Index

_

_AtomBondContainer (class in schrodinger.structure) _AtomCollection (class in schrodinger.structure) _AtomIterator (class in schrodinger.structure) _BaseWriter (class in schrodinger.structure) _Chain (class in schrodinger.structure) _Molecule (class in schrodinger.structure) _NotSortable (class in schrodinger.structure) _ReaderWriterContextManager (class in schrodinger.structure) _Residue (class in schrodinger.structure) _ResidueIterator (class in schrodinger.structure) _Ring (class in schrodinger.structure)

_RingEdgeIterator (class in schrodinger.structure) _StructureAtom (class in schrodinger.structure) _StructureAtomContainer (class in schrodinger.structure) _StructureAtomProperty (class in schrodinger.structure) _StructureBond (class in schrodinger.structure) _StructureBondContainer (class in schrodinger.structure) _StructureBondProperty (class in schrodinger.structure) _StructureChainIterator (class in schrodinger.structure) _StructureMoleculeIterator (class in schrodinger.structure) _StructureProperty (class in schrodinger.structure) _StructureRingIterator (class in schrodinger.structure)

A

a (schrodinger.infra.phase.PhpFastShapePair attribute) A_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) A_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) A_VACUUM (schrodinger.application.matsci.nano.tube.NanoTube attribute) ABAB (schrodinger.application.matsci.nano.constants.Constants attribute) ABCD (schrodinger.application.matsci.nano.constants.Constants attribute) AbstractAligner (class in schrodinger.protein.align) AbstractExportPanel (class in schrodinger.application.livedesign.ld_export) AbstractExportSetupPanel (class in schrodinger.application.livedesign.ld_export) AbstractExportTableModel (class in schrodinger.application.livedesign.panel_components) AbstractFunctionTask (class in schrodinger.tasks.tasks_) AbstractJobTask (class in schrodinger.tasks.jobtasks) AbstractParamMapper (class in schrodinger.models.mappers) AbstractSequenceElement (class in schrodinger.protein.residue) AbstractTask (class in schrodinger.tasks.tasks) (class in schrodinger.tasks.tasks_) AbstractTaskReporter (class in schrodinger.tasks.runners) accept() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.bioluminate.propfilter.ValueSelectionDialog method) (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.matsci.jobdirdlg.NewJobDirDialog method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.mswidgets.SolventDialog method) (schrodinger.application.matsci.reordergui.ReorderAtomsDialog method) (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog method) (schrodinger.ui.chooseligand.ChooseLigandDialog method) (schrodinger.ui.picking.MaestrolessPickLigandDialog method) accept_reject_parse() (in module schrodinger.application.desmond.replica_exchange_review) accepted (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) ACCEPTED_FRAMEWORK_COLOR (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) ACCEPTOR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) AcceptorConstraint (class in schrodinger.application.glide.glide) AccessType (class in schrodinger.models.mappers) ACCURACY_LEVELS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) ACCURATE (schrodinger.application.matsci.qualityslider.QualitySlider attribute) ACIDIC_HYDROPHILIC (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) ack() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) action_factory (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) activate() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) active_atom_pairs() (in module schrodinger.application.jaguar.autots_bonding) active_jobs (schrodinger.job.queue.JobDJ attribute) active_reactant_atom_pairs() (in module schrodinger.application.jaguar.autots_bonding) active_total (schrodinger.application.desmond.cms.Cms attribute) ActiveBondSearchFailure ActiveCoord (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) ActiveDecoyFingerprintAnalyzer (class in schrodinger.analysis.enrichment) activeSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) activeSubTabName() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) adapt_st_reader() (in module schrodinger.analysis.reaction) adapter() (in module schrodinger.models.json) adaptor (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) add() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.packages.energygroup.EnergyComponent method) (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.graphics3d.common.Group method) (schrodinger.job.queue.LinkedList method) (schrodinger.job.queue.RunningJobs method) (schrodinger.project_surface.SurfaceDict method) (schrodinger.structutils.color.ColorScheme method) add_amide_constraints() (in module schrodinger.structutils.rgroup_enumerate) add_and_parse_SMILES() (in module schrodinger.application.desmond.report_helper) add_atom_highlight() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) add_atoms_onto_tree() (in module schrodinger.application.desmond.reorder_atom) add_attachment_points() (schrodinger.application.canvas.r_group.Data method) add_attribute_aliases() (in module schrodinger.application.jaguar.results) add_bonds_in_rings() (schrodinger.application.canvas.r_group.Data method) add_child() (schrodinger.application.desmond.reorder_atom.Node method) add_cms_property() (in module schrodinger.application.matsci.desmondutils) add_code() (schrodinger.infra.mmcheck.ReturnCode method) add_core() (schrodinger.application.canvas.r_group.Data method) add_core_bonds() (schrodinger.application.canvas.r_group.Data method) add_core_ct() (schrodinger.application.canvas.r_group.Data method) add_ct_data() (in module schrodinger.application.canvas.r_group) add_ct_offset() (schrodinger.application.canvas.r_group.Data method) add_cubic_chorus_box_props() (in module schrodinger.application.matsci.desmondutils) add_current_to_states() (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) add_descriptors() (in module schrodinger.structutils.rgroup_enumerate) add_desmond_ms_logo() (in module schrodinger.application.matsci.mswidgets) add_disulfide_bond() (in module schrodinger.protein.residue) add_error() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.licensing.licadmin.ServerInfo method) add_functional_rings() (schrodinger.application.canvas.r_group.Data method) add_ghost_solvent() (in module schrodinger.application.desmond.gcmc_utils) add_ghost_solvent_file() (in module schrodinger.application.desmond.gcmc_utils) add_histo() (in module schrodinger.application.desmond.event_analysis.pl_image_tools) add_host_lists() (in module schrodinger.pipeline.pipeline) add_hydrogens() (in module schrodinger.structutils.build) (schrodinger.application.desmond.fep_struc.SchrodStruc method) ADD_HYPO_PT (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) ADD_HYPO_WS (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) add_jaguar_files_to_jc_backend() (in module schrodinger.application.matsci.jaguarworkflows) add_job_launch_log() (in module schrodinger.maestro.maestro) add_jobcontrol_diagnostic_options() (in module schrodinger.utils.cmdline) add_jobcontrol_options() (in module schrodinger.utils.cmdline) add_keyword_parser_argument() (in module schrodinger.application.matsci.jobutils) add_kwarg() (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method) add_labeled_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) add_local_type_force_field_to_job_builder() (in module schrodinger.application.matsci.cgforcefield) add_methyl_ring() (in module schrodinger.application.canvas.r_group) add_methyl_standard() (in module schrodinger.application.canvas.r_group) add_multi_job_finalizer() (in module schrodinger.job.queue) add_neighbor_charges_to_jaginput() (in module schrodinger.application.matsci.clusterstruct) add_output() (schrodinger.application.desmond.enhsamp.Env method) (schrodinger.application.licensing.licerror.LicenseError method) add_overlapEnergyTable() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) add_package_dir_to_path() (in module schrodinger.application.utils) add_para_job_options() (in module schrodinger.application.macromodel.paraUtils) add_parser_opts() (in module schrodinger.application.matsci.equilibrium_md) add_plugin() (in module schrodinger.application.desmond.config) add_point() (schrodinger.protein.analysis.Report.data_set method) (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method) add_position() (schrodinger.application.canvas.r_group.Data method) add_prepared_props() (in module schrodinger.application.prepwizard) add_property_value() (schrodinger.application.canvas.r_group.Data method) add_qe_parallel_parser_arguments() (in module schrodinger.application.matsci.espresso.utils) add_r_group() (schrodinger.application.canvas.r_group.Data method) add_r_groups_to_atom() (schrodinger.application.canvas.r_group.Data method) add_replicas_dF_table() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) add_rest_region() (in module schrodinger.application.desmond.rest_inp) add_restart_parser_arguments() (in module schrodinger.application.matsci.jobutils) add_rg_ct() (schrodinger.application.canvas.r_group.Data method) add_rings() (schrodinger.application.canvas.r_group.Data method) add_save_desmond_files_parser_argument() (in module schrodinger.application.matsci.jobutils) add_signature() (schrodinger.application.licensing.flexlm.Feature method) add_signatures() (schrodinger.application.licensing.flexlm.License method) add_smiles() (in module schrodinger.structutils.smilesfilter) add_spacer() (in module schrodinger.application.desmond.report_helper) add_standard_options() (in module schrodinger.utils.cmdline) add_static() (schrodinger.application.desmond.enhsamp.Env method) add_subjob_files_to_backend() (in module schrodinger.application.matsci.jobutils) add_table() (in module schrodinger.application.desmond.report_helper) add_tag() (schrodinger.utils.sea.Sea method) add_temp_hydrogen() (in module schrodinger.application.matsci.rxn_path) add_to_data() (in module schrodinger.application.canvas.r_group) add_var() (schrodinger.application.desmond.enhsamp.binding method) add_vtable() (in module schrodinger.application.desmond.report_helper) add_water_constraints() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) add_xsd_types_to_dict() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) add_zmatrix_lines() (in module schrodinger.application.matsci.zmutils) addActionItem() (schrodinger.application.bioluminate.bwidgets.RowActionItem method) addActions() (schrodinger.application.bioluminate.actions.factory.Factory method) addAlignmentAxesToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addAlignToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addAnalyzer() (schrodinger.application.desmond.packages.staf.GeomCalc method) addAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method) addAngleRestraint() (schrodinger.structutils.minimize.Minimizer method) addAnnotationAction() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) addAntibodyNumberingToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addAtom() (schrodinger.application.desmond.packages.msys.Residue method) (schrodinger.application.desmond.packages.msys.System method) (schrodinger.structure.Structure method) addAtomGroupRow() (schrodinger.application.desmond.gui.AtomGroupFrame method) addAtomProp() (schrodinger.application.desmond.packages.msys.System method) addAtoms() (schrodinger.structure.Structure method) addAttachmentPoint() (schrodinger.application.desmond.fep_mapping.AtomMappingData method) addAttr() (schrodinger.infra.phase.PhpHypoAdaptor method) addAutoGpuCbToLayout() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) addAuxTable() (schrodinger.application.desmond.packages.msys.System method) addBidentateLigand() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) addBond() (schrodinger.application.desmond.packages.msys.Atom method) (schrodinger.structure.Structure method) (schrodinger.structure._StructureAtom method) addBondProp() (schrodinger.application.desmond.packages.msys.System method) addBonds() (schrodinger.structure.Structure method) addBranchingAtoms() (schrodinger.application.matsci.amorphous.PolymerToFragments method) addc() (schrodinger.application.macromodel.utils.ComUtil method) addCanvasKPLSOptions() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS static method) addChain() (schrodinger.application.desmond.packages.msys.Ct method) (schrodinger.application.desmond.packages.msys.System method) (schrodinger.protein.getpdb_utility.Code method) addCharges() (schrodinger.application.matsci.clusterstruct.SpeciesData method) addChild() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) addChildren() (schrodinger.application.desmond.antlr3.tree.BaseTree method) addCnst() (schrodinger.infra.phase.PhpHypoAdaptor method) addColumn() (schrodinger.application.desmond.gui.TableModel method) addCommandLineOptions() (schrodinger.job.app.App method) addConsButtonPressed() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) addConsensusToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addConstantProperties() (schrodinger.application.matsci.cgforcefield.FFIOParam method) addConstraint() (schrodinger.application.glide.glide.ConstraintGroup method) (schrodinger.infra.phase.PhpSiteConstrainer method) addConstraintGroup() (schrodinger.application.glide.glide.Dock method) addContext() (schrodinger.application.bioluminate.actions.factory.Factory method) addCoord() (schrodinger.application.matsci.zmutils.ZAtom method) addCoordinate() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) addCostProperties() (schrodinger.application.ligprep.ionizer.Ionizer method) addCriterion() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) addCt() (schrodinger.application.desmond.packages.msys.System method) (schrodinger.infra.phase.PhpHypoAdaptor method) addCustom() (schrodinger.application.desmond.packages.staf.GeomCalc method) addCV() (schrodinger.application.desmond.meta.Meta method) addData() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit method) addDefinition() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) AddDefinitionDialog (class in schrodinger.ui.ligfilter) addDefinitionsFromFile() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) addDesignator() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) addDesmondPBC() (schrodinger.application.matsci.amorphous.Scaffold method) addDispFlag() (schrodinger.tasks.jobtasks.JobConfig method) addDistance() (schrodinger.application.desmond.packages.staf.GeomCalc method) addDistanceRestraint() (schrodinger.structutils.minimize.Minimizer method) addDisulfideBond() (schrodinger.protein.alignment.ProteinAlignment method) addEdge() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) addEigenpair() (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.trajectory.prody.pca.PCA method) addEnv() (schrodinger.job.launcher.Launcher method) addExcludedVolumes() (schrodinger.application.phase.phase_markers.PhaseXvolMarkers method) addExpectedInput() (schrodinger.pipeline.stage.Stage method) addExpectedKeyword() (schrodinger.pipeline.stages.qsite.QSiteStage method) addExpectedOutput() (schrodinger.pipeline.stage.Stage method) addext() (in module schrodinger.trajectory.prody.writenmd) addFeatureDefinitionPresets() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) addFeaturesForWorkspaceLigands() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addFeatureTypeEquivalencies() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) addFinalizer() (schrodinger.job.queue.BaseJob method) addFindToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addForceInputFile() (schrodinger.job.launcher.Launcher method) addFromFile() (schrodinger.project_surface.SurfaceDict method) addGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) addGPGPUGroupToLayout() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.application.desmond.gui.DesmondRestGuiConfigDialog method) addGPGPUTableToLayout() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) addGroupPrereq() (schrodinger.job.queue.BaseJob method) addHostFlag() (schrodinger.tasks.jobtasks.JobConfig method) addHydrogenCap() (schrodinger.application.qsite.input.QSiteInput method) addHydrogens() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) addHypoFromPT() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addHypoFromWorkspace() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addHypothesisFromEntry() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) addImportToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addInputFile() (schrodinger.job.app.App method) (schrodinger.job.launcher.Launcher method) addIonProperties() (schrodinger.application.ligprep.ionizer.Ionizer method) addIons() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) addIvol() (schrodinger.infra.phase.PhpHypoAdaptor method) addJaguarMarker (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute) addJaguarMarkerForRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel method) addJob() (schrodinger.job.queue.JobDJ method) addKey() (schrodinger.utils.ligfilter.Definition method) addKwargs() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property static method) addLicense() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) (schrodinger.job.launcher.Launcher method) addLigandDesignator() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) addLigands() (schrodinger.infra.phase.PhpProject method) addLine() (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ExtraSectionData method) addLogFile() (schrodinger.job.app.App method) (schrodinger.job.launcher.Launcher method) addMapping() (schrodinger.models.mappers.AbstractParamMapper method) addMask() (schrodinger.infra.phase.PhpHypoAdaptor method) addMember() (schrodinger.application.matsci.clusterstruct.SpeciesData method) addMonodentateLigand() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) addNamedProperties() (schrodinger.application.matsci.cgforcefield.FFIOParam method) (schrodinger.application.matsci.cgforcefield.FFIOSite method) addNavigationNode() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) addNew() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) addNewConstraint() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) addNewEndpoint() (schrodinger.application.livedesign.panel_components.EndpointSelectionPopup method) AddNewLineEdit (class in schrodinger.application.livedesign.panel_components) addNewLiveReport() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) addNode() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) addNonbondedFromSchema() (schrodinger.application.desmond.packages.msys.System method) addNormalsToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addNumericLineEdit() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) addOneRow() (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) addOptions() (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog method) (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method) addOrReplaceSeqs() (schrodinger.protein.alignment.BaseAlignment method) addOutputFile() (schrodinger.job.launcher.Launcher method) (schrodinger.pipeline.stage.Stage method) addOutputFileBE() (schrodinger.job.app.App method) addOutputFileFE() (schrodinger.job.app.App method) addPair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) addParam() (schrodinger.application.desmond.packages.msys.ParamTable method) addParams() (schrodinger.application.matsci.cgforcefield.FFIOParam method) addPath() (schrodinger.application.livedesign.panel_components.PathTreeDict method) addPattern() (schrodinger.ui.ligfilter.LigfilterFrame method) addPatternCriterion() (schrodinger.ui.ligfilter.LigfilterFrame method) addPBCProperties() (schrodinger.application.matsci.amorphous.Scaffold method) addPkaMarkers() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) addPlanarAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method) addPointsToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addPosFrozen() (schrodinger.structutils.minimize.Minimizer method) addPosition() (schrodinger.application.desmond.packages.staf.GeomCalc method) addPosResRow() (schrodinger.application.desmond.gui.RestraintsTab method) addPosRestraint() (schrodinger.structutils.minimize.Minimizer method) addPredefinedCriterion() (schrodinger.ui.ligfilter.LigfilterFrame method) addPrereq() (schrodinger.job.queue.BaseJob method) addPreviousFreezerFile() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.StructureGenome method) addProduct() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) addProjects() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) addProjFlag() (schrodinger.tasks.jobtasks.JobConfig method) addProp() (schrodinger.application.desmond.packages.msys.ParamTable method) (schrodinger.infra.phase.PhpHypoAdaptor method) addPropCriterion() (schrodinger.ui.ligfilter.LigfilterFrame method) addProperties() (schrodinger.application.matsci.cgforcefield.ForceField method) addProperty() (in module schrodinger.infra.propedit) addpropop1Modified() (schrodinger.ui.ligfilter.LigfilterFrame method) addPropsToStructure() (schrodinger.application.matsci.amorphous.Monomer static method) addQMCut() (schrodinger.application.qsite.input.QSiteInput method) addQMMolecule() (schrodinger.application.qsite.input.QSiteInput method) addQsar() (schrodinger.infra.phase.PhpHypoAdaptor method) addRad() (schrodinger.infra.phase.PhpHypoAdaptor method) addRandomChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) addRandomChannelsFromAll() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) addRandomChannelsOnTheFly() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) addReactant() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) addReactionInstance() (schrodinger.analysis.reaction.RetroSynthesisNode method) addRefCtMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addRequiredOutputFile() (schrodinger.job.launcher.Launcher method) addResidue() (schrodinger.application.desmond.packages.msys.Chain method) (schrodinger.application.desmond.packages.msys.System method) addResidues() (schrodinger.application.bioluminate.protein.PrimeConfig method) (schrodinger.protein.alignment.BaseAlignment method) addResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method) addRestraints() (schrodinger.application.desmond.restraint.RestraintBuilder method) addResultServerFlag() (schrodinger.tasks.jobtasks.JobConfig method) addRow() (schrodinger.application.desmond.fep_gui.PathModel method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) addRule() (schrodinger.infra.phase.PhpFeatureRules method) (schrodinger.utils.colorscheme.MM_CScheme method) addRules() (schrodinger.infra.phase.PhpHypoAdaptor method) addSalt() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) addScriptArgs() (schrodinger.job.launcher.Launcher method) addSegmentPlaneIntersectionsToTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) addSeq() (schrodinger.protein.alignment.BaseAlignment method) addSeqs() (schrodinger.protein.alignment.BaseAlignment method) addSeqsByIndices() (schrodinger.protein.alignment.BaseAlignment method) addSite() (schrodinger.infra.phase.PhpHypoAdaptor method) addSiteData() (schrodinger.infra.phase.PhpDeltaHypo method) addSiteMaskData() (schrodinger.infra.phase.PhpSiteMask method) addSiteMaskGroup() (schrodinger.infra.phase.PhpSiteMask method) addSites() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addSpaceGroupPBC() (schrodinger.application.matsci.amorphous.Scaffold method) addSphere() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.infra.phase.PhpExclVol method) addStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) (schrodinger.pipeline.input.LinearWriter method) (schrodinger.pipeline.input.Writer method) addStaticDummyAtom() (in module schrodinger.infra.phase) addStaticFragmentPatterns() (schrodinger.infra.phase.PhpFeatureDefinition method) addStructProperties() (schrodinger.application.matsci.amorphous.PolymerToFragments method) addStructureFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addSubMenu() (schrodinger.application.bioluminate.actions.factory.Factory method) addSubprocessStackedWidget() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) addSubTabMarker() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) addSubTabs() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) addSurfaceToProject() (schrodinger.project_surface.ProjectSurface class method) addTable() (schrodinger.application.desmond.packages.msys.System method) (schrodinger.application.desmond.packages.restrain.Restraints method) addTableFromSchema() (schrodinger.application.desmond.packages.msys.System method) addTempHydrogens() (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule method) addTempInputFile() (schrodinger.job.launcher.Launcher method) addTerm() (schrodinger.application.desmond.packages.msys.TermTable method) (schrodinger.application.desmond.packages.restrain.Restraints method) addTermProp() (schrodinger.application.desmond.packages.msys.TermTable method) addTmpLaunchDirFlag() (schrodinger.tasks.jobtasks.JobConfig method) addToChain() (schrodinger.application.matsci.amorphous.BaseMoiety method) ADDTOENTRY (schrodinger.job.launchparams.ProjectDisposition attribute) addToFFST() (schrodinger.application.matsci.cgforcefield.FFIOParam method) addToJaguarInput() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ExtraSectionData method) addTol() (schrodinger.infra.phase.PhpHypoAdaptor method) addTolByType() (schrodinger.infra.phase.PhpHypoAdaptor method) addTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) addToolBars() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addTorsion() (schrodinger.application.desmond.packages.staf.GeomCalc method) addTorsionRestraint() (schrodinger.structutils.minimize.Minimizer method) addToWorkspace() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant method) addUndoRedoToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) addVacuum() (schrodinger.application.matsci.nano.slab.Surface method) addVar() (schrodinger.pipeline.input.LinearWriter method) (schrodinger.pipeline.input.Writer method) addVector() (schrodinger.application.desmond.packages.staf.GeomCalc method) addViewnameFlag() (schrodinger.tasks.jobtasks.JobConfig method) addXvol() (schrodinger.infra.phase.PhpHypoAdaptor method) addXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) adf() (schrodinger.application.macromodel.utils.ComUtil method) adjust() (schrodinger.structure.Structure method) adjustACellClashVDWScale() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) adjustACellDensity() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) adjustAtomIds() (schrodinger.application.matsci.amorphous.PolymerFragment method) adjustDihedral() (schrodinger.protein.captermini.CapTermini method) ADOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) advance() (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) advanceSelection() (schrodinger.application.matsci.reordergui.ReferenceFrame method) advice (schrodinger.application.licensing.licerror.LicenseError attribute) AdvLabel (class in schrodinger.application.desmond.cwidget) (class in schrodinger.application.desmond.fep_gui) AdvOptionsFrame (class in schrodinger.application.desmond.gui) af2SettingsGetValue() (schrodinger.ui.picking.MaestrolessPickResidueDialog method) af2SettingsSetValue() (schrodinger.ui.picking.MaestrolessPickResidueDialog method) after_upper_edge() (in module schrodinger.application.matsci.nano.xtal) afterStep() (schrodinger.infra.phase.PhpProject method) AFTERSUPERPOSITION (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) AGGREGATE_CALCULATIONS (schrodinger.application.bioluminate.protein.PropertyCalculator attribute) AHEAD (schrodinger.application.matsci.nano.xtal.PBCBond attribute) AHo (schrodinger.protein.annotation.AntibodyCDRScheme attribute) ahomo_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) aid_match() (in module schrodinger.application.desmond.packages.topo) AIDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) aids2gids() (in module schrodinger.application.desmond.packages.topo) AlchemAsl (class in schrodinger.application.desmond.replica_sid_generator) Alchemist (class in schrodinger.application.matsci.enumeration) ALDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) alie_analysis() (in module schrodinger.application.jaguar.textparser) alie_analysis_precision (schrodinger.application.jaguar.results.JaguarResults attribute) alie_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) align() (schrodinger.structutils.structalign.StructAlign method) align_alignment() (in module schrodinger.protein.sequence) align_all_molecules() (in module schrodinger.application.jaguar.autots_rmsd) align_chmmol() (in module schrodinger.application.desmond.depictor) align_from_chains() (in module schrodinger.protein.sequence) align_path_strs() (in module schrodinger.application.jaguar.autots_rmsd) ALIGN_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) align_weight (schrodinger.infra.phase.PhpHypoOptimizerSettings attribute) alignCenterCollect() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) alignCoordinates() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method) alignCt() (schrodinger.infra.phase.PhpFastShape method) alignCtPy() (schrodinger.infra.phase.PhpFastShape method) alignedRMSD() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method) alignLigands() (schrodinger.infra.phase.PhpProject method) alignment (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) alignmentAboutToBeCleared (schrodinger.protein.alignment.AlignmentSignals attribute) alignmentCleared (schrodinger.protein.alignment.AlignmentSignals attribute) AlignmentException alignmentLengthAboutToChange (schrodinger.protein.alignment.AlignmentSignals attribute) alignmentLengthChanged (schrodinger.protein.alignment.AlignmentSignals attribute) alignmentLocked() (schrodinger.protein.alignment.BaseAlignment method) AlignmentSignals (class in schrodinger.protein.alignment) alignOnXAxis() (schrodinger.application.matsci.amorphous.Monomer method) alignPolyhedron() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) alignSites() (schrodinger.structutils.sitealign.BindingSiteAligner method) alignStructure() (schrodinger.structutils.structalign.StructAlign method) alignStructWithPlane() (schrodinger.application.matsci.espresso.qeinput.StructureType method) alignToVector() (schrodinger.application.matsci.amorphous.BaseMoiety method) ALL (schrodinger.utils.pandasutils.WhichColumns attribute) (schrodinger.utils.pandasutils.WhichRows attribute) all_annotations (schrodinger.protein.alignment.BaseAlignment attribute) all_basisnames() (in module schrodinger.application.jaguar.jaguar_keyword_utils) ALL_CONSTRAINTS_BUTTON (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) all_dftnames() (in module schrodinger.application.jaguar.jaguar_keyword_utils) all_fnames_in_dir() (in module schrodinger.application.desmond.packages.cui) all_jobs (schrodinger.job.queue.JobDJ attribute) all_keywords() (in module schrodinger.application.jaguar.jaguar_keyword_utils) all_meaningful_keywords() (in module schrodinger.application.jaguar.jaguar_keyword_utils) all_multicomb() (in module schrodinger.application.desmond.autopartition) all_properties() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) ALL_RANDOM_CHANNELS (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) ALL_RESIDUES (schrodinger.application.bioluminate.protein.PrimeConfig attribute) (schrodinger.ui.picking.MaestrolessPickResidueDialog attribute) all_rows (schrodinger.project.EntryGroup attribute) (schrodinger.project.Project attribute) ALL_SEARCH_ALONG (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) ALL_SMARTS (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) ALL_STRUCS (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) all_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer attribute) ALL_TYPES (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) allaid_gids (schrodinger.application.desmond.cms.Cms attribute) allCoordinatesDeleted (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) allDescriptorFullLabels() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method) allFacesIntersected() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) ALLINDICIES (schrodinger.application.matsci.nano.sheet.Grow attribute) allInteractingResidues() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) allow_add_live_reports (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel attribute) ALLOW_ADSORPTION_ONTO (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) ALLOW_ADSORPTION_ONTO_METAVAR (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) ALLOWED_FP_TYPES (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) ALLOWED_TO_MATCH (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) allPrimitives() (schrodinger.graphics3d.common.Group method) allTransmutationsCompleted() (schrodinger.application.matsci.enumeration.Alchemist method) (schrodinger.application.matsci.enumeration.ElementAlchemist method) (schrodinger.application.matsci.enumeration.VacancyAlchemist method) ALPHA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) ALPHA_ORBITALS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) ALPHA_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) alpha_polar() (in module schrodinger.application.jaguar.textparser)

alpha_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute) ALPHA_THRESH (schrodinger.application.matsci.mecp_mod.MECPStep attribute) alphabet (schrodinger.protein.sequence.NucleicAcidSequence attribute) (schrodinger.protein.sequence.ProteinSequence attribute) (schrodinger.protein.sequence.Sequence attribute) (schrodinger.protein.sequence.StrictProteinSequence attribute) alreadyParsedRule() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) ALSO_REG_BOND_KEY (schrodinger.application.matsci.nano.xtal.PBCBond attribute) alt_matches() (schrodinger.application.licensing.flexlm.Feature method) alt_xyz (schrodinger.structure._StructureAtom attribute) alumo_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) alwaysLocal() (schrodinger.job.app.App method) AMBIVALENT (schrodinger.protein.residue.BETA_STRAND_PROPENSITY attribute) (schrodinger.protein.residue.HELIX_PROPENSITY attribute) (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) (schrodinger.protein.residue.STERIC_GROUP attribute) (schrodinger.protein.residue.TURN_PROPENSITY attribute) AmorphousCellBuilder (class in schrodinger.application.matsci.amorphous) Analysis (class in schrodinger.application.desmond.title_to_hex) ANALYSIS (schrodinger.application.matsci.desmondutils.MSJStringer attribute) ANALYSIS_DIR_NAME (schrodinger.application.desmond.title_to_hex.Analysis attribute) ANALYSIS_TYPE (schrodinger.application.matsci.desmondutils.MSJStringer attribute) analyze() (in module schrodinger.application.desmond.packages.analysis) (schrodinger.application.desmond.packages.msys.System method) (schrodinger.protein.analysis.Report.Bfactor_data_set method) (schrodinger.protein.analysis.Report.Gfactor_summary_data_set method) (schrodinger.protein.analysis.Report.backbone_dihedral_data_set method) (schrodinger.protein.analysis.Report.bond_angle_data_set method) (schrodinger.protein.analysis.Report.bond_length_data_set method) (schrodinger.protein.analysis.Report.chirality_data_set method) (schrodinger.protein.analysis.Report.data_set method) (schrodinger.protein.analysis.Report.gamma_Bfactor_data_set method) (schrodinger.protein.analysis.Report.improper_torsion_data_set method) (schrodinger.protein.analysis.Report.missing_atoms_data_set method) (schrodinger.protein.analysis.Report.peptide_planarity_data_set method) (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method) (schrodinger.protein.analysis.Report.sidechain_dihedral_data_set method) (schrodinger.protein.analysis.Report.sidechain_planarity_data_set method) (schrodinger.protein.analysis.Report.steric_clash_data_set method) analyze_data() (schrodinger.application.desmond.bennett.CalcBAR method) analyze_it() (schrodinger.application.desmond.title_to_hex.Analysis method) analyze_pair() (schrodinger.protein.analysis.Report.steric_clash_data_set method) analyzeBetweenGroups() (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer method) AnalyzeEnergyOptions (class in schrodinger.application.prime.gui.analyze_energy) AnalyzeEnergyWidget (class in schrodinger.application.prime.gui.analyze_energy) analyzeFingerprints() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) analyzeGroups() (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer method) AnalyzeStageData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) analyzeStructures() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) (schrodinger.application.livedesign.maestro_data_types.DockedPoses method) (schrodinger.application.livedesign.maestro_data_types.Ligands method) (schrodinger.application.livedesign.maestro_data_types.OrganometallicCompounds method) analyzeWithinGroups() (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer method) Angle (class in schrodinger.application.desmond.packages.analysis) ANGLE (schrodinger.application.matsci.rxn_path.Coord attribute) angle (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) (schrodinger.structutils.interactions.pi.PiPiInteraction attribute) angle_bend_energy() (in module schrodinger.application.qsite.output) ANGLE_DEP_TRANSPARENCY (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) angle_iterator() (in module schrodinger.structutils.analyze) ANGLE_TOL (schrodinger.application.matsci.mecp_mod.BFGS attribute) ANGLELARGE (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) ANGLEMEDIUM (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) (schrodinger.application.matsci.nano.tube.NanoSheet attribute) ANGLESMALL (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) ANGLEWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) ANIMATION_TIME (schrodinger.application.desmond.feputils.LabelSpinner attribute) animationTimeElapsed (schrodinger.application.desmond.feputils.LabelSpinner attribute) anion_frame_coordination() (in module schrodinger.application.matsci.mlearn.features) AnionCation (schrodinger.structutils.interactions.salt_bridge.OrderBy attribute) annotate() (schrodinger.application.combiglide.combenumdock.CgHydrogenFragmentAnnotator method) (schrodinger.application.desmond.fep_scholar_util.MappingAnnotator method) AnnotatedSystem (class in schrodinger.application.desmond.packages.msys) annotation_types (schrodinger.protein.sequence.Sequence attribute) AnnotationClass (schrodinger.protein.sequence.NucleicAcidSequence attribute) (schrodinger.protein.sequence.ProteinSequence attribute) (schrodinger.protein.sequence.Sequence attribute) annotationTitleChanged (schrodinger.protein.alignment.AlignmentSignals attribute) (schrodinger.protein.sequence.Sequence attribute) ANTIBODY (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) antibody_cdr (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) ANTIBODY_NUM_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) AntibodyCDR (class in schrodinger.protein.annotation) AntibodyCDRLabel (class in schrodinger.protein.annotation) AntibodyCDRScheme (class in schrodinger.protein.annotation) AntibodyNumberingToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) ANTIGEN (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) ANTIGEN_TYPE (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) antlr_version (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) antlr_version_str (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) ANTLRFileStream (class in schrodinger.application.desmond.antlr3.streams) ANTLRInputStream (class in schrodinger.application.desmond.antlr3.streams) ANTLRStringStream (class in schrodinger.application.desmond.antlr3.streams) ANY_CONTACT (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) aposteri_e() (in module schrodinger.application.jaguar.textparser) App (class in schrodinger.job.app) APPEND (schrodinger.job.launchparams.ProjectDisposition attribute) append() (schrodinger.application.desmond.ffiostructure.FFIOStructure method) (schrodinger.application.desmond.packages.msys.Ct method) (schrodinger.application.desmond.packages.msys.System method) (schrodinger.application.livedesign.export_controller.DataMapWriter method) (schrodinger.application.qsite.input.QMRegion method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmkv.MMKVArgList method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.infra.phase.PhpExclVol method) (schrodinger.protein.sequence.Sequence method) (schrodinger.structure.MaestroWriter method) (schrodinger.structure.Mol2Writer method) (schrodinger.structure.MultiFileStructureWriter method) (schrodinger.structure.PDBWriter method) (schrodinger.structure.SDWriter method) (schrodinger.structure.SmilesCsvWriter method) (schrodinger.structure.SmilesStructure method) (schrodinger.structure.SmilesWriter method) (schrodinger.structure.Structure method) (schrodinger.structure.StructureWriter method) (schrodinger.structure.TextualStructure method) (schrodinger.structutils.filter.Filter method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.multifpfile.MultiFPFileWriter method) (schrodinger.utils.sea.List method) append_comment() (in module schrodinger.application.desmond.util) APPEND_FIT (schrodinger.job.launchparams.ProjectDisposition attribute) append_outfiles_to_recover_file() (in module schrodinger.application.jaguar.utils) append_path() (in module schrodinger.utils.env) append_project_command() (in module schrodinger.maestro.maestro) appendAdditionalViewInformation() (schrodinger.application.livedesign.export_controller.ExportController method) appendChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) appendConfigFlags() (schrodinger.tasks.jobtasks.AbstractJobTask method) appendFile() (schrodinger.application.combiglide.combenumdock.createFragmentDelegate method) (schrodinger.application.combiglide.combenumdock.simpleEnumDockDelegate method) appendFlags() (schrodinger.tasks.jobtasks.JobConfig method) appendFromModel() (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) APPENDINPLACE (schrodinger.job.launchparams.ProjectDisposition attribute) APPENDINPLACE_FIT (schrodinger.job.launchparams.ProjectDisposition attribute) appendLigand() (schrodinger.application.glide.poseviewconvert.Complex method) appendNewCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) appendReceptor() (schrodinger.application.glide.poseviewconvert.Complex method) appendRepository() (schrodinger.infra.fast3d.Engine method) appendRule() (schrodinger.infra.fast3d.Generalizer method) appendStruct() (schrodinger.application.combiglide.combenumdock.collectionViewerModel method) appendSubalignment() (schrodinger.protein.alignment.BaseAlignment method) APPENDUNGROUPED (schrodinger.job.launchparams.ProjectDisposition attribute) apply() (in module schrodinger.application.desmond.packages.msys.posre) (schrodinger.analysis.reaction.Reaction method) (schrodinger.application.desmond.gaussian_filter.GaussianFilter method) (schrodinger.structutils.color.ColorScheme method) (schrodinger.utils.sea.List method) (schrodinger.utils.sea.Map method) (schrodinger.utils.sea.Sea method) apply_color_scheme() (in module schrodinger.structutils.color) apply_exclusion() (in module schrodinger.application.desmond.r_group_asl) apply_jaguar_atom_naming() (in module schrodinger.application.jaguar.input) apply_pkas() (schrodinger.protein.assignment.ProtAssign method) apply_state() (in module schrodinger.application.prepwizard) apply_state_and_calc_score() (in module schrodinger.application.prepwizard) apply_transform() (in module schrodinger.analysis.transformations) apply_transforms() (in module schrodinger.analysis.transformations) apply_uniform_operator_weights() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) applyContextDependentDefaults() (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.GlideJob method) applyCurrentCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) applyCurrentSelection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) ApplyDihedralGeometry() (in module schrodinger.application.desmond.packages.msys) applyEnergyFilter() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) applyEntryData() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) applyFF() (schrodinger.application.matsci.cgforcefield.ForceField method) applyGoldsteinSingles() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) applyGroupSelections() (schrodinger.ui.residueselector.MutationSelectorFrame method) applyRampToColorSchemeRules() (schrodinger.utils.colorscheme.ColorSchemeManager method) applyRule() (schrodinger.utils.colorscheme.MM_CSchemeRule method) applyScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) (schrodinger.utils.colorscheme.MM_CScheme method) applySchemeDescriptive() (schrodinger.utils.colorscheme.ColorSchemeManager method) applySettings() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.tasks.jobtasks.JobConfig method) applyStyle() (schrodinger.structure._Chain method) (schrodinger.structure.Structure method) (schrodinger.structure._Molecule method) (schrodinger.structure._Residue method) (schrodinger.structure._Ring method) applyToDimers() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) applyToJaguarInput() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.OverrideKeywords method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords method) approx_eq() (in module schrodinger.application.bioluminate.interaction_calculator) approximateVolume() (schrodinger.application.matsci.amorphous.Scaffold method) archive_job_data() (in module schrodinger.application.matsci.jobutils) archive_wm() (in module schrodinger.application.watermap.utils) ArchivedProjectException are_conformers() (in module schrodinger.application.jaguar.autots_rmsd) (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) are_consistently_ordered_conformers() (in module schrodinger.application.jaguar.autots_rmsd) are_same_structure() (in module schrodinger.application.jaguar.autots_rmsd) are_sts_the_same() (in module schrodinger.structutils.createfragments) are_times_insane() (in module schrodinger.application.desmond.fepana) areAtomsOrtho() (schrodinger.structutils.assignbondorders.AssignBondOrders method) areBound() (schrodinger.structure.Structure method) areCOsPara() (schrodinger.structutils.assignbondorders.AssignBondOrders method) ArgumentParserError ark_str() (schrodinger.application.desmond.replica_sid_generator.FEPReport method) ARMCHAIR (schrodinger.application.matsci.nano.constants.Constants attribute) ARMCHAIR_BY_ONE_BASE (schrodinger.application.matsci.nano.sheet.Grow attribute) aromatic (schrodinger.application.desmond.packages.msys.Atom attribute) AROMATIC (schrodinger.protein.residue.STERIC_GROUP attribute) aromatic() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method) AROMATIC_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) AROMATIC_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) AROMATIC_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) Array_Prop (class in schrodinger.application.desmond.simulation_block_data) ArrayCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) ArraySyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) (class in schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) Arrow (class in schrodinger.graphics3d.arrow) ARROW_RADII (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) ArrowCore (class in schrodinger.graphics3d.arrow) ARROWDOWN (schrodinger.maestro.markers.Icons attribute) asDict() (schrodinger.analysis.reaction.Reaction method) (schrodinger.analysis.reaction.ReagentClass method) asdict() (schrodinger.utils.mmutil.StringStringMap method) asDock() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) asea_copy() (in module schrodinger.utils.sea) aset() (schrodinger.application.macromodel.utils.ComUtil method) asFrame() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) asGrid() (schrodinger.application.bioluminate.bwidgets.ImportWidget method) asJSON() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) asl (schrodinger.protein.assignment.ProtAssign.amide_changeable attribute) (schrodinger.protein.assignment.ProtAssign.amine_changeable attribute) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable attribute) (schrodinger.protein.assignment.ProtAssign.changeable attribute) (schrodinger.protein.assignment.ProtAssign.histidine_changeable attribute) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable attribute) (schrodinger.protein.assignment.ProtAssign.water_changeable attribute) asl() (schrodinger.application.desmond.maestro.NewEntry method) asl2gids() (in module schrodinger.application.desmond.packages.topo) ASL_IONS (schrodinger.application.bioluminate.protein.Consensus attribute) (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) ASL_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) ASL_LIGAND (schrodinger.application.bioluminate.protein.Consensus attribute) (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) ASL_WATER (schrodinger.application.bioluminate.protein.Consensus attribute) (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) AslCriterion (class in schrodinger.utils.ligfilter) AslException AslLigandSearcher (class in schrodinger.structutils.analyze) ASLObject (class in schrodinger.application.desmond.enhsamp) aslselect_atom() (in module schrodinger.application.desmond.cms) asNamedTuple() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) asp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) asp_tot_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) aspectScale() (in module schrodinger.application.desmond.report_helper) assaySelected (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) AssaySelectionLineEdit (class in schrodinger.application.livedesign.panel_components) AssaySelectionPopup (class in schrodinger.application.livedesign.panel_components) AssaySelectionPopUpDelegate (class in schrodinger.application.livedesign.panel_components) assign() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.structutils.assignbondorders.AssignBondOrders method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) assign_best_combinations() (schrodinger.protein.assignment.ProtAssign method) assign_bond_orders() (in module schrodinger.application.matsci.nano.xtal) assign_bond_orders_w_mmlewis() (in module schrodinger.application.matsci.nano.xtal) assign_bonded_params() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util) assign_cluster_combination() (schrodinger.protein.assignment.ProtAssign method) assign_combination() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) assign_ff() (in module schrodinger.application.bioluminate.escomp) assign_markers() (in module schrodinger.application.matsci.amorphous) assign_pdb_names() (in module schrodinger.protein.pdbname) assign_phased() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util) assign_setup() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util) assign_space_group() (in module schrodinger.application.matsci.nano.xtal) assign_st() (in module schrodinger.structutils.assignbondorders) assign_state() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) assign_state_of_changeable() (schrodinger.protein.assignment.ProtAssign method) assignActives() (schrodinger.infra.phase.PhpProject method) assignAromaticBonders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignAromaticRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignAromaticRingGroup() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignAromaticRingOrders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) AssignBondOrderAndFormalCharge() (in module schrodinger.application.desmond.packages.msys) AssignBondOrders (class in schrodinger.structutils.assignbondorders) assignChainOrders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignDefaultGroups() (schrodinger.infra.phase.PhpProject method) assignGroupDoubleBonds() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignGroups() (schrodinger.infra.phase.PhpProject method) assignGroupTripleBonds() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignInactives() (schrodinger.infra.phase.PhpProject method) assignQsarSet() (schrodinger.infra.phase.PhpProject method) assignRingAtomIds() (schrodinger.application.matsci.amorphous.PolymerToFragments method) assignTemplatedSubstructures() (schrodinger.structutils.assignbondorders.AssignBondOrders method) assignTripleBonds() (schrodinger.structutils.assignbondorders.AssignBondOrders method) ASSOCIATION_TYPE (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) ASSUME_ISOLATED_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) ASU_LABEL_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) ASU_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) at_surface (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) at_time_near() (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method) (schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method) at_values (schrodinger.application.jaguar.scan.Scan attribute) atid2atomsel() (schrodinger.application.desmond.meta.CmsModel method) Atom (class in schrodinger.application.desmond.packages.msys) (class in schrodinger.application.desmond.packages.viparr1.viparr.viparr) (class in schrodinger.utils.sea) ATOM (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) atom (schrodinger.structure._AtomCollection attribute) (schrodinger.structure.Structure attribute) (schrodinger.structure.TextualStructure attribute) atom() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) (schrodinger.application.desmond.packages.msys.System method) (schrodinger.application.glide.glide.AcceptorConstraint method) (schrodinger.application.glide.glide.DonorConstraint method) (schrodinger.application.glide.glide.MetalConstraint method) atom_clicked (schrodinger.application.matsci.reordergui.StructureListWidget attribute) atom_color (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) atom_highlighted (schrodinger.application.matsci.reordergui.StructureView attribute) atom_idx (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) atom_index (schrodinger.structutils.rgroup_enumerate.RGroup attribute) atom_index() (schrodinger.application.desmond.reorder_atom.Node method) atom_indexes (schrodinger.structutils.analyze.Ligand attribute) atom_indices (schrodinger.application.bioluminate.protein.Consensus attribute) atom_is_nonpolar() (in module schrodinger.application.bioluminate.protein) ATOM_LABELS (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) atom_mapping (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) atom_movement (schrodinger.infra.phase.PhpAlignCoreOptions attribute) atom_name (schrodinger.structure._StructureAtom attribute) atom_name_regex (in module schrodinger.application.jaguar.gui.utils) atom_name_sort_key() (in module schrodinger.application.jaguar.gui.utils) atom_props (schrodinger.application.desmond.packages.msys.System attribute) atom_selection_dialog() (in module schrodinger.maestro.maestro) atom_style (schrodinger.structure._StructureAtom attribute) atom_total (schrodinger.application.jaguar.results.JaguarResults attribute) (schrodinger.structure.Structure attribute) atom_type (schrodinger.application.desmond.fep_scholar_util.MetaAtom attribute) ATOM_TYPE (schrodinger.application.jaguar.structure_isomorphism.AutoTSAtomMapper attribute) atom_type (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) (schrodinger.structure._StructureAtom attribute) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) atom_type_name (schrodinger.structure._StructureAtom attribute) atom_typeMM (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) ATOM_TYPING_SCHEMES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) AtomBasis (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) AtomBasisSetDelegate (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) atomClasses (schrodinger.infra.phase.PhpQSARModel attribute) AtomGroup (class in schrodinger.application.desmond.cms) ATOMGROUP_PREFIX (schrodinger.application.desmond.cms.Cms attribute) AtomGroupDelegate (class in schrodinger.application.desmond.gui) AtomGroupFrame (class in schrodinger.application.desmond.gui) AtomGroupModel (class in schrodinger.application.desmond.gui) AtomGroupRow (class in schrodinger.application.desmond.gui) atomic_charge_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) atomic_number (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.structure._StructureAtom attribute) ATOMIC_SYMBOL (schrodinger.application.matsci.nano.constants.Constants attribute) ATOMIC_SYMBOLS (in module schrodinger.application.matsci.atomicsymbols) atomic_weight (schrodinger.structure._StructureAtom attribute) AtomMappingData (class in schrodinger.application.desmond.fep_mapping) AtomMarker (class in schrodinger.maestro.markers) atomPicked() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) atomPropType() (schrodinger.application.desmond.packages.msys.System method) atoms (schrodinger.application.bioluminate.protein.Consensus attribute) (schrodinger.application.desmond.packages.msys.Bond attribute) (schrodinger.application.desmond.packages.msys.Ct attribute) (schrodinger.application.desmond.packages.msys.Residue attribute) (schrodinger.application.desmond.packages.msys.System attribute) (schrodinger.application.desmond.packages.msys.Term attribute) ATOMS (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) atoms (schrodinger.infra.phase.PhpIntCoord attribute) (schrodinger.infra.phase.PhpSiteWithAtoms attribute) (schrodinger.protein.analysis.Report.data_set.data_point attribute) atoms() (schrodinger.application.desmond.packages.msys.Graph method) (schrodinger.application.glide.glide.AcceptorConstraint method) (schrodinger.application.glide.glide.DonorConstraint method) (schrodinger.application.glide.glide.MetalConstraint method) atoms_within_3_bonds() (in module schrodinger.application.desmond.reorder_atom) atomsasl() (in module schrodinger.application.prepwizard) Atomsel (class in schrodinger.application.desmond.packages.msys.atomsel) atomsel() (schrodinger.application.desmond.enhsamp.ASLObject method) (schrodinger.application.desmond.packages.msys.System method) AtomSelectionDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) atomsGroupedBy() (schrodinger.application.desmond.packages.msys.System method) AtomsInRingError AtomTyper (class in schrodinger.application.bindingsite.atomtyping) atomTypingCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) attach_fragment() (in module schrodinger.structutils.build) attach_structure() (in module schrodinger.structutils.build) attachCap() (schrodinger.protein.captermini.CapTermini method) AttachmentAtoms (class in schrodinger.application.matsci.amorphous) attachSidechains() (schrodinger.structutils.rgroup_enumerate.RgroupEnumerator method) ATTRACTION (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) attrib (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute attribute) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement attribute) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup attribute) attribute_groups (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) attributes (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) AttrTarget (class in schrodinger.models.mappers) ATYPE_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) AUTO (schrodinger.application.desmond.packages.traj.Fmt attribute) auto_partition() (in module schrodinger.application.desmond.autopartition) autoIncreaseThreshold() (schrodinger.infra.fast3d.Engine method) autoMap() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) Automatic (schrodinger.application.jaguar.gui.utils.SpinTreatment attribute) AUTOMATIC_BAND (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) AutomaticJobnameMixin (class in schrodinger.application.jaguar.gui.base_panel) autoPlace() (schrodinger.protein.membrane.Membrane_Model method) autoPlaceByMolecule() (schrodinger.protein.membrane.Membrane_Model method) autoprojectsync_call() (in module schrodinger.application.desmond.maestro) AutoTSAtomMapper (class in schrodinger.application.jaguar.structure_isomorphism) auxinfo (schrodinger.application.desmond.packages.msys.InChI attribute) auxtable() (schrodinger.application.desmond.packages.msys.System method) auxtable_names (schrodinger.application.desmond.packages.msys.System attribute) auxtables (schrodinger.application.desmond.packages.msys.System attribute) available_color_schemes() (in module schrodinger.structutils.color) available_tokens() (schrodinger.application.licensing.licadmin.LicenseResource method) averageAndSort() (schrodinger.application.matsci.coarsegrain.Internals method) avg_anion_anion_short_distance() (in module schrodinger.application.matsci.mlearn.features) avg_atomic_vol() (in module schrodinger.application.matsci.mlearn.features) avg_element_anion_short_distance() (in module schrodinger.application.matsci.mlearn.features) avg_element_element_short_distance() (in module schrodinger.application.matsci.mlearn.features) avg_element_neighbor_count() (in module schrodinger.application.matsci.mlearn.features) avg_neighbor_count() (in module schrodinger.application.matsci.mlearn.features) avg_neighbor_ion() (in module schrodinger.application.matsci.mlearn.features) avg_sublattice_eneg() (in module schrodinger.application.matsci.mlearn.features) avg_sublattice_neighbor_count() (in module schrodinger.application.matsci.mlearn.features) avg_sublattice_neighbor_ion() (in module schrodinger.application.matsci.mlearn.features) avgInternals() (schrodinger.application.matsci.coarsegrain.Internals method) AXES (schrodinger.application.matsci.amorphous.Box attribute) axis (schrodinger.application.desmond.packages.msys.molfile.Grid attribute) AxisDirector (class in schrodinger.application.desmond.packages.analysis)

B

b (schrodinger.graphics3d.arrow.MaestroArrow attribute) (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.graphics3d.torus.MaestroTorus attribute) (schrodinger.infra.phase.PhpFastShapePair attribute) B_FACTOR (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) b_factor (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) B_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) B_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) back() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) back_transparency (schrodinger.surface.Surface attribute) backbone_dihedrals (in module schrodinger.protein.analysis_params) BACKBONE_INTERACTION (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) BACKBONE_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) backClicked() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) backend() (schrodinger.job.app.App method) backtrack() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) BacktrackingFailed backup_file() (in module schrodinger.job.queue) backupFile() (in module schrodinger.trajectory.prody.writenmd) BackwardsReader (class in schrodinger.pipeline.pipeutils) balance_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) balance_alie_precision (schrodinger.application.jaguar.results.JaguarResults attribute) balance_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) balance_esp_precision (schrodinger.application.jaguar.results.JaguarResults attribute) balance_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) ball_atom() (in module schrodinger.application.desmond.maestro) (schrodinger.application.desmond.maestro.Workspace method) BandshapeSpectrumFile (class in schrodinger.application.matsci.bandshape_utils) BandStructure (class in schrodinger.application.matsci.espresso.qeoutput) BandsType (class in schrodinger.application.matsci.espresso.qeinput) baroMethodChanged() (schrodinger.application.desmond.gui.EnsembleTab method) base_evaluator() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) base_name (schrodinger.tasks.tasks.AbstractTask attribute) base_nameChanged (schrodinger.tasks.tasks.AbstractTask attribute) BaseAlignment (class in schrodinger.protein.alignment) BaseAtomMapper (class in schrodinger.application.jaguar.structure_isomorphism) basedir() (schrodinger.utils.installation_check.TestJobDJ method) BaseFeaturizer (class in schrodinger.application.matsci.mlearn.base) BaseFunctionTask (class in schrodinger.tasks.tasks) BaseInteractiveEnumeration (class in schrodinger.application.combiglide.combenumdock) BaseJaguarPanel (class in schrodinger.application.jaguar.gui.base_panel) BaseJob (class in schrodinger.job.queue) BaseLDTreeItemWrapper (class in schrodinger.application.livedesign.panel_components) BaseLiveReportSelectionPopup (class in schrodinger.application.livedesign.panel_components) BaseMaestroData (class in schrodinger.application.livedesign.maestro_data_types) BaseMoiety (class in schrodinger.application.matsci.amorphous) BaseMutableParam (class in schrodinger.models.parameters) basename() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method) BaseRecognizer (class in schrodinger.application.desmond.antlr3.recognizers) BaseSearchTreeWidgetHelper (class in schrodinger.application.livedesign.panel_components) BaseSelectionPopup (class in schrodinger.application.livedesign.panel_components) BaseSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab) (class in schrodinger.application.jaguar.gui.tabs.properties_tab) BaseTab (class in schrodinger.application.jaguar.gui.tabs.base_tab) BaseTree (class in schrodinger.application.desmond.antlr3.tree) BaseTreeAdaptor (class in schrodinger.application.desmond.antlr3.tree) BASIC_HYDROPHILIC (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) BasicAligner (class in schrodinger.protein.align) Basis (class in schrodinger.application.jaguar.gui.input_tab_widgets) BASIS (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) basis (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) BASIS (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) basis_changed (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin attribute) basis_is_supported_for_functional() (in module schrodinger.application.jaguar.jaguar_keyword_utils) basis_set() (in module schrodinger.application.jaguar.textparser) basis_set_is_valid() (in module schrodinger.application.jaguar.reactiq_validation) basisChanged (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) basisname_in_list() (in module schrodinger.application.jaguar.jaguar_keyword_utils) BasisSelector (class in schrodinger.application.jaguar.gui.basis_selector) BasisSelectorLineEdit (class in schrodinger.application.jaguar.gui.basis_selector) BasisSet (class in schrodinger.application.jaguar.basis) BasisSetColumns (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) BasisSetModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetProxyModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisSetSelector (class in schrodinger.application.matsci.chargegui) BasisSetSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set) BasisSetTableView (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) BasisType (class in schrodinger.application.matsci.espresso.qeinput) BATCHES_INCLUDE_TARGETS (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) (schrodinger.application.livedesign.maestro_data_types.Complexes attribute) batchIteration() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) BC_EFIELD_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) BC_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) bc_type (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) BC_W_KEY (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) bcc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) bctet1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) bctet2() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) becomeRoot() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) before_lower_edge() (in module schrodinger.application.matsci.nano.xtal) beforeStep() (schrodinger.infra.phase.PhpProject method) BEFORESUPERPOSITION (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) begin (schrodinger.utils.colorscheme.MMrange attribute) begin() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.infra.phase.PhpTextFileReader method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method)

begin_drawing() (in module schrodinger.application.desmond.maestro) beginBacktrack() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) beginGroup() (schrodinger.utils.preferences.Preferences method) beginResync() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) BEHIND (schrodinger.application.matsci.nano.xtal.PBCBond attribute) bennett() (schrodinger.application.desmond.bennett.CalcBAR method) best_scoring_element() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) beta_au() (in module schrodinger.application.jaguar.utils) beta_kcalmol() (in module schrodinger.application.jaguar.utils) BETA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) BETA_ORBITALS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) BETA_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) beta_polar() (in module schrodinger.application.jaguar.textparser) beta_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute) BETA_STRAND_PROPENSITY (class in schrodinger.protein.residue) beta_strand_propensity (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) between_groups_global_max (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer attribute) between_groups_global_min (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer attribute) BFGS (class in schrodinger.application.matsci.mecp_mod) bhomo_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) BIDENTATE (in module schrodinger.application.matsci.buildcomplex) BILAYERSEP (schrodinger.application.matsci.nano.constants.Constants attribute) BILAYERSHIFT (schrodinger.application.matsci.nano.constants.Constants attribute) bin_edges (schrodinger.analysis.enrichment.StatisticalSummary attribute) bin_structures_by_property() (in module schrodinger.application.matsci.reaction_workflow_utils) BinaryThreadSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) (class in schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) Bind (class in schrodinger.application.desmond.enhsamp) bind() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) binding (class in schrodinger.application.desmond.enhsamp) BindingSiteAligner (class in schrodinger.structutils.sitealign) bins() (schrodinger.application.desmond.packages.analysis.Rdf method) BIT_EXT (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) bitCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) bits (schrodinger.infra.phase.PhpPackedFp attribute) Bitset (class in schrodinger.infra.mmbitset) bitset_to_list() (in module schrodinger.utils.multifpfile) bitSetOff() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) bitSetOn() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) BiunivocalMap (class in schrodinger.application.matsci.qexsd.qespresso.utils.mapping) BLANK_PATTERN (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions attribute) BlankableSpinBox (class in schrodinger.application.jaguar.gui.input_tab_widgets) BlankableSpinBoxDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) BlankDebugEventListener (class in schrodinger.application.desmond.antlr3.debug) BLKSIZE (schrodinger.pipeline.pipeutils.BackwardsReader attribute) blobs() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) Block (class in schrodinger.application.desmond.simulation_block_test) block() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) BLOCK_NAME (schrodinger.application.prime.residue_interaction.InteractionReader attribute) BlockingFunctionTask (class in schrodinger.tasks.tasks) (class in schrodinger.tasks.tasks_) blumo_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) bodyToNode() (in module schrodinger.application.desmond.enhsamp) boltzmann_probability() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) Bond (class in schrodinger.application.desmond.packages.msys) BOND (schrodinger.application.matsci.rxn_path.Coord attribute) bond (schrodinger.structure._StructureAtom attribute) (schrodinger.structure.Structure attribute) bond() (schrodinger.application.desmond.packages.msys.System method) bond_crossover() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) bond_in_ring() (in module schrodinger.application.canvas.r_group) bond_iterator() (in module schrodinger.structutils.analyze) bond_length_cache (schrodinger.application.matsci.amorphous.BaseMoiety attribute) BOND_ORDERS_CHOICES (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BOND_ORDERS_DEFAULT (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) bond_props (schrodinger.application.desmond.packages.msys.System attribute) bond_stretch_energy() (in module schrodinger.application.qsite.output) BOND_SUM_THRESH (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule attribute) bond_total (schrodinger.structure._StructureAtom attribute) BondCharge (class in schrodinger.application.jaguar.results) bondchg_repulsion_energy() (in module schrodinger.application.qsite.output) bonded_atoms (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.structure._StructureAtom attribute) bonded_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) bondedAtomIdInSameRes() (schrodinger.application.matsci.amorphous.PolymerToFragments method) BondError BONDING_CHOICES (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BONDING_DEFAULT (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) BONDLENGTH (schrodinger.application.matsci.nano.constants.Constants attribute) bondMatchingEdges() (schrodinger.application.matsci.nano.tube.NanoTube method) bondPair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) BONDPENALTYTHRESH (schrodinger.application.matsci.rxn_path.ReactionPath attribute) bondPropType() (schrodinger.application.desmond.packages.msys.System method) bondRemainingNodes() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) BondRotator (class in schrodinger.application.desmond.torsion_related) bonds (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.application.desmond.packages.msys.Ct attribute) (schrodinger.application.desmond.packages.msys.System attribute) bondToH() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) BondType (class in schrodinger.structure) BONDWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) boolean() (in module schrodinger.utils.sea) BooleanDatabaseCriterion (class in schrodinger.application.bioluminate.propfilter) BoolParam (class in schrodinger.models.parameters) bootstrap() (in module schrodinger.application.desmond.bennett) BoundaryType (class in schrodinger.application.matsci.espresso.qeinput) boundingBoxCallback() (schrodinger.graphics3d.common.Group method) BoundingInformation() (in module schrodinger.analysis.visanalysis.volumedatastructureutils) BoundingInformationL() (in module schrodinger.analysis.visanalysis.volumedatastructureutils) Box (class in schrodinger.application.matsci.amorphous) (class in schrodinger.graphics3d.box) box (schrodinger.application.desmond.packages.analysis.Pbc attribute) (schrodinger.application.desmond.packages.topo.DuckFrame attribute) (schrodinger.application.desmond.packages.traj.Frame attribute) box_col_major (schrodinger.application.desmond.packages.topo.DuckFrame attribute) (schrodinger.application.desmond.packages.traj.Frame attribute) BoxSize (class in schrodinger.application.desmond.simulation_block_test) BoxWithInnerHull (class in schrodinger.application.matsci.amorphous) BREAK (schrodinger.maestro.markers.Icons attribute) BREAK_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) breakIntoMols() (schrodinger.application.matsci.amorphous.PolymerToFragments method) breakTemplatePolymer() (schrodinger.application.matsci.amorphous.Monomer method) BrownieMSJStringer (class in schrodinger.application.matsci.desmondutils) browse() (schrodinger.application.desmond.cwidget.FileEntry method) browse_for_collection_dir() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) browseDirectory() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) browseForNewCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) browseSystemFile() (schrodinger.application.desmond.gui.InputGroup method) build() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) build_cell() (in module schrodinger.application.matsci.nano.sheet) build_kwargs() (in module schrodinger.application.matsci.nano.particle) build_receptor_ligand_map() (in module schrodinger.application.livedesign.ld_utils) buildAllAttr() (schrodinger.infra.phase.PhpHypoAdaptor method) buildBilayer() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) buildCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) buildCellDriver() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) buildChannelStrDef() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) buildComboBox() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) buildCovariance() (schrodinger.trajectory.prody.pca.PCA method) buildCrystalSuperCell() (schrodinger.application.matsci.nano.xtal.Crystal method) buildCrystalUnitCell() (schrodinger.application.matsci.nano.xtal.Crystal method) buildDerivedAttributes() (schrodinger.application.jaguar.output.JaguarOutput method) buildDockedLigandsMap() (schrodinger.pipeline.stages.glide.DockingStage method) BuilderGrowInCellMixin (class in schrodinger.application.matsci.amorphous) BuilderWithClashDetection (class in schrodinger.application.matsci.amorphous) buildingBlocksHaveRings() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) buildLabel() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) buildLattice() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) buildLayer() (schrodinger.application.matsci.nano.interface_mod.Interface method) buildLayers() (schrodinger.application.matsci.nano.interface_mod.Interface method) buildLineEdit() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) buildMultiWallTube() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) buildNanoTubeSheet() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) buildQsarModel() (schrodinger.infra.phase.PhpProject method) buildReorderList() (schrodinger.application.matsci.rxn_channel.rxn_channel.Products method) buildSlab() (schrodinger.application.matsci.nano.slab.Surface method) buildTemplateList() (schrodinger.application.matsci.builderwidgets.SketcherBox method) buildTube() (schrodinger.application.matsci.nano.tube.NanoTube method) buildUnitCell() (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) Bulk (class in schrodinger.application.desmond.packages.energygroup) bumpIndexes() (schrodinger.application.matsci.zmutils.ZAtom method) (schrodinger.application.matsci.zmutils.ZMatrix method) BURIED (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) busy_icon_exec() (in module schrodinger.application.desmond.util) buttonChanged() (schrodinger.application.matsci.qualityslider.QualitySlider method) bval (schrodinger.utils.sea.Atom attribute) (schrodinger.utils.sea.List attribute) (schrodinger.utils.sea.Map attribute)

C

c (schrodinger.infra.phase.PhpFastShapePair attribute) c6() (schrodinger.application.desmond.cms.Vdw method) C_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) C_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) c_v() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) C_VACUUM (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) cache_hostname_plink() (in module schrodinger.utils.sshconfig) cached_property (class in schrodinger.infra.util) cached_topo_descriptor() (in module schrodinger.application.canvas.topo_descriptors) calc_agg_scores() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) calc_average_vdw_coeff() (in module schrodinger.application.desmond.cms) calc_block_average() (in module schrodinger.application.desmond.simulation_block_data) calc_complementarity() (in module schrodinger.application.bioluminate.escomp) calc_complementarity_by_atom() (in module schrodinger.application.bioluminate.escomp) (in module schrodinger.application.bioluminate.surfcomp) calc_contrib() (in module schrodinger.application.desmond.fepana) calc_convergence_rate() (in module schrodinger.application.desmond.fepana) calc_forward_reversed_work_overlap() (in module schrodinger.application.desmond.fepana) calc_free_energy_for_abfe_cross_link() (in module schrodinger.application.desmond.fepana) calc_free_energy_for_abfe_cross_link_xu() (in module schrodinger.application.desmond.fepana) calc_freeenergy_rtime_function() (in module schrodinger.application.desmond.fepana) calc_freeenergy_stime_function() (in module schrodinger.application.desmond.fepana) calc_freeenergy_time_function() (in module schrodinger.application.desmond.fepana) calc_lambda_sim_matrix() (in module schrodinger.application.desmond.fepana) calc_lambda_window_overlap() (in module schrodinger.application.desmond.fepana) calc_ligand_size() (in module schrodinger.application.glide.glide) calc_long_range_dispersion_energy() (in module schrodinger.application.desmond.fepana) calc_prob_profile() (in module schrodinger.application.desmond.ana) calc_time_curve() (in module schrodinger.application.desmond.fepana) calc_time_series() (in module schrodinger.application.desmond.ana) calc_total_complementarity() (in module schrodinger.application.bioluminate.escomp) (in module schrodinger.application.bioluminate.surfcomp) calc_type() (in module schrodinger.application.jaguar.textparser) calc_volume() (in module schrodinger.application.desmond.fep_net_charge) calc_work_prob_distr() (in module schrodinger.application.desmond.fepana) calcActivesInN() (schrodinger.analysis.enrichment.Calculator method) calcActivesInNStar() (schrodinger.analysis.enrichment.Calculator method) CalcAngle() (in module schrodinger.application.desmond.packages.msys) calcAngle() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) calcAUAC() (schrodinger.analysis.enrichment.Calculator method) calcAveNumberOutrankingDecoys() (schrodinger.analysis.enrichment.Calculator method) CalcBAR (class in schrodinger.application.desmond.bennett) calcBEDROC() (schrodinger.analysis.enrichment.Calculator method) calcBondScore() (schrodinger.structutils.assignbondorders.AssignBondOrders method) calcConsensusScore() (schrodinger.pipeline.stages.combine.DataFusionMergeStage method) calcCovariance() (in module schrodinger.trajectory.prody.crosscorrelation) calcCrossCorr() (in module schrodinger.trajectory.prody.crosscorrelation) calcDEF() (schrodinger.analysis.enrichment.Calculator method) calcDEFP() (schrodinger.analysis.enrichment.Calculator method) calcDEFStar() (schrodinger.analysis.enrichment.Calculator method) CalcDihedral() (in module schrodinger.application.desmond.packages.msys) calcDihedral() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) CalcDistance() (in module schrodinger.application.desmond.packages.msys) calcDistance() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) calcEF() (schrodinger.analysis.enrichment.Calculator method) calcEFF() (schrodinger.analysis.enrichment.Calculator method) calcEFP() (schrodinger.analysis.enrichment.Calculator method) calcEFStar() (schrodinger.analysis.enrichment.Calculator method) calcFOD() (schrodinger.analysis.enrichment.Calculator method) calcMinimumDiff() (schrodinger.application.desmond.packages.analysis.Pbc method) calcMinimumImage() (schrodinger.application.desmond.packages.analysis.Pbc method) calcModes() (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.trajectory.prody.pca.PCA method) calcMWUROC() (schrodinger.analysis.enrichment.Calculator method) calcPlanarAngle() (schrodinger.trajectory.pbc_manager.PBCMeasureMananger method) CalcPlanarity() (in module schrodinger.application.desmond.packages.msys) calcProperty() (in module schrodinger.infra.propedit) calcRIE() (schrodinger.analysis.enrichment.Calculator method) calcROC() (schrodinger.analysis.enrichment.Calculator method) calcsDone() (schrodinger.application.matsci.jaguarworkflows.Step method) calculate() (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) (schrodinger.application.bioluminate.protein.PropertyCalculator method) (schrodinger.application.canvas.r_group.RGroupFinder method) (schrodinger.structutils.rmsd.ConformerRmsd method) calculate_average_angle() (in module schrodinger.structutils.assignbondorders) calculate_binding_modes() (in module schrodinger.application.phase.hypothesis_binding_modes) calculate_dihedral() (in module schrodinger.structutils.assignbondorders) calculate_in_place_rmsd() (in module schrodinger.structutils.rmsd) calculate_njobs() (in module schrodinger.job.jobcontrol) calculate_num_protons() (in module schrodinger.application.jaguar.gui.utils) calculate_planarity() (in module schrodinger.structutils.assignbondorders) calculate_principle_moments() (in module schrodinger.structutils.analyze) calculate_RIP() (in module schrodinger.application.desmond.fep_net_charge) calculate_sasa() (in module schrodinger.structutils.analyze) calculate_sasa_by_atom() (in module schrodinger.structutils.analyze) calculate_sasa_by_residue() (in module schrodinger.structutils.analyze) calculate_stats() (schrodinger.application.glide.glideanalysis.PoseLibrary method) calculate_total_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) CalculateContainingVolume() (in module schrodinger.analysis.visanalysis.volumedatautils) calculateCoords() (schrodinger.graphics3d.arrow.MaestroArrow method) calculateEnergy() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) calculateEnergyDifference() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) calculateInter() (schrodinger.structutils.interactions.salt_bridge.SaltBridgeFinder method) calculateIntra() (schrodinger.structutils.interactions.salt_bridge.SaltBridgeFinder method) calculateMatrix() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.structutils.sitealign.BindingSiteAligner method) calculateMembraneBox() (schrodinger.protein.membrane.Membrane_Model method) calculateMetrics() (schrodinger.analysis.enrichment.Calculator method) calculateMutationsList() (schrodinger.application.bioluminate.protein.Mutator method) calculateOverResidues() (schrodinger.application.bioluminate.protein.PropertyCalculator method) calculateProbeRadius() (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab method) calculateSensitivity() (schrodinger.analysis.enrichment.Calculator method) calculateSimilarity() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.infra.phase.PhpSite method) calculateSpecificity() (schrodinger.analysis.enrichment.Calculator method) calculateTopologicalDescriptors() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method) calculateVolume() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) CALCULATION_MODE (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget attribute) Calculator (class in schrodinger.analysis.enrichment) calcZScores() (schrodinger.pipeline.stages.combine.DataFusionMergeStage method) calDensity() (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) call() (in module schrodinger.utils.subprocess) callback (schrodinger.application.jaguar.textparser.TextParser attribute) (schrodinger.application.qsite.output.QSiteTextParser attribute) callback() (in module schrodinger.application.jaguar.textparser) (in module schrodinger.application.mopac.results2012) (in module schrodinger.application.qsite.output) callbacks (schrodinger.application.mopac.results2012.Mopac2012TextParser attribute) can_atom_hydrogen_bond() (in module schrodinger.structutils.analyze) can_write_file() (in module schrodinger.application.licensing.licadmin) cancelPressed() (schrodinger.application.desmond.gui.AdvOptionsFrame method) cancelSubmitted() (schrodinger.job.queue.JobControlJob method) canonical_filename() (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.licensing.licadmin.LicenseResource method) canonicalize() (in module schrodinger.application.desmond.config) (schrodinger.structutils.smiles.SmilesGenerator method) canonicalize_atom_names() (in module schrodinger.application.jaguar.autots_bonding) canonicalize_ligand() (in module schrodinger.application.desmond.automatic_analysis_generator) canorb() (in module schrodinger.application.jaguar.textparser) canStart() (schrodinger.application.matsci.jaguarworkflows.Step method) Canvas2DSimilarityStage (class in schrodinger.pipeline.stages.canvas) CanvasFingerprintCluster (class in schrodinger.application.canvas.cluster) CanvasFingerprintClusterCLI (class in schrodinger.application.canvas.cluster) CanvasFingerprintClusterGUI (class in schrodinger.application.canvas.clustergui) CanvasFingerprintGenerator (class in schrodinger.application.canvas.fingerprint) CanvasFingerprintGeneratorCLI (class in schrodinger.application.canvas.fingerprint) CanvasFingerprintGeneratorGUI (class in schrodinger.application.canvas.fingerprintgui) CanvasFingerprintSimilarity (class in schrodinger.application.canvas.similarity) CanvasFingerprintSimilarityCLI (class in schrodinger.application.canvas.similarity) CanvasFingerprintSimilarityGUI (class in schrodinger.application.canvas.similaritygui) canvasfp_fpreader() (in module schrodinger.application.hitexpander) CanvasKPLS (class in schrodinger.application.matsci.genetic_optimization.genetic_optimization) CanvasSimilarityNotImplemented cap_termini() (in module schrodinger.protein.captermini) capacity() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) cappedResidues() (schrodinger.protein.captermini.CapTermini method) CAPPING_BOND_LENGTH (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) CAPPINGELEMENT (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) capResidues() (schrodinger.protein.captermini.CapTermini method) capSequences() (schrodinger.protein.captermini.CapTermini method) CapTermini (class in schrodinger.protein.captermini) CAPTION (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) Capture (class in schrodinger.infra.mmerr) CARTESIAN (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) CARTESIANWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) Cascader (class in schrodinger.application.matsci.amorphous) CascadingCheckboxItem (class in schrodinger.application.livedesign.panel_components) CaseInsensitiveString (class in schrodinger.application.jaguar.jaguar_diff) cast_type (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) cat() (in module schrodinger.utils.fileutils) catch_jag_errors() (in module schrodinger.application.jaguar.gui.utils) catch_last_added() (in module schrodinger.application.bioluminate.ssv.viewer) catch_subprocess_errors() (in module schrodinger.utils.sysinfo) category (schrodinger.application.desmond.packages.msys.TermTable attribute) CategoryOrderError cation_centroid (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) cation_structure (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) CationPiInteraction (class in schrodinger.structutils.interactions.pi) catOpText() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) Cavity (class in schrodinger.application.bindingsite.cavutils) cavity_depth (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) CCDStructureMismatchError cd() (in module schrodinger.utils.installation_check) cell (schrodinger.application.desmond.packages.msys.System attribute) CELL_DYNAMICS_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_FACTOR_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_FIX_XY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) CELL_PADDING (schrodinger.application.report2d.PicturePrinter attribute) cellClearData() (schrodinger.infra.table.Table method) CellControlType (class in schrodinger.application.matsci.espresso.qeinput) cellHasData() (schrodinger.infra.table.Table method) CellRunInfo (class in schrodinger.application.matsci.jobutils) CELSIUS (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) center (schrodinger.application.desmond.packages.msys.Residue attribute) (schrodinger.application.desmond.packages.msys.System attribute) CENTER (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) center() (in module schrodinger.application.desmond.packages.topo) center_cms() (in module schrodinger.application.desmond.packages.topo) center_ct() (in module schrodinger.application.desmond.packages.staf) center_fr() (in module schrodinger.application.desmond.packages.staf) center_of_mass() (in module schrodinger.structutils.analyze) center_widget_in_table_cell() (in module schrodinger.application.matsci.mswidgets) centerAndRotate() (schrodinger.structutils.ringspear.SpearRing method) CenteredSoluteAnalysis (class in schrodinger.application.desmond.packages.staf) CENTERING (schrodinger.application.matsci.nano.xtal.SpaceGroups attribute) CENTERING_OPERATIONS_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) CENTERING_OPERS (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) CenterOf (class in schrodinger.application.desmond.packages.analysis) CenterOfMotion (in module schrodinger.application.desmond.packages.analysis) Centroid (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.structutils.interactions.pi) centroid (schrodinger.structutils.analyze.Ligand attribute) (schrodinger.structutils.ringspear.SpearRing attribute) cgen() (schrodinger.application.macromodel.utils.ComUtil method) CGFFIOStructure (class in schrodinger.application.matsci.cgforcefield) CGForceFieldSelector (class in schrodinger.application.matsci.cgforcefieldgui) CgHydrogenFragmentAnnotator (class in schrodinger.application.combiglide.combenumdock) cgResidueToAllAtom() (schrodinger.application.matsci.amorphous.PolymerToFragments method) Chain (class in schrodinger.application.desmond.packages.msys) (class in schrodinger.protein.getpdb_utility) CHAIN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain (schrodinger.application.desmond.packages.msys.Residue attribute) (schrodinger.application.qsite.input.Cut attribute) (schrodinger.structure.Structure attribute) (schrodinger.structure.TextualStructure attribute) (schrodinger.structure._Residue attribute) (schrodinger.structure._StructureAtom attribute) chain() (schrodinger.application.desmond.packages.msys.System method) CHAIN_FR_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) CHAIN_FR_SIM (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) CHAIN_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chain_name (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) CHAIN_SIM (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) chainNames() (schrodinger.structure._StructureChainIterator method) chains (schrodinger.application.desmond.packages.msys.Ct attribute) (schrodinger.application.desmond.packages.msys.System attribute) change_pka() (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) change_plot_colors() (in module schrodinger.application.desmond.report_helper) change_working_directory() (in module schrodinger.utils.fileutils) changeBasis() (schrodinger.application.matsci.nano.tube.NanoSheet method) changeCoord() (schrodinger.application.matsci.zmutils.ZAtom method) changed (schrodinger.application.combiglide.combenumdock.editableViewerTable attribute) changeLayer() (schrodinger.application.matsci.sliceplot.SlicePlot method) changeMarkerAtomsToTempElement() (schrodinger.application.matsci.builderwidgets.SketcherBox method) changeMoleculeForParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) changePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) changeProtFile() (schrodinger.application.desmond.gui.RelaxFrame method) changesSaved() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) changeTemp() (schrodinger.application.desmond.gui.EnsembleClassFrame method) changeTemplateDirectory() (schrodinger.application.matsci.builderwidgets.TemplateManager method) CHANNEL_FILE (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) ChannelDefinition (class in schrodinger.application.matsci.rxn_channel.rxn_channel) ChannelDefinitions (class in schrodinger.application.matsci.rxn_channel.rxn_channel) Channels (class in schrodinger.application.matsci.rxn_channel.rxn_channel) charge (schrodinger.application.desmond.packages.msys.Atom attribute) CHARGE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) charge (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) CHARGE (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) charge (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) CHARGE (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) charge (schrodinger.application.matsci.cgforcefield.VDWData attribute) CHARGE (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute) charge (schrodinger.protein.residue.Residue attribute) charge_is_conserved() (in module schrodinger.application.jaguar.reactiq_validation) charge_is_consistent() (in module schrodinger.application.jaguar.reactiq_validation) charge_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) CHARGE_SPIN_INCONSISTANT_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) ChargeConstraint (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) ChargeConstraintRow (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsColumns (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeConstraintsSubTab (class in schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints) ChargeConstraintsTableView (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) CHARGED_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) CHARGED_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) CHARGED_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) chargedStrucsPresent() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) ChargeFilterStage (class in schrodinger.pipeline.stages.filtering) ChargePropertySelector (class in schrodinger.application.matsci.chargegui) charges_from_ct (schrodinger.structutils.minimize.Minimizer attribute) ChargeSelectorDelegate (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets) ChargeSelectorLineEdit (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector) charPositionInLine (schrodinger.application.desmond.antlr3.tree.CommonTree attribute) CharStream (class in schrodinger.application.desmond.antlr3.streams) chdir (class in schrodinger.utils.fileutils) chdir() (in module schrodinger.application.desmond.util) CHECK (schrodinger.maestro.markers.Icons attribute) check() (schrodinger.application.desmond.enhanced_sampling.FcnTypes.ArraySyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.Syntax method) (schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes.ArraySyntax method) (schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes.Syntax method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) check1_subst_code() (in module schrodinger.application.desmond.fep_mapping) (in module schrodinger.application.desmond.fep_util) check_attachment_point() (in module schrodinger.structutils.rgroup_enumerate) check_call() (in module schrodinger.utils.subprocess) check_canvas_license() (in module schrodinger.application.canvas.topo_descriptors) check_compatible_forcefield() (in module schrodinger.application.desmond.starter.generator.fep_plus) check_conflicts() (in module schrodinger.application.jaguar.reactiq_validation) check_conformers() (in module schrodinger.application.matsci.reaction_workflow_utils) check_consistency() (in module schrodinger.application.desmond.packages.topo) check_coordinates_changed() (in module schrodinger.application.matsci.freevolume) check_ff_assignment() (in module schrodinger.application.matsci.reaction_workflow_utils) check_file_exist() (in module schrodinger.application.matsci.equilibrium_md) check_file_exists() (in module schrodinger.application.desmond.starter.ui.fep_plus) check_for_spears() (in module schrodinger.structutils.ringspear) check_formula() (in module schrodinger.infra.propedit) check_fp_availability() (in module schrodinger.application.hitexpander) check_hbond() (schrodinger.protein.analysis.Report.primex_steric_clash_data_set method) (schrodinger.protein.analysis.Report.steric_clash_data_set method) check_if_lattice_properties_exist() (in module schrodinger.application.matsci.nano.particle) check_key() (schrodinger.application.mopac.results71.MopacResults71 method) check_key_pair() (in module schrodinger.utils.sshconfig) check_license() (in module schrodinger.application.matsci.jobutils) check_map() (in module schrodinger.utils.sea) check_map2() (in module schrodinger.utils.sea) check_mapping() (in module schrodinger.application.desmond.fep_mapping) check_memory_use() (in module schrodinger.application.mopac.results2012) check_module() (in module schrodinger.application.bioluminate.validate_imported_modules) check_options() (in module schrodinger.application.matsci.equilibrium_md) check_output() (in module schrodinger.utils.subprocess) check_reaction_wf_structures() (in module schrodinger.application.matsci.reaction_workflow_utils) check_restrain_diffs() (in module schrodinger.application.desmond.gconfig) check_rule() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) check_running_as_root() (in module schrodinger.utils.installation_check) check_sanity() (in module schrodinger.application.desmond.cms) check_st_valences() (in module schrodinger.application.prepwizard) check_subjob_output() (schrodinger.pipeline.stages.glide.DockingStage method) check_subset_existence() (in module schrodinger.pipeline.stages.phase) check_subst_code() (in module schrodinger.application.desmond.fep_util) check_system() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.SysType method) (schrodinger.application.desmond.systype.WatermapTyper static method) check_valid_key() (in module schrodinger.job.launchapi) checkAlignment() (schrodinger.application.matsci.nano.particle.CheckInput method) checkAll() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) (schrodinger.application.matsci.nano.sheet.CheckInput method) (schrodinger.application.matsci.nano.tube.CheckInput method) checkAndProcessAllowAdsorptionOnto() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkArgs() (schrodinger.structutils.createfragments.FragmentCreator method) checkASU() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkAtomUniqueness() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition method) checkAtomZeroIndex() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition method) checkBasisSets() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetProxyModel method) checkBilayerSep() (schrodinger.application.matsci.nano.check.CheckInput method) checkBilayerShift() (schrodinger.application.matsci.nano.check.CheckInput method) checkBilayerStackType() (schrodinger.application.matsci.nano.check.CheckInput method) checkBlockTau() (schrodinger.application.matsci.equilibrium_md.MixInBlockStd method) checkBondingAndTranslate() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkBondlength() (schrodinger.application.matsci.nano.check.CheckInput method) checkCanvasKPLSModelFile() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS static method) checkCellDims() (schrodinger.application.matsci.nano.check.CheckInput method) checkChannelDefs() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkChannelDefsVsReactants() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkChannelUniqueness() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkChargeAndMultiplicity() (schrodinger.application.matsci.mecp_mod.CheckInput static method) checkChargesMultiplicitiesStates() (schrodinger.application.matsci.mecp_mod.CheckInput static method) checkCompatibleTypes() (in module schrodinger.infra.propedit) checkConflicts() (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.GlideJob method) checkConformationalSearch() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkConnectivity() (schrodinger.application.matsci.rxn_path.CheckInput method) checkConstantVol() (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) checkConstraintCoords() (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) checkCT() (in module schrodinger.infra.propedit) checkDefinition() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition method) checkDefStrFormat() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition method) checkDielectric() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) checkDissociationBondLength() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkedFeatures() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) checkEdgetypes() (schrodinger.application.matsci.nano.check.CheckInput method) checkElements() (schrodinger.application.matsci.nano.check.CheckInput method) checkElitism() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkExcitedStatesType() (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController method) checkExistingFile() (schrodinger.application.matsci.nano.check.CheckInput method) checkFields() (schrodinger.application.livedesign.ld_export.ExportThreadRunner method) checkFile() (schrodinger.pipeline.stage.Stage method) checkFileExists() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkFiles() (schrodinger.pipeline.stage.Stage method) checkForceFieldLicense() (schrodinger.application.glide.glide.GlideJob method) checkForClashes() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) checkForCollectionChanges() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) checkForCombLibChanges() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) checkForCompletion() (schrodinger.pipeline.stages.qikprop.QikPropStage method) checkForInterStructureClashes() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) checkForIntraStructureClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) checkForMatch() (schrodinger.application.bioluminate.propfilter.BooleanDatabaseCriterion method) (schrodinger.application.bioluminate.propfilter.NumericalDatabaseCriterion method) (schrodinger.application.bioluminate.propfilter.StringDatabaseCriterion method) checkForPaletteChanges() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) checkForRings() (schrodinger.application.matsci.montecarlo.ClashChecker method) checkFractionalDefs() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkFractionalRedundancies() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkFragmentLibs() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkFreezers() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkGenerations() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkGuess() (schrodinger.application.matsci.rxn_path.CheckInput method) checkHost() (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) checkIfNotAdsorbable() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkIfNotSimpleBond() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkin() (schrodinger.infra.licensing.License method) (schrodinger.utils.license.License method) checkIndicies() (schrodinger.application.matsci.nano.check.CheckInput method) checkInitialPopulation() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkInoculate() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) CheckInput (class in schrodinger.application.matsci.genetic_optimization.genetic_optimization) (class in schrodinger.application.matsci.mecp_mod) (class in schrodinger.application.matsci.nano.check) (class in schrodinger.application.matsci.nano.particle) (class in schrodinger.application.matsci.nano.sheet) (class in schrodinger.application.matsci.nano.slab) (class in schrodinger.application.matsci.nano.tube) (class in schrodinger.application.matsci.nano.xtal) (class in schrodinger.application.matsci.rxn_channel.rxn_channel) (class in schrodinger.application.matsci.rxn_path) checkInput() (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.slab.Surface method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) checkInputFile() (schrodinger.application.matsci.nano.xtal.CheckInput method) (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkInputFiles() (schrodinger.application.matsci.rxn_path.CheckInput method) checkInputParams() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization method) (schrodinger.application.matsci.nano.xtal.Crystal method) (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) checkInputs() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.glide.DockingStage method) checkInterpolation() (schrodinger.application.matsci.rxn_path.CheckInput method) checkIntersectingBond() (schrodinger.application.matsci.nano.particle.Nanoparticle method) checkJaguarKwargs() (schrodinger.application.matsci.mecp_mod.CheckInput static method) checkJobName() (schrodinger.application.matsci.rxn_path.CheckInput method) checkKeywordsLE() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) checkLatticeAngleValues() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkLatticeMaxVolume() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkLatticeParameters() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkLicense() (schrodinger.infra.phase.PhpLicenseGeneric method) checkLigands() (schrodinger.application.livedesign.maestro_data_types.Complexes method) checkMaeExt() (schrodinger.application.matsci.nano.check.CheckInput method) checkMaeFile() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) CHECKMARK (schrodinger.maestro.markers.Icons attribute) checkMemoryLimit() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) checkMillerIndices() (schrodinger.application.matsci.nano.plane.CrystalPlane method) checkMixPrevious() (schrodinger.application.matsci.rxn_path.CheckInput method) checkMultipleMappings() (in module schrodinger.application.canvas.r_group) checkMultiplicity() (schrodinger.application.jaguar.gui.base_panel.ExcitedStateValidatorMixin method) checkMultiplicityProperty() (schrodinger.application.jaguar.gui.base_panel.PropertiesValidatorMixin method) checkNewCoordinate() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) checkNodeFile() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkNoRxnComplex() (schrodinger.application.matsci.rxn_path.CheckInput method) checkNumAtoms() (schrodinger.application.livedesign.maestro_data_types.TargetlessBase method) checkNumBilayers() (schrodinger.application.matsci.nano.check.CheckInput method) checkNumCells() (schrodinger.application.matsci.nano.check.CheckInput method) checkNumEntries() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) checkNumNodes() (schrodinger.application.livedesign.maestro_data_types.DockedPoses method) (schrodinger.application.livedesign.maestro_data_types.IndividualStructureBase method) checkNumRandomChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkNumUnitCellParams() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkNumWalls() (schrodinger.application.matsci.nano.check.CheckInput method) checkOK() (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.Code method) (schrodinger.protein.getpdb_utility.WholePDB method) checkOperators() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkOrigin() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkout() (schrodinger.application.licensing.licadmin.LicenseResource method) checkOutputFile() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) checkParallelization() (schrodinger.application.matsci.mecp_mod.CheckInput static method) checkParameters() (schrodinger.pipeline.stage.Stage method) checkPkaAtom() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) checkPkaAtoms() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) CHECKPOINT (schrodinger.application.matsci.desmondutils.MSJStringer attribute) checkPopulationParam() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkPresumedTs() (schrodinger.application.matsci.rxn_path.CheckInput method) checkProducts() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) checkProperties() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkProperty() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property method) checkPropertyType() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) checkRandomChannelsInput() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkRandomSeed() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkRandomTypes() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkRates() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkReactants() (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput method) checkReactions() (schrodinger.analysis.reaction.RouteNode method) checkReorder() (schrodinger.application.matsci.rxn_path.CheckInput method) checkRequiredProperties() (schrodinger.application.matsci.amorphous.BaseMoiety method) checkResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method) checkReverseInterpolation() (schrodinger.application.matsci.rxn_path.CheckInput method) checkRunning() (schrodinger.application.licensing.licadmin.LocalServerProcess method) checkSample() (schrodinger.application.matsci.rxn_path.CheckInput method) checkScaling() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkScanCoords() (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) checkSelection() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkSetTimeInterval() (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) checkShapeParams() (schrodinger.application.matsci.nano.particle.CheckInput method) checkSlabThickness() (schrodinger.application.matsci.nano.slab.CheckInput static method) checkSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) checkSpaceGroup() (schrodinger.application.matsci.nano.xtal.CheckInput method) checkStaticFrag() (in module schrodinger.infra.phase) checkStructure() (schrodinger.structutils.filter.Filter method) (schrodinger.structutils.filter.SingleFilter method) (schrodinger.structutils.filter.SinglePropFilter method) (schrodinger.structutils.filter.SingleSmartsFilter method) checkStructurePairs() (schrodinger.application.matsci.rxn_path.CheckInput method) checkStructures() (schrodinger.application.matsci.rxn_path.CheckInput method) checkTargets() (schrodinger.application.livedesign.maestro_data_types.Complexes method) (schrodinger.application.livedesign.maestro_data_types.DockedPoses method) checkTau() (schrodinger.application.matsci.equilibrium_md.TrjBase method) checkTermFrag() (schrodinger.application.matsci.nano.check.CheckInput method) checkTerminationParams() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkTournamentSize() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkTpp() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CheckInput method) checkUpToIndex() (schrodinger.application.matsci.nano.check.CheckInput method) checkUserNames() (schrodinger.application.bioluminate.propfilter.PropertySelectorWithRanges method) checkUserOutputs() (schrodinger.pipeline.pipeline.Pipeline method) checkValidity() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.EnsembleClassFrame method) (schrodinger.application.desmond.gui.EnsembleTab method) (schrodinger.application.desmond.gui.IntegrationTab method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.MinOutputFrame method) (schrodinger.application.desmond.gui.MinimizerFrame method) (schrodinger.application.desmond.gui.OutputTab method) (schrodinger.application.desmond.gui.RandVelFrame method) (schrodinger.application.desmond.gui.RelaxFrame method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.gui.SimOptionsFrame method) checkValidOneLetterCodes() (schrodinger.application.matsci.amorphous.Moieties method) checkValidWeights() (schrodinger.application.matsci.amorphous.Moieties method) checkVel() (schrodinger.application.matsci.equilibrium_md.TrjBase method) checkWallSep() (schrodinger.application.matsci.nano.check.CheckInput method) checkWeights() (in module schrodinger.trajectory.prody.ensemble) (schrodinger.application.matsci.rxn_path.CheckInput method) children() (schrodinger.application.desmond.reorder_atom.Node method) chiral_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) chirality (schrodinger.structure._StructureAtom attribute) chirality_is_conserved() (in module schrodinger.application.jaguar.chirality) chm_bluebird (class in schrodinger.application.canvas.utils) chm_excel (class in schrodinger.application.canvas.utils) chm_sparse_bitset_from_string() (in module schrodinger.structutils.interactionfp) ChmColumnUIDFilterPtr (class in schrodinger.application.canvas.base) ChmCSVTools (class in schrodinger.application.canvas.utils) ChmMolPtr (class in schrodinger.application.canvas.base) ChmRowUIDFilterPtr (class in schrodinger.application.canvas.base) CHOICE_OFF (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) CHOICE_ON (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) choiceChanged (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector attribute) Choices (class in schrodinger.application.jaguar.reactiq_keywords) choose_ligand() (in module schrodinger.ui.chooseligand) chooseEntry() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) ChooseLigandDialog (class in schrodinger.ui.chooseligand) ChooseLigandModel (class in schrodinger.ui.chooseligand) chooseSolvent() (schrodinger.application.matsci.mswidgets.CompactSolventSelector method) chop() (in module schrodinger.utils.cgxutils) CHORUS_BOX_A_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_AZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_B_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BASE_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_BZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_C_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CX_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) CHORUS_BOX_CZ_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) Chothia (schrodinger.protein.annotation.AntibodyCDRScheme attribute) CIS (in module schrodinger.application.matsci.buildcomplex) cis_excitation_energies() (in module schrodinger.application.jaguar.textparser) CLASH (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) clash_iterator() (in module schrodinger.structutils.interactions.steric_clash) clash_volume() (in module schrodinger.structutils.interactions.steric_clash) ClashChecker (class in schrodinger.application.matsci.montecarlo) CLASS_KWARGS (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) ClassEvaluator (class in schrodinger.application.matsci.genetic_optimization.genetic_optimization) classFractions (schrodinger.infra.phase.PhpQSARModel attribute) ClassicToken (class in schrodinger.application.desmond.antlr3.tokens) clean() (schrodinger.application.bioluminate.protein.Refiner method) clean_basisname() (in module schrodinger.application.jaguar.jaguar_keyword_utils) clean_drawing() (in module schrodinger.application.desmond.maestro) clean_st() (in module schrodinger.application.jaguar.autots_bonding) clean_string() (in module schrodinger.application.matsci.jobutils) cleanAndUniquify() (schrodinger.application.matsci.jobutils.StringCleaner method) cleanup() (in module schrodinger.application.desmond.fep_mapping) (in module schrodinger.application.desmond.fep_net_charge) (schrodinger.application.glide.glide.ConstraintGroup method) (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.glide.glide.Gridgen method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.protein.assignment.ProtAssign method) cleanup_external() (in module schrodinger.application.mopac.utils) cleanup_time() (in module schrodinger.application.desmond.fepana) cleanupIntermediateFiles() (schrodinger.pipeline.pipeline.Pipeline method) cleanUpPBCBonds() (schrodinger.application.matsci.nano.xtal.PBCBonds method) cleanupTempFiles() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) clear() (in module schrodinger.infra.propedit) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.desmond.fep_gui.PathModel method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.application.desmond.fep_scholar_util.FEPStructureObject method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.phase.featureselector.FeatureSelector method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.graphics3d.common.Group method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.infra.phase.PhpDeltaHypo method) (schrodinger.infra.phase.PhpExclVol method) (schrodinger.infra.phase.PhpFeatureData method) (schrodinger.infra.phase.PhpFeatureDefinition method) (schrodinger.infra.phase.PhpFeatureRules method) (schrodinger.infra.phase.PhpHiCluster method) (schrodinger.infra.phase.PhpQSAR method) (schrodinger.infra.phase.PhpSiteConstrainer method) (schrodinger.infra.phase.PhpSiteMask method) (schrodinger.protein.membrane.Membrane_Model method) (schrodinger.structure._StructureProperty method) (schrodinger.ui.residueselector.MutationSelectorFrame method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) (schrodinger.utils.preferences.Preferences method) (schrodinger.utils.scollections.IdentityDict method) clear_all_tag() (schrodinger.utils.sea.Sea method) clear_asu_and_fractional_properties() (in module schrodinger.application.matsci.nano.xtal) clear_atom_props() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) clear_autots_atom_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_bond_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_autots_st_properties() (in module schrodinger.application.jaguar.autots_bonding) clear_cache() (schrodinger.application.desmond.packages.traj.Source method) clear_input() (schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter method) (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method) clear_layout() (in module schrodinger.ui.residueselector) clear_marker_properties() (in module schrodinger.application.matsci.builderwidgets) clear_restrain() (schrodinger.application.desmond.cms.Cms method) clearActions() (schrodinger.application.bioluminate.actions.factory.Factory method) clearAllConstraints() (schrodinger.application.jaguar.input.JaguarInput method) clearAslText() (schrodinger.application.matsci.mswidgets.MdAtomSelector method) clearAtomicBases() (schrodinger.application.jaguar.input.JaguarInput method) clearChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) clearClusters() (schrodinger.infra.phase.PhpHiCluster method) clearCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) clearCombdef() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) clearConstraintsIfMultiStrucTab() (schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin method) clearConstraintsIfProject() (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin method) clearConstraintsIfWorkspace() (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) clearDataForEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) clearDataSet() (schrodinger.infra.phase.PhpQSAR method) clearDefaultCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) clearGraph() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) clearJobs() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) clearLabels() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) clearLigands() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) clearLR() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) clearModel() (schrodinger.infra.phase.PhpQSAR method) clearPalette() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) clearReadErrors() (schrodinger.structure.FormatReader method) (schrodinger.structure.StructureReader method) clearResources() (schrodinger.application.licensing.licadmin.LocalServerProcess method) ClearResults() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) clearRowIfEmpty() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate method) clearRows() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) clearRules() (schrodinger.utils.colorscheme.MM_CScheme method) clearSelected() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) clearSelection() (schrodinger.application.phase.featureselector.FeatureModel method) (schrodinger.application.phase.phase_markers.PhaseMarkers method) clearSiteMaskGroups() (schrodinger.infra.phase.PhpSiteMask method) clearSketcher() (schrodinger.application.matsci.builderwidgets.SketcherBox method) clearStructs() (schrodinger.application.combiglide.combenumdock.collectionViewerModel method) clearView() (schrodinger.application.desmond.fep_gui.StrucListModel method) click() (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) client (schrodinger.application.glide.http_client.GlideServerManager attribute) clone() (schrodinger.application.desmond.packages.msys.System method) (schrodinger.application.matsci.genetic_optimization.genetic_optimization.StructureGenome method) (schrodinger.application.qsite.input.Cut method) (schrodinger.application.qsite.input.HydrogenCap method) (schrodinger.utils.sea.Map method) clone_buffer_violations() (in module schrodinger.application.desmond.packages.msys.groups) CloneSystem() (in module schrodinger.application.desmond.packages.msys) CLOSABLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) close() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) (schrodinger.application.desmond.ffiostructure.CMSReader method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.livedesign.export_controller.DataMapWriter method) (schrodinger.infra.mmgpgpu.ifstream method) (schrodinger.infra.mmgpgpu.ofstream method) (schrodinger.infra.mmjob.ifstream method) (schrodinger.infra.mmjob.ofstream method) (schrodinger.infra.mmsurf.ifstream method) (schrodinger.infra.mmsurf.ofstream method) (schrodinger.project.Project method) (schrodinger.structure.MaestroReader method) (schrodinger.structure.MaestroTextReader method) (schrodinger.structure.MaestroWriter method) (schrodinger.structure.Mol2Reader method) (schrodinger.structure.Mol2Writer method) (schrodinger.structure.MultiFileStructureWriter method) (schrodinger.structure.PDBReader method) (schrodinger.structure.PDBWriter method) (schrodinger.structure.SDReader method) (schrodinger.structure.SDWriter method) (schrodinger.structure.SmilesCsvWriter method) (schrodinger.structure.SmilesWriter method) (schrodinger.structure.StructureReader method) (schrodinger.structure.StructureWriter method) (schrodinger.utils.cgxutils.FragmentLibrary method) (schrodinger.utils.colorscheme.ifstream method) (schrodinger.utils.colorscheme.ofstream method) (schrodinger.utils.multifpfile.MultiFPFile method) (schrodinger.utils.multifpfile.MultiFPFileWriter method) (schrodinger.utils.pymol.PymolInstance method) (schrodinger.utils.pymol.PymolScriptInstance method)

close_contact_action (schrodinger.infra.phase.PhpAlignCoreOptions attribute) close_contact_tol (schrodinger.infra.phase.PhpAlignCoreOptions attribute) CLOSE_LIG_DIST (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) close_output() (schrodinger.application.desmond.bennett.CalcBAR method) closeBlockIfNecessary() (schrodinger.structure.Structure method) (schrodinger.structure.TextualStructure method) closeContactFailure() (schrodinger.infra.phase.PhpAlignCore method) closeDialog() (schrodinger.application.desmond.gui.AdvOptionsFrame method) closeEvent() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.matsci.sliceplot.SlicePlot method) closeFeatureEditDialog (schrodinger.application.phase.phase_markers.PhaseMarkers attribute) closeFile() (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.WholePDB method) closeFiles() (schrodinger.protein.getpdb_utility.Code method) closePalette() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) closePanel() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) closeProject() (schrodinger.infra.phase.PhpProject method) closeWindow() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) ClustalAligner (class in schrodinger.protein.align) cluster() (in module schrodinger.application.desmond.packages.analysis) (schrodinger.protein.assignment.ProtAssign method) cluster1 (schrodinger.infra.phase.PhpHiClusterPair attribute) cluster2 (schrodinger.infra.phase.PhpHiClusterPair attribute) clusterDM() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) clusterFP() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) clustering_distance (schrodinger.protein.assignment.ProtAssign attribute) ClusterStatisticsPlotDialog (class in schrodinger.application.canvas.clustergui) ClusterValues (class in schrodinger.analysis.cluster) CluUtil (class in schrodinger.application.macromodel.utils) CM_TO_ANGSTROM (schrodinger.application.matsci.nano.xtal.Crystal attribute) cmd (schrodinger.application.licensing.licerror.LicenseError attribute) CmdJobTask (class in schrodinger.tasks.jobtasks) CmdlineTaskReporter (class in schrodinger.tasks.runners) cmdlist (schrodinger.infra.mmjob.JobLaunchOptions attribute) cmdlist_to_cmd() (in module schrodinger.tasks.jobtasks) cmp() (schrodinger.application.jaguar.results.BondCharge method) (schrodinger.application.jaguar.results.Dipole method) (schrodinger.application.jaguar.results.Orbital method) (schrodinger.application.jaguar.results.ThermoProp method) Cms (class in schrodinger.application.desmond.cms) cms_atom() (in module schrodinger.application.desmond.packages.topo) cms_file (schrodinger.project.ProjectRow attribute) cms_structure_reader (schrodinger.project.ProjectRow attribute) CmsModel (class in schrodinger.application.desmond.meta) CMSReader (class in schrodinger.application.desmond.ffiostructure) CNSData (class in schrodinger.application.desmond.cns_io) coalesce() (schrodinger.application.desmond.packages.msys.TermTable method) coalesceTables() (schrodinger.application.desmond.packages.msys.System method) COARSE (schrodinger.application.matsci.qualityslider.QualitySlider attribute) Coc (class in schrodinger.application.desmond.packages.analysis) Code (class in schrodinger.protein.getpdb_utility) code (schrodinger.application.licensing.licerror.LicenseError attribute) COLINEAR_THRESH (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule attribute) collapseAll() (schrodinger.application.matsci.mswidgets.MultiStageArea method) collapsed (schrodinger.project.EntryGroup attribute) collectInternals() (schrodinger.application.matsci.rxn_path.ReactionCoords method) collectIonCandidates() (schrodinger.application.ligprep.ionizer.Ionizer method) collectionChanged() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) collectionRefreshed() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) collectionViewerModel (class in schrodinger.application.combiglide.combenumdock) Color (class in schrodinger.structutils.color) color (schrodinger.structure._StructureAtom attribute) (schrodinger.surface.Surface attribute) color() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) color_arg_to_rgb() (in module schrodinger.graphics3d.common) color_potential_surface() (in module schrodinger.application.bioluminate.escomp) color_scheme (schrodinger.surface.Surface attribute) color_source (schrodinger.surface.Surface attribute) ColorBy (class in schrodinger.surface) colorByMolecule() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) colorByRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) ColorFrom (class in schrodinger.surface) coloring() (schrodinger.surface.Surface method) ColorRamp (class in schrodinger.structutils.color) ColorScheme (class in schrodinger.structutils.color) ColorSchemeManager (class in schrodinger.utils.colorscheme) colorSurfByPatches() (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) COLUMN (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.FullTable attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitTable attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesModelHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka attribute) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetTableView attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute) Column (schrodinger.application.livedesign.panel_components.ExportTableView attribute) (schrodinger.application.phase.featureselector.FeatureModel attribute) (schrodinger.application.phase.phase_widgets.HypothesisModel attribute) (schrodinger.ui.picking.PickResidueModel attribute) column() (schrodinger.application.livedesign.panel_components.ColumnCheckboxItem method) ColumnCheckboxItem (class in schrodinger.application.livedesign.panel_components) columnCount() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.desmond.fep_gui.PathModel method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.PatternModel method) columnGetDataName() (schrodinger.infra.table.Table method) columnGetDataType() (schrodinger.infra.table.Table method) columnGetName() (schrodinger.infra.table.Table method) columnGetPersistent() (schrodinger.infra.table.Table method) columnGetProperty() (schrodinger.infra.table.Table method) columnGetVisible() (schrodinger.infra.table.Table method) columnGetWidth() (schrodinger.infra.table.Table method) columnHasAllSameResidues() (schrodinger.protein.alignment.BaseAlignment method) COLUMNS (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) columns() (schrodinger.protein.alignment.BaseAlignment method) ColumnSelectionListView (class in schrodinger.application.livedesign.panel_components) ColumnSelectionModel (class in schrodinger.application.livedesign.panel_components) ColumnSelectionProxyModel (class in schrodinger.application.livedesign.panel_components) columnSetName() (schrodinger.infra.table.Table method) columnSetPersistent() (schrodinger.infra.table.Table method) columnSetProperty() (schrodinger.infra.table.Table method) columnSetVisible() (schrodinger.infra.table.Table method) columnSetWidth() (schrodinger.infra.table.Table method) Com (class in schrodinger.application.desmond.packages.analysis) COMBIGLD_REPLACEMENTS (schrodinger.application.matsci.rxn_path.CheckInput attribute) combine_rings() (in module schrodinger.application.desmond.r_group_asl) combine_sentences() (in module schrodinger.application.jaguar.gui.basis_selector) combine_two_structures() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) combine_vdw() (in module schrodinger.application.desmond.cms) combineAndReorder() (schrodinger.application.matsci.rxn_channel.rxn_channel.Products method) CombinedUi (class in schrodinger.application.jaguar.gui.tabs.base_tab) combineFollows() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) combineMapWith() (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule method) CombineStage (class in schrodinger.pipeline.stages.combine) COMBO_TEXT (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) ComboRadioSelector (class in schrodinger.application.jaguar.gui.tabs.theory_tab) command() (in module schrodinger.maestro.maestro) (schrodinger.ui.chooseligand.TestApp method) command_callback_add() (in module schrodinger.maestro.maestro) command_callback_remove() (in module schrodinger.maestro.maestro) CommandError CommandLine (class in schrodinger.application.desmond.packages.cui) commandLine() (schrodinger.job.app.App method) commandLineOptions() (schrodinger.application.jaguar.input.GenOptions method) commence() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) commit() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.desmond.maestro.Workspace method) commitDataToSelected (schrodinger.application.jaguar.gui.input_tab_widgets.CommitMultipleDelegate attribute) commitDataToSelected() (schrodinger.application.jaguar.gui.utils.ProjTableLikeView method) commitMasterData() (schrodinger.infra.phase.PhpProject method) CommitMultipleDelegate (class in schrodinger.application.jaguar.gui.input_tab_widgets) CommonErrorNode (class in schrodinger.application.desmond.antlr3.tree) CommonToken (class in schrodinger.application.desmond.antlr3.tokens) CommonTokenStream (class in schrodinger.application.desmond.antlr3.streams) CommonTree (class in schrodinger.application.desmond.antlr3.tree) CommonTreeAdaptor (class in schrodinger.application.desmond.antlr3.tree) CommonTreeNodeStream (class in schrodinger.application.desmond.antlr3.tree) comp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) comp_atoms() (in module schrodinger.application.desmond.packages.topo) COMP_SCORE (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) CompactSolventSelector (class in schrodinger.application.matsci.mswidgets) comparator() (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) compare_angle() (in module schrodinger.application.jaguar.jaguar_diff) compare_consistently_ordered_structures() (in module schrodinger.application.jaguar.autots_rmsd) compare_eneseq() (in module schrodinger.application.desmond.packages.gdesmond_utils) compare_float() (in module schrodinger.application.jaguar.jaguar_diff) compare_lists() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) compare_molecular_formulas() (in module schrodinger.application.matsci.reorder) compare_molecule_lists() (in module schrodinger.application.jaguar.autots_rmsd) compare_structures() (in module schrodinger.application.jaguar.autots_rmsd) compareFeatureDef() (schrodinger.infra.phase.PhpProject method) ComparisonFrame (class in schrodinger.application.matsci.reordergui) ComparisonListWidget (class in schrodinger.application.matsci.reordergui) compAtomFromRefAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) compile_xy() (in module schrodinger.application.desmond.gchart) compileResults() (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator method) complete_bonding() (in module schrodinger.application.matsci.nano.xtal) completedJobids() (schrodinger.utils.installation_check.TestJobDJ method) completePolymer() (schrodinger.application.matsci.amorphous.Initiator method) Complex (class in schrodinger.application.glide.poseviewconvert) COMPLEX_HOTREGION (schrodinger.application.desmond.constants.REST_PROPERTIES attribute) COMPLEX_SIZE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) ComplexBuilder (class in schrodinger.application.matsci.buildcomplex) Complexes (class in schrodinger.application.livedesign.maestro_data_types) ComplexTemplateSketcher (class in schrodinger.application.matsci.builderwidgets) COMPONENT_LIST (schrodinger.application.desmond.packages.energygroup.Energy attribute) CompositeAnalyzer (class in schrodinger.application.desmond.packages.staf) CompositeDynamicAslAnalyzer (class in schrodinger.application.desmond.packages.staf) COMPOSITION_FLAG (schrodinger.application.matsci.jobutils.MultijobDriver attribute) COMPOSITION_FLAG_SHORT (schrodinger.application.matsci.jobutils.MultijobDriver attribute) CompoundParam (class in schrodinger.models.parameters) COMPRESS (schrodinger.application.matsci.desmondutils.MSJStringer attribute) compress() (in module schrodinger.pipeline.stages.glide) (in module schrodinger.pipeline.stages.ligprep) compress_residue_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) compute_alogp() (in module schrodinger.application.medchem.property) compute_and_populate_charges() (in module schrodinger.application.matsci.clusterstruct) compute_esp_charges() (in module schrodinger.application.matsci.clusterstruct) compute_max_internal_distance() (in module schrodinger.application.matsci.coarsegrain) compute_medchem_properties() (in module schrodinger.application.medchem.property) compute_mw() (in module schrodinger.application.medchem.property) compute_net_charge_correction() (in module schrodinger.application.desmond.fep_net_charge) compute_net_charge_corrections() (in module schrodinger.application.desmond.fep_net_charge) compute_num_hbond_acceptors() (in module schrodinger.application.medchem.property) compute_num_hbond_donors() (in module schrodinger.application.medchem.property) compute_num_rot_bonds() (in module schrodinger.application.medchem.property) compute_polar_surf_area() (in module schrodinger.application.medchem.property) compute_rip_correction() (in module schrodinger.application.desmond.fep_net_charge) compute_rmse() (in module schrodinger.application.desmond.correlation_tau) compute_smiles() (in module schrodinger.application.medchem.property) compute_std_conc_gibbs_energy() (in module schrodinger.application.jaguar.utils) compute_title() (in module schrodinger.application.medchem.property) computeContextSensitiveRuleFOLLOW() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) computeErrorRecoverySet() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) computeFES() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis method) computeRCorr() (schrodinger.infra.phase.PhpQSAR method) computeShapeSim() (schrodinger.infra.phase.PhpFastShape method) computeShapeSimPy() (schrodinger.infra.phase.PhpFastShape method) computeStats() (schrodinger.infra.phase.PhpQSAR method) computeTokenTypes() (in module schrodinger.application.desmond.antlr3.treewizard) ComputeTopologicalIds() (in module schrodinger.application.desmond.packages.msys) ComUtil (class in schrodinger.application.macromodel.utils) ComUtil_2010 (class in schrodinger.application.macromodel.utils) ComUtilAppSci (class in schrodinger.application.macromodel.utils) CONCAT (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) concat (schrodinger.application.desmond.config.TAG_SPECS attribute) concat() (in module schrodinger.application.desmond.packages.traj) concatenate_cfgs() (in module schrodinger.application.desmond.gconfig) config (schrodinger.application.glide.http_client.GlideServerManager attribute) ConfigError configure_local_ssh_setup() (in module schrodinger.utils.sshconfig) configureBonds() (schrodinger.application.matsci.nano.particle.Nanoparticle method) confirmOverwriting() (schrodinger.application.desmond.fep_gui.DesmondApp method) conformerBlockPositions() (in module schrodinger.infra.phase) ConformerError ConformerRmsd (class in schrodinger.structutils.rmsd) ConformerRmsdX (class in schrodinger.application.jaguar.rmsd) (class in schrodinger.structutils.rmsd) ConfSearch (class in schrodinger.application.macromodel.input) ConfSearchStage (class in schrodinger.pipeline.stages.macromodel) conglomerate_rings() (in module schrodinger.application.canvas.r_group) connect() (in module schrodinger.structutils.build) connect_atoms() (in module schrodinger.application.matsci.nano.xtal) connectAction() (schrodinger.application.bioluminate.actions.factory.Factory method) CONNECTED (schrodinger.application.desmond.restraint.GeneratorTypes attribute) connected_atoms (schrodinger.application.desmond.fep_scholar_util.MetaAtom attribute) connecting_mass() (in module schrodinger.application.desmond.automatic_analysis_generator) ConnectionError ConnectionStorage (class in schrodinger.application.combiglide.combenumdock) (class in schrodinger.application.combiglide.connection_storage) CONNECTIVITYCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) connectSlot() (schrodinger.application.bioluminate.actions.factory.SAction method) connectToCells() (schrodinger.application.matsci.nano.xtal.PBCBonds method) connectToLD() (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) Consensus (class in schrodinger.application.bioluminate.protein) (class in schrodinger.protein.annotation) consensus_freq (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) consensus_seq (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) consensus_symbols (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) CONSENSUS_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) consensusCounterions() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) consensusLigands() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) ConsensusToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) consensusWaters() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) CONST (class in schrodinger.application.desmond.envir) constant_fold() (schrodinger.application.desmond.enhsamp.FcnCall method) (schrodinger.application.desmond.enhsamp.Node method) CONSTANT_PROPERTIES (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) (schrodinger.application.matsci.cgforcefield.FFIOSite attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) Constants (class in schrodinger.application.desmond.constants) (class in schrodinger.application.matsci.nano.constants) (class in schrodinger.application.matsci.rxn_channel.rxn_channel) constrainAll() (schrodinger.application.matsci.zmutils.ZAtom method) (schrodinger.application.matsci.zmutils.ZMatrix method) constrainAtomXYZ() (schrodinger.application.jaguar.input.JaguarInput method) constrainCoord() (schrodinger.application.matsci.zmutils.ZAtom method) constrainInternal() (schrodinger.application.jaguar.input.JaguarInput method) Constraint (class in schrodinger.application.desmond.cms) (class in schrodinger.application.glide.glide) CONSTRAINT_SCORE (schrodinger.protein.align.PairwiseAligner attribute) ConstraintCoordinateColumns (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinateData (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesDelegate (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesModel (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) ConstraintCoordinatesProxyModel (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) constraintCount() (schrodinger.application.jaguar.input.JaguarInput method) ConstraintGroup (class in schrodinger.application.glide.glide) constraints() (schrodinger.application.jaguar.input.JaguarInput method) CONSTRAINTS_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab attribute) construct_lists() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) constructHostArg() (schrodinger.job.launchparams.LaunchParameters method) consume() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer method) consumeCommandLine() (schrodinger.job.launchparams.LaunchParameters method) consumeHiddenToken() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) consumeInitialHiddenTokens() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) consumeNode() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) consumeToken() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) consumeUntil() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) CONTACT_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) contains() (schrodinger.utils.preferences.Preferences method) containsMultipleCores() (schrodinger.application.combiglide.combenumdock.ConnectionStorage method) (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) containsVariant() (schrodinger.infra.phase.PhpFeatureRules method) contextMenuEvent() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) contextMenuRequested() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) continueResBackbone() (schrodinger.application.matsci.amorphous.PolymerToFragments method) contract_by_molecule() (in module schrodinger.application.matsci.clusterstruct) contract_structure() (in module schrodinger.application.matsci.clusterstruct) contractToCentroid() (schrodinger.structutils.ringspear.SpearRing method) ControlType (class in schrodinger.application.matsci.espresso.qeinput) conv_bool() (in module schrodinger.infra.propedit) converge_search() (in module schrodinger.application.macromodel.apps) convergence_category() (in module schrodinger.application.jaguar.textparser) CONVERGENCE_CRITERIA (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) CONVERGENCE_SCHEME_OPTS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) convergenceTypeChanged() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) conversion_maps_builder() (in module schrodinger.application.matsci.qexsd.qespresso.converters) convert() (schrodinger.infra.phase.PhpHypoAdaptor method) convert_attachment_point() (in module schrodinger.structutils.rgroup_enumerate) convert_ct2graph() (in module schrodinger.application.desmond.r_group_asl) convert_data() (in module schrodinger.application.desmond.fep_mapping) convert_file() (in module schrodinger.infra.epydoc_to_sphinx) convert_gibbs_energy_to_std_conc() (in module schrodinger.application.jaguar.utils) convert_muts_file() (schrodinger.application.bioluminate.protein.Mutator static method) convert_nm_and_wavenumber() (in module schrodinger.application.matsci.spectra) convert_old_marker_props_to_new() (in module schrodinger.application.matsci.builderwidgets) convert_prj() (in module schrodinger.application.livedesign.export_controller) convert_prjzip() (in module schrodinger.application.livedesign.export_controller) convert_project_hypotheses() (in module schrodinger.application.phase.pt_hypothesis) convert_res_file() (schrodinger.application.bioluminate.protein.Mutator class method) convert_res_list() (schrodinger.application.bioluminate.protein.Mutator class method) convert_res_to_muts() (schrodinger.application.bioluminate.protein.Mutator static method) convert_residue_list() (schrodinger.application.bioluminate.protein.Mutator static method) convert_rga_data() (in module schrodinger.application.desmond.fep_mapping) convert_selenomethionines() (in module schrodinger.application.prepwizard) convert_sparse_dict_to_list() (in module schrodinger.application.mopac.utils) convert_string() (in module schrodinger.infra.mmim) convert_structure_sequence_for_pattern_search() (in module schrodinger.protein.sequence) convertDataToPlot() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis static method) convertPlotToData() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis static method) convertQimageToImage() (in module schrodinger.application.desmond.report_helper) convertSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) ConvertStage (class in schrodinger.pipeline.stages.convert) convertToCartesian() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) convertToClassToken() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) convertToEnv() (schrodinger.job.launchparams.LaunchParameters method) convertToJLaunchOptions() (schrodinger.job.launchparams.LaunchParameters method) ConvertToRdkit() (in module schrodinger.application.desmond.packages.msys) convertToStatic() (schrodinger.infra.phase.PhpHypoAdaptor method) convertToZMatrix() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) ConvexPolyhedron (class in schrodinger.application.matsci.shapes) Coord (class in schrodinger.application.matsci.rxn_path) COORD_LETTERS (schrodinger.application.matsci.zmutils.ZAtom attribute) COORD_NAME (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) COORD_TYPE (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) COORDINATE_ANGLE_INCREMENT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_ANGLE_OFFSET (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_DISTANCE_INCREMENT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_DISTANCE_OFFSET (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_FUNCS (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateData attribute) COORDINATE_OPTS (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) coordinateAdded (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinateData (class in schrodinger.application.jaguar.gui.tabs.coordinates) coordinateDeleted (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) coordinateDeselected (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinateDialog (class in schrodinger.application.jaguar.gui.base_panel) CoordinateFrame (schrodinger.analysis.visanalysis.volumedata.VolumeData attribute) CoordinateMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) CoordinatePicker (class in schrodinger.application.jaguar.gui.tabs.coordinates) Coordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) coordinateSelected (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) CoordinatesModel (class in schrodinger.application.jaguar.gui.tabs.coordinates) CoordinateTab (class in schrodinger.application.jaguar.gui.tabs.coordinates) coordinateTypeChanged() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker method) CoordinationSite (class in schrodinger.application.matsci.siteselector.siteselector) coords (schrodinger.application.matsci.espresso.qeoutput.KptLegend attribute) (schrodinger.infra.phase.PhpIntCoord attribute) coords_frozen1() (in module schrodinger.application.jaguar.textparser) coords_frozen2() (in module schrodinger.application.jaguar.textparser) coords_harmonic() (in module schrodinger.application.jaguar.textparser) coords_ind() (in module schrodinger.application.jaguar.textparser) coords_nred() (in module schrodinger.application.jaguar.textparser) coords_opt() (in module schrodinger.application.jaguar.textparser) coordsMatch() (in module schrodinger.infra.phase) copy() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) (schrodinger.application.desmond.ffiostructure.FFIOStructure method) (schrodinger.application.desmond.packages.traj.Frame method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.PerAtomBasisRow method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow method) (schrodinger.application.matsci.genetic_optimization.genetic_optimization.StructureGenome method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method) (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.structure.Structure method) (schrodinger.structutils.color.ColorScheme method) (schrodinger.surface.Surface method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) copy_atom_properties() (in module schrodinger.application.matsci.desmondutils) copy_autots_atom_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_bond_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_autots_st_properties() (in module schrodinger.application.jaguar.autots_bonding) copy_bonding() (in module schrodinger.application.jaguar.autots_bonding) copy_file() (in module schrodinger.application.jaguar.file_logger) copy_structure_properties() (in module schrodinger.application.livedesign.ld_utils) copy_structure_property_value() (in module schrodinger.application.livedesign.ld_utils) copyalgn() (schrodinger.application.macromodel.utils.ComUtil method) copyCanvasKPLSModelFiles() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS method) copyChargeMultBasisFromModel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) copyColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) copyColorSchemeByObject() (schrodinger.utils.colorscheme.ColorSchemeManager method) copyColorSchemeRule() (schrodinger.utils.colorscheme.ColorSchemeManager method) copyFile() (schrodinger.infra.phase.PhpProject method) copyProperty() (in module schrodinger.infra.propedit) copyRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel method) copyStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) copyToClipboard() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) CORE_LOCALIZATION_METHODS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) coreSketch() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) correct_restr() (in module schrodinger.application.desmond.fepana) correlation_type() (in module schrodinger.application.jaguar.textparser) count (schrodinger.analysis.enrichment.StatisticalSummary attribute) (schrodinger.application.licensing.licerror.LicenseError attribute) count() (in module schrodinger.application.macromodel.tools) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.utils.mmutil.StringStringMap method) count_atom_hbonds() (in module schrodinger.protein.captermini) count_atoms_in_smarts() (in module schrodinger.structutils.analyze) count_heavy_atoms() (in module schrodinger.application.desmond.r_group_asl) count_ligands() (in module schrodinger.application.hitexpander) count_num_strucs() (in module schrodinger.application.jaguar.gui.utils) count_phosphates_and_sulfurs() (in module schrodinger.application.prepwizard) count_structures() (in module schrodinger.structure) count_traj_frames() (in module schrodinger.application.desmond.gui) countChanged (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) countClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection static method) Counter (class in schrodinger.application.desmond.util) countHeavyAtoms() (in module schrodinger.application.desmond.r_group_asl) countRoots() (in module schrodinger.pipeline.pipeutils) countStructuresMaeOrSD() (in module schrodinger.infra.phase) countTotalStructures() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) coupler (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) coupler_marker (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) COV_FACTOR (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) COV_MIN (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) COV_OFFSET (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) COVALENT_LIGAND (schrodinger.application.desmond.constants.FEP_TYPES attribute) CovalentDockingComplexes (class in schrodinger.application.livedesign.maestro_data_types) CovalentFEPEdgeData (class in schrodinger.application.desmond.fep_edge_data) CovalentMsjGenerator (class in schrodinger.application.desmond.mapper_msj_generator) CPU_UNIT_LABEL (schrodinger.application.matsci.guibase.PerStrucConfigDialog attribute) (schrodinger.application.matsci.guibase.PerStrucSingleGpuConfigDialog attribute) cpus (schrodinger.tasks.jobtasks.JobConfig attribute) (schrodinger.tasks.jobtasks.JobOptions attribute) cpusChanged (schrodinger.tasks.jobtasks.JobConfig attribute) (schrodinger.tasks.jobtasks.JobOptions attribute) cpx_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_forward (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_forward_dg (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_end_time_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_ensemble (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_ff (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_rest_exchanges (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_result (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute) cpx_salt_info (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_salt_molecules (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_sid_lp_results (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) cpx_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_sid_pl_results (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_sid_protein_residues (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_sid_snapshot_times_ps (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_sid_snashot_times_ps (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_sim_time (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_start_time_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_temperature (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_timestep_interval (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_timestep_list (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_total_atoms (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_total_replicas (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cpx_total_waters (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) cradius (schrodinger.application.matsci.elementalprops.ElementalProperties attribute) create() (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.infra.phase.PhpComplex method) create_alignment_from_chains() (in module schrodinger.protein.sequence) create_archive_file() (in module schrodinger.application.licensing.licadmin) create_argument_parser() (in module schrodinger.utils.cmdline) create_atom_marker() (in module schrodinger.maestro.maestro) create_atom_pair_marker() (in module schrodinger.maestro.maestro) create_atom_quad_marker() (in module schrodinger.maestro.maestro) create_atom_tag() (in module schrodinger.application.desmond.maestro) (schrodinger.application.desmond.maestro.Workspace method) create_atom_triple_marker() (in module schrodinger.maestro.maestro) create_cg_system() (in module schrodinger.application.matsci.cgforcefield) create_cms_from_mae() (in module schrodinger.application.desmond.repair_cms) create_cone() (in module schrodinger.maestro.maestro) create_contour_plot_on_figure() (in module schrodinger.application.desmond.mplchart) create_cylinder() (in module schrodinger.maestro.maestro) create_dimer_structures() (in module schrodinger.application.matsci.clusterstruct) create_distance_cell() (in module schrodinger.application.matsci.clusterstruct) (in module schrodinger.structutils.measure) (in module schrodinger.structutils.ringspear) create_disulfide_bonds() (in module schrodinger.application.prepwizard) create_entry_from_workspace() (in module schrodinger.maestro.maestro) create_fragment_structure() (in module schrodinger.structutils.rgroup_enumerate) create_full_system_from_comp() (in module schrodinger.application.desmond.repair_cms) create_hard_link() (in module schrodinger.utils.fileutils) create_hybrid() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) create_hypo (schrodinger.application.phase.input.InputSpecs attribute) create_isosurface_from_grid_data() (in module schrodinger.surface) create_job() (in module schrodinger.application.matsci.jaguarworkflows) create_job_dir (schrodinger.tasks.jobtasks.JobOptions attribute) create_job_dirChanged (schrodinger.tasks.jobtasks.JobOptions attribute) create_live_report() (in module schrodinger.application.livedesign.ld_export) create_logger() (in module schrodinger.application.matsci.textlogger) create_model_xyz_axes() (in module schrodinger.maestro.maestro) create_mpl_plot_on_figure() (in module schrodinger.application.desmond.mplchart) create_msj() (in module schrodinger.application.matsci.desmondutils) create_multiline_text() (in module schrodinger.maestro.maestro) create_nearest_neighbor_cluster() (in module schrodinger.application.matsci.clusterstruct) create_new_box() (in module schrodinger.application.matsci.nano.xtal) create_new_structure() (in module schrodinger.structure) create_non_pbc_cluster() (in module schrodinger.application.matsci.clusterstruct) create_normal() (in module schrodinger.graphics3d.common) create_nx_graph() (in module schrodinger.structutils.analyze) create_pbc() (in module schrodinger.application.matsci.clusterstruct) (in module schrodinger.structutils.ringspear) create_polygon() (in module schrodinger.maestro.maestro) create_polyhedron() (in module schrodinger.maestro.maestro) create_queue() (in module schrodinger.application.matsci.jaguarworkflows) CREATE_RADIOBUTTON_NAMES (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) create_reagent_library() (in module schrodinger.analysis.reaction) create_restart_jobcmd() (in module schrodinger.application.matsci.jobutils) create_restart_launcher() (in module schrodinger.application.matsci.jobutils) create_run_dir() (in module schrodinger.application.matsci.jobutils) create_single_line_text() (in module schrodinger.maestro.maestro) create_single_line_z_buffered_text() (in module schrodinger.maestro.maestro) create_sketcher() (in module schrodinger.application.desmond.fep_edge_report_maker) create_smap() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) create_soft_links() (schrodinger.application.desmond.title_to_hex.Analysis method) create_sphere() (in module schrodinger.maestro.maestro) create_stub_license() (in module schrodinger.application.licensing.licadmin) create_surface() (in module schrodinger.application.bioluminate.surfcomp) create_surface_on_figure() (in module schrodinger.application.desmond.mplchart) create_torsions_plot() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) create_torus() (in module schrodinger.maestro.maestro) create_workdir() (schrodinger.application.desmond.title_to_hex.Analysis method) create_workflows() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) create_xvol (schrodinger.application.phase.input.InputSpecs attribute) createActions() (schrodinger.application.bioluminate.actions.factory.Factory method) createAdditionalViewInformation() (schrodinger.application.livedesign.export_controller.ExportController method) createAlignFile() (schrodinger.application.bioluminate.protein.PrimeStructure method) createCell() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) createChargeProperties() (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) createClusters() (schrodinger.infra.phase.PhpHiCluster method) createCmd() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) createCombLibSelectFile() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) createComplex() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) createConfOptions() (in module schrodinger.infra.phase) createConformers() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) createControlButtons() (schrodinger.application.matsci.mswidgets.StageFrame method) createDataMapFile() (schrodinger.application.livedesign.export_controller.ExportController method) createEditor() (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.TempItemDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBoxDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate method) createEndSubFragment() (schrodinger.application.matsci.amorphous.PolymerToFragments method) createExcludedVolumeClash() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createExcludedVolumeReceptor() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createExcludedVolumeShell() (schrodinger.application.phase.create_xvol.ExcludedVolumeGenerator method) createFFIOBlock() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) createFragForInitiator() (schrodinger.application.matsci.amorphous.PolymerToFragments method) createFragmentDelegate (class in schrodinger.application.combiglide.combenumdock) createFromToken() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) createFromType() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) createGPGPUTable() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) createIconsIfNecessary() (schrodinger.application.matsci.mswidgets.StageFrame method) createImportWidget() (schrodinger.application.bioluminate.bwidgets.ImportWidget method) createInterfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) createIter() (schrodinger.application.bioluminate.interaction_calculator.PiStackFinder class method) createJob() (schrodinger.application.matsci.jaguarworkflows.Step method) createLabel() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) createLabels() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) CreateLike() (in module schrodinger.analysis.visanalysis.volumedatautils) createLocateSite() (in module schrodinger.infra.phase) createMap() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) createModel() (schrodinger.infra.phase.PhpQSAR method) createNode() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) CreateParamTable() (in module schrodinger.application.desmond.packages.msys) createPrjzip() (schrodinger.application.livedesign.export_controller.ExportController method) createReorderedEntry() (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) createRowInCollectionTable() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) createSection() (schrodinger.application.jaguar.input.JaguarInput method) createSequence() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) createSites() (schrodinger.infra.phase.PhpProject method) createSketcher() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) createSlab() (schrodinger.application.matsci.sliceplot.SlicePlot method) createStage() (schrodinger.pipeline.pipeline.Pipeline method) createStaticFrag() (in module schrodinger.infra.phase) createStaticMol() (in module schrodinger.infra.phase) createStaticSite() (in module schrodinger.infra.phase) createString() (schrodinger.application.matsci.desmondutils.MSJStringer method) createSubsetForCompsWithoutSites() (schrodinger.pipeline.stages.phase.DBConfSitesStage method) createSubWidgets() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) createSurfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) CreateSystem() (in module schrodinger.application.desmond.packages.msys) createTemplateFile() (schrodinger.application.bioluminate.protein.PrimeStructure method) createTip4pFfio() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) createToken() (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) createUniqueElement() (schrodinger.application.matsci.espresso.qeinput.MagSpecies method) createVectorAtoms() (schrodinger.protein.membrane.Membrane_Model method) CreateWhenNeeded (class in schrodinger.infra.util) createWithPayload() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.desmond.antlr3.treewizard.TreePatternTreeAdaptor method) CriteriaListModel (class in schrodinger.application.bioluminate.propfilter) (class in schrodinger.ui.ligfilter) Criterion (class in schrodinger.utils.ligfilter) criterion_changed (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector attribute) criterionChanged() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) CriterionParser (class in schrodinger.utils.ligfilter) CriticalPointsFailure crop_image() (in module schrodinger.application.desmond.report_helper) crossprod() (in module schrodinger.application.desmond.cms) crossValidateModel() (schrodinger.infra.phase.PhpQSAR method) Crystal (class in schrodinger.application.matsci.nano.xtal) CRYSTAL_ENVIRON (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) CRYSTAL_SYSTEM (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) CRYSTAL_SYSTEM_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) CRYSTAL_SYSTEMS (schrodinger.application.matsci.nano.xtal.SpaceGroups attribute) CrystalPlane (class in schrodinger.application.matsci.nano.plane) CrystalSystems (class in schrodinger.application.matsci.nano.xtal) CrystalSystems.Cubic (class in schrodinger.application.matsci.nano.xtal) CrystalSystems.Hexagonal (class in schrodinger.application.matsci.nano.xtal) CrystalSystems.Monoclinic (class in schrodinger.application.matsci.nano.xtal) CrystalSystems.Orthorhombic (class in schrodinger.application.matsci.nano.xtal) CrystalSystems.Tetragonal (class in schrodinger.application.matsci.nano.xtal) CrystalSystems.Triclinic (class in schrodinger.application.matsci.nano.xtal) CrystalSystems.Trigonal (class in schrodinger.application.matsci.nano.xtal) CSTART (schrodinger.application.matsci.cgforcefield.FFIODihedral attribute) (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) csv_file_ext (schrodinger.analysis.enrichment.Calculator attribute) Ct (class in schrodinger.application.desmond.packages.msys) ct (schrodinger.application.desmond.maestro.Workspace attribute) (schrodinger.application.desmond.packages.msys.Chain attribute) ct() (schrodinger.application.desmond.packages.msys.System method) ct2chmmol() (in module schrodinger.application.desmond.depictor) ct_to_multipart() (schrodinger.application.glide.http_client.HTTPClient method) CtAtoms() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util) CtBonds() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util) cts (schrodinger.application.desmond.packages.msys.System attribute) Cube (class in schrodinger.application.matsci.shapes) (class in schrodinger.graphics3d.polyhedron) Cubeoctahedron (class in schrodinger.application.matsci.shapes) cubic() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) CUBIC_NAME (schrodinger.application.matsci.nano.xtal.CrystalSystems attribute) current_filename (schrodinger.structure.MultiFileStructureReader attribute) CURRENT_VAL (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) currentCategory() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) currentChoice() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) currentCriterion() (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) currentDataType() (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) currentHost() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.fep_gui.GPUAndCPURESTFEPConfigDialog method) currentProjectID() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) currentProjectName() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) currentRMSD() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method) currentScheme() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) currentSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) currentText() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) curvatures() (schrodinger.surface.Surface method) CUSTOM (schrodinger.job.launchparams.ProjectDisposition attribute) custom_functional() (in module schrodinger.application.jaguar.textparser) CUSTOM_HYPO_TEXT (schrodinger.application.phase.featureselector.FeatureModel attribute) custom_is_list() (in module schrodinger.application.inputconfig) custom_is_string_list() (in module schrodinger.application.inputconfig) CUSTOM_KEY (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) customDirChanged (schrodinger.application.matsci.builderwidgets.TemplateManager attribute) CustomGPUComboBox (class in schrodinger.application.desmond.fep_gui) CustomMaestroAnalysis (class in schrodinger.application.desmond.packages.staf) Cut (class in schrodinger.application.qsite.input) cutAwayExcess() (schrodinger.application.matsci.nano.particle.Nanoparticle method) cutOutNanoSheet() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) CV (class in schrodinger.application.desmond.meta) CVAngle (class in schrodinger.application.desmond.meta) cvangle_floor_template (schrodinger.application.desmond.meta.CVAngle attribute) cvangle_grp_template (schrodinger.application.desmond.meta.CVAngle attribute) cvangle_template (schrodinger.application.desmond.meta.CVAngle attribute) cvangle_wall_template (schrodinger.application.desmond.meta.CVAngle attribute) CVDihedral (class in schrodinger.application.desmond.meta) cvdihedral_grp_template (schrodinger.application.desmond.meta.CVDihedral attribute) cvdihedral_template (schrodinger.application.desmond.meta.CVDihedral attribute) CVDist (class in schrodinger.application.desmond.meta) cvdist_floor_template (schrodinger.application.desmond.meta.CVDist attribute) (schrodinger.application.desmond.meta.CVzdist attribute) cvdist_grp_template (schrodinger.application.desmond.meta.CVDist attribute) cvdist_template (schrodinger.application.desmond.meta.CVDist attribute) cvdist_wall_template (schrodinger.application.desmond.meta.CVDist attribute) (schrodinger.application.desmond.meta.CVzdist attribute) CVrgyr (class in schrodinger.application.desmond.meta) CVrgyr_mass (class in schrodinger.application.desmond.meta) cvrgyr_mass_template (schrodinger.application.desmond.meta.CVrgyr_mass attribute) cvrgyr_template (schrodinger.application.desmond.meta.CVrgyr attribute) CVrmsd (class in schrodinger.application.desmond.meta) cvrmsd_conf_template (schrodinger.application.desmond.meta.CVrmsd_symm attribute) cvrmsd_setup_template (schrodinger.application.desmond.meta.CVrmsd_symm attribute) CVrmsd_symm (class in schrodinger.application.desmond.meta) cvrmsd_template (schrodinger.application.desmond.meta.CVrmsd attribute) (schrodinger.application.desmond.meta.CVrmsd_symm attribute) cvrmsd_weights_template (schrodinger.application.desmond.meta.CVrmsd attribute) CVwhim (class in schrodinger.application.desmond.meta) cvwhim_template (schrodinger.application.desmond.meta.CVwhim attribute) CVzdist (class in schrodinger.application.desmond.meta) CVzdist0 (class in schrodinger.application.desmond.meta) cvzdist0_template (schrodinger.application.desmond.meta.CVzdist0 attribute) cvzdist_template (schrodinger.application.desmond.meta.CVzdist attribute) cycle() (schrodinger.application.bioluminate.bwidgets.LoadingIcon method) Cylinder (class in schrodinger.application.matsci.shapes)

D

d12 (schrodinger.infra.phase.PhpHiClusterPair attribute) darken_colors_by_cavity_depth (schrodinger.surface.Surface attribute) Data (class in schrodinger.application.canvas.r_group) data (schrodinger.application.desmond.packages.msys.molfile.Grid attribute) (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) DATA (schrodinger.job.util.DirectoryType attribute) data() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.desmond.fep_gui.PathModel method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.desmond.packages.msys.Atom method) (schrodinger.application.desmond.packages.msys.Bond method) (schrodinger.application.desmond.packages.msys.Chain method) (schrodinger.application.desmond.packages.msys.Ct method) (schrodinger.application.desmond.packages.msys.Residue method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.livedesign.panel_components.EndpointSelectionModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.PatternModel method) DATA_CLASSES (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData attribute) data_name (schrodinger.application.livedesign.data_classes.LDData attribute) dataChanged (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget attribute) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates attribute) (schrodinger.ui.residueselector.MutationSelectorFrame attribute) (schrodinger.ui.residueselector.MutationSelectorPopUp attribute) dataChanged() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView method) DataClass (schrodinger.models.parameters.BoolParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.FloatParam attribute) (schrodinger.models.parameters.IntParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.Param attribute) (schrodinger.models.parameters.SetParam attribute) (schrodinger.models.parameters.StringParam attribute) dataDir() (schrodinger.infra.fast3d.Engine static method) DataFusionMergeStage (class in schrodinger.pipeline.stages.combine) DataMapWriter (class in schrodinger.application.livedesign.export_controller) DataModel (class in schrodinger.application.bioluminate.protein_report_widget) dataName() (schrodinger.structure.PropertyName method) DataPointLocator (class in schrodinger.analysis.visanalysis.volumedatautils) DataType (class in schrodinger.application.matsci.espresso.qeinput) Dative (schrodinger.structure.BondType attribute) db_file (schrodinger.structutils.shuffle.Shuffler attribute) DBConfSitesStage (class in schrodinger.pipeline.stages.phase) DBExportStage (class in schrodinger.pipeline.stages.phase) dbg (schrodinger.application.desmond.antlr3.debug.DebugParser attribute) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream attribute) DBManageStage (class in schrodinger.pipeline.stages.phase) DDRIVE (schrodinger.maestro.markers.Icons attribute) deactivate() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) deactivateTabs() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) debug (schrodinger.application.glide.glideanalysis.PoseLibrary attribute) debug() (in module schrodinger.application.desmond.fep_gui) (in module schrodinger.structutils.assignbondorders) (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.pipeline.stage.Stage method) debug_maefile (schrodinger.infra.phase.PhpAlignCoreOptions attribute) debug_mols() (in module schrodinger.analysis.reaction) debugbond() (in module schrodinger.structutils.assignbondorders) debugbonders() (in module schrodinger.structutils.assignbondorders) debugEnabled() (schrodinger.job.launchapi.JobSpecification method) DebugEventListener (class in schrodinger.application.desmond.antlr3.debug) DebugEventSocketProxy (class in schrodinger.application.desmond.antlr3.debug) debuggroup() (in module schrodinger.structutils.assignbondorders) DebugParser (class in schrodinger.application.desmond.antlr3.debug) DebugTokenStream (class in schrodinger.application.desmond.antlr3.debug) DebugTreeAdaptor (class in schrodinger.application.desmond.antlr3.debug) decl() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) decl_meta() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) decl_output() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) declare_template (schrodinger.application.desmond.meta.Meta attribute) decode() (schrodinger.application.desmond.packages.restrain.Restraints static method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method) decode_base64_cmd() (in module schrodinger.application.matsci.textlogger) decomp_rawfep_structure() (in module schrodinger.application.desmond.cms) decompose_to_comp_ct() (in module schrodinger.application.desmond.repair_cms) deconverge() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) decorateAxes() (schrodinger.application.matsci.sliceplot.SlicePlot method) decr() (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) DECREMENT() (in module schrodinger.application.desmond.fep_scholar_util) decrement_state_of_changeable() (schrodinger.protein.assignment.ProtAssign method) DEE_Backtracking (class in schrodinger.application.canvas.r_group_dee) DEE_EnergyMatrix (class in schrodinger.application.canvas.r_group_dee) deep_update() (in module schrodinger.application.matsci.espresso.qeinput) deepCopy() (schrodinger.application.matsci.amorphous.PolymerFragment method) default (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword attribute) DEFAULT (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Slab attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) default() (schrodinger.models.json.JSONEncoder method) default_accounter() (in module schrodinger.application.desmond.starter.starter) DEFAULT_ATOM_TYPING_SCHEMES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) default_basis() (in module schrodinger.application.jaguar.basis) DEFAULT_BIN_WIDTH (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) default_custom_fraglib() (in module schrodinger.utils.cgxutils) DEFAULT_DATA (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) DEFAULT_DEBUGGER_PORT (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy attribute) default_disp (schrodinger.tasks.jobtasks.JobOptions attribute) default_dispChanged (schrodinger.tasks.jobtasks.JobOptions attribute) DEFAULT_ENVIRON (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) DEFAULT_FILTERS (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) DEFAULT_ICON_HEIGHT (schrodinger.application.desmond.feputils.LabelSpinner attribute) default_logging_config() (in module schrodinger.utils.log) DEFAULT_MAE_EXT (schrodinger.application.matsci.nano.constants.Constants attribute) default_method (schrodinger.application.mopac.mopac_launchers.MopacLauncher attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher2012 attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher71 attribute) DEFAULT_ORBITAL (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) DEFAULT_PROGRAM_NAME (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream attribute) DEFAULT_RANDOM_TYPES (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) DEFAULT_SETTING (class in schrodinger.application.desmond.config) DEFAULT_SORT_COLUMN (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel attribute) DEFAULT_SORT_ORDER (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) DEFAULT_SUB_TAB_VISIBILITY (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) default_text (schrodinger.application.livedesign.panel_components.AddNewLineEdit attribute) DEFAULT_TOKEN_CHANNEL (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) DEFAULT_TOOLBARS (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) DEFAULT_TRANSPARENCY (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings attribute) DEFAULT_WEIGHT (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow attribute) defaultConfig() (schrodinger.infra.fast3d.Volumizer static method) defaultCustomRepository() (schrodinger.infra.fast3d.Engine static method) DefaultFactoryDict (class in schrodinger.utils.scollections) DefaultFactoryDictMixin (class in schrodinger.utils.scollections) DEFAULTMSG (schrodinger.application.matsci.nano.check.CheckInput attribute) defaultRepositories() (schrodinger.infra.fast3d.Engine static method) DEFAULTS (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) (schrodinger.application.matsci.espresso.qeinput.BasisType attribute) (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) (schrodinger.application.matsci.espresso.qeinput.ControlType attribute) (schrodinger.application.matsci.espresso.qeinput.DftType attribute) (schrodinger.application.matsci.espresso.qeinput.DftUType attribute) (schrodinger.application.matsci.espresso.qeinput.ElectronControlType attribute) (schrodinger.application.matsci.espresso.qeinput.EsmType attribute) (schrodinger.application.matsci.espresso.qeinput.FreePositionsType attribute) (schrodinger.application.matsci.espresso.qeinput.HybridType attribute) (schrodinger.application.matsci.espresso.qeinput.IonControlType attribute) (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) (schrodinger.application.matsci.espresso.qeinput.MdType attribute) (schrodinger.application.matsci.espresso.qeinput.NEBPathType attribute) (schrodinger.application.matsci.espresso.qeinput.PHControlType attribute) (schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType attribute) (schrodinger.application.matsci.espresso.qeinput.SpinType attribute) (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) (schrodinger.application.matsci.espresso.qeinput.VdwType attribute) DefaultTargetMixin (class in schrodinger.models.mappers) define_options() (in module schrodinger.application.desmond.starter.ui.cmdline) DefineASLDialog (class in schrodinger.application.matsci.mswidgets) defineBox() (schrodinger.application.matsci.amorphous.Scaffold method) defineBoxFromNonPBCStruct() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineBoxFromPBC() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineBoxFromScaffold() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) defineDimensions() (schrodinger.application.matsci.nano.tube.NanoSheet method) definedShadowBonds() (schrodinger.application.matsci.cgforcefield.ForceField static method) defineInternals() (schrodinger.application.matsci.cgforcefield.ForceField method) defineMappings() (schrodinger.models.mappers.MapperMixin method) definePanelSettings() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) defineVectors() (schrodinger.application.matsci.nano.tube.NanoSheet method) defineVoids() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) Definition (class in schrodinger.utils.ligfilter) DEFINITION_ID (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) DefinitionParser (class in schrodinger.utils.ligfilter) DefinitionViewerDialog (class in schrodinger.ui.ligfilter) degree() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method) (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) del_atom_props() (in module schrodinger.application.matsci.nano.interface_mod) del_chorus_props() (in module schrodinger.application.matsci.nano.xtal) del_from_carat() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) delAtomProp() (schrodinger.application.desmond.packages.msys.System method) delAtoms() (schrodinger.application.desmond.packages.msys.System method) delAuxTable() (schrodinger.application.desmond.packages.msys.System method) delBondProp() (schrodinger.application.desmond.packages.msys.System method) delBonds() (schrodinger.application.desmond.packages.msys.System method) delChains() (schrodinger.application.desmond.packages.msys.System method) delChiralMatchAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) delConnectivity() (schrodinger.application.matsci.amorphous.PolymerToFragments method) delDanglingTermAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) DelegatingIndentedHelpFormatter (class in schrodinger.utils.cmdline) deletable (schrodinger.project.ProjectRow attribute) delete() (in module schrodinger.infra.propedit) (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.project.ProjectRow method) (schrodinger.project_surface.ProjectSurface method) (schrodinger.structure._StructureBond method) (schrodinger.surface.Surface method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) delete_all_atom_group() (schrodinger.application.desmond.cms.Cms method) delete_atom() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) delete_atom_group() (schrodinger.application.desmond.cms.Cms method) delete_atom_property() (in module schrodinger.application.desmond.struc) delete_atom_tag() (schrodinger.application.desmond.maestro.Workspace method) delete_atoms() (schrodinger.protein.assignment.ProtAssign method) DELETE_BOTH (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) delete_cms_property() (in module schrodinger.application.matsci.desmondutils) DELETE_CONSTRAINT (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) delete_ct_property() (in module schrodinger.application.desmond.struc) delete_duplicate_atoms() (in module schrodinger.application.matsci.nano.xtal) delete_fepio() (in module schrodinger.application.desmond.cms) delete_ghosts() (in module schrodinger.application.jaguar.autots_bonding) delete_group_properties() (in module schrodinger.application.matsci.smartsutils) delete_hydrogens() (in module schrodinger.structutils.build) delete_pbc_bonds() (in module schrodinger.application.matsci.nano.xtal) delete_project_commands() (in module schrodinger.maestro.maestro) DELETE_PROPERTY (schrodinger.application.matsci.enumeration.VacancyAlchemist attribute) DELETE_SCAN (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog attribute) delete_temp_project_directory() (in module schrodinger.project) DELETE_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) delete_zobs() (in module schrodinger.structutils.build) deleteAll() (schrodinger.ui.ligfilter.AddDefinitionDialog method) deleteAllAtoms() (in module schrodinger.infra.phase) deleteAllRestraints() (schrodinger.structutils.minimize.Minimizer method) deleteAllRows() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.infra.table.Table method) deleteAtomGroupRow() (schrodinger.application.desmond.gui.AtomGroupFrame method) deleteAtoms() (schrodinger.application.matsci.enumeration.VacancyAlchemist method) (schrodinger.structure.Structure method) deleteAtomsByAsl() (schrodinger.application.desmond.maestro.NewEntry method) deleteAttr() (schrodinger.infra.phase.PhpHypoAdaptor method) deleteBond() (schrodinger.structure._StructureAtom method) (schrodinger.structure.Structure method) deleteByEntry() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) deleteBySequences() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) deleteChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) deleteCollectionRow() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) deleteColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) deleteColorSchemeRules() (schrodinger.utils.colorscheme.ColorSchemeManager method) deleteColumn() (schrodinger.infra.table.Table method) deleteCtVector() (in module schrodinger.infra.phase) deleteCurrentRow() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) deleteEntry() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) deleteExportMap() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) deleteFile() (schrodinger.utils.colorscheme.MM_CScheme method) deleteHypotheses() (schrodinger.infra.phase.PhpProject method) deleteKey() (schrodinger.application.jaguar.input.JaguarInput method) deleteKeys() (schrodinger.application.jaguar.input.JaguarInput method) deleteLigands() (schrodinger.infra.phase.PhpProject method) deleteMapping() (schrodinger.application.livedesign.ld_export.ExportMapManager method) DeleteOp (class in schrodinger.application.desmond.antlr3.streams) deleteOtherBranches() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) deletePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) deleteParticipant (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) deletePosResRow() (schrodinger.application.desmond.gui.RestraintsTab method) deleteProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) deleteQsarModels() (schrodinger.infra.phase.PhpProject method) deleteRow() (schrodinger.infra.table.Table method) (schrodinger.project.Project method) deleteSection() (schrodinger.application.jaguar.input.JaguarInput method) deleteSite() (schrodinger.infra.phase.PhpHypoAdaptor method) deleteSiteFast() (schrodinger.infra.phase.PhpHypoAdaptor method) deleteSolventFromSt() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) deleteStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) deleteStructure() (schrodinger.application.jaguar.input.JaguarInput method) deleteTemplate() (schrodinger.application.matsci.builderwidgets.TemplateManager method) deleteTmpHydrogens() (schrodinger.application.matsci.rxn_channel.rxn_channel.Products method) deleteVectorAtoms() (schrodinger.protein.membrane.Membrane_Model method) deletion_penalty (schrodinger.structutils.structalign.StructAlign attribute) delimiter (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) delKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) delProp() (schrodinger.application.desmond.packages.msys.ParamTable method) delResidues() (schrodinger.application.desmond.packages.msys.System method) delta_delta_g (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) DeltaEnergy (class in schrodinger.application.desmond.fepana) deltaGIsChecked() (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab method) deltaXYZ (schrodinger.infra.phase.PhpDeltaHypoSite attribute) delTempHydrogens() (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule method) delTermProp() (schrodinger.application.desmond.packages.msys.TermTable method) delTermsWithAtom() (schrodinger.application.desmond.packages.msys.TermTable method) delZigZagMatchAtoms() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) DendrogramPlotDialog (class in schrodinger.application.canvas.clustergui) DENSEAROUND (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) density (schrodinger.application.jaguar.gui.utils.Solvent attribute) Depictor() (in module schrodinger.application.desmond.depictor) depreference_call() (in module schrodinger.application.desmond.maestro) deproxy() (schrodinger.application.desmond.reorder_atom.Node method) depth (schrodinger.application.matsci.cgforcefield.ShadowData attribute) depth() (schrodinger.analysis.reaction.RouteNode method) (schrodinger.application.desmond.reorder_atom.Node method) desalt_structure() (in module schrodinger.structutils.build) description (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword attribute) (schrodinger.application.licensing.licerror.LicenseError attribute) (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) (schrodinger.application.livedesign.maestro_data_types.Complexes attribute) (schrodinger.application.livedesign.maestro_data_types.CovalentDockingComplexes attribute) (schrodinger.application.livedesign.maestro_data_types.DockedPoses attribute) (schrodinger.application.livedesign.maestro_data_types.Ligands attribute) (schrodinger.application.livedesign.maestro_data_types.OrganometallicCompounds attribute) DESCRIPTION (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Slab attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) Descriptor (class in schrodinger.application.canvas.topo_descriptors) (class in schrodinger.application.matsci.order_parameter_mod)

descriptor (schrodinger.protein.analysis.Report.data_set.data_point attribute) DESCRIPTOR_DICT (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions attribute) deselectAll() (schrodinger.ui.residueselector.MutationSelectorFrame method) deselected (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite attribute) deselectSelectedSites() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) deserialize() (schrodinger.application.desmond.picklejar.PickleJar static method) deserialize_conformations() (in module schrodinger.utils.cgxutils) DESMOND_DATA_DIR (schrodinger.application.desmond.envir.CONST attribute) DESMOND_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute) DESMOND_LIB_DIR (schrodinger.application.desmond.envir.CONST attribute) DESMOND_VERSION (schrodinger.application.desmond.envir.CONST attribute) DesmondApp (class in schrodinger.application.desmond.fep_gui) DesmondBasicConfigDialog (class in schrodinger.application.desmond.gui) DesmondBoxSize (class in schrodinger.application.desmond.system_builder_util) DesmondGuiConfigDialog (class in schrodinger.application.desmond.gui) DesmondRestGuiConfigDialog (class in schrodinger.application.desmond.gui) DesmondTyper (class in schrodinger.application.desmond.systype) detailsData() (schrodinger.application.bioluminate.patch_utils.patch_finder.Patch method) detect() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) DetectionError determine_attachment_bonds() (in module schrodinger.application.canvas.r_group) determine_attachments() (in module schrodinger.application.canvas.r_group) determine_box_size() (in module schrodinger.application.matsci.desmondutils) determine_jobtype() (in module schrodinger.application.inputconfig) determine_rgroup_indexes() (in module schrodinger.application.canvas.r_group) determine_rings_in_attachments() (in module schrodinger.application.canvas.r_group) determineAromaticAtomType() (schrodinger.structutils.assignbondorders.AssignBondOrders method) determineAromaticAtomTypes() (schrodinger.structutils.assignbondorders.AssignBondOrders method) determineBasisVectors() (schrodinger.application.matsci.nano.xtal.Crystal method) determineCouplerLocation() (schrodinger.application.matsci.amorphous.BaseMoiety method) determineLatticeNumbering() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) DFA (class in schrodinger.application.desmond.antlr3.dfa) DFA12_accept (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_eof (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_eot (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_max (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_min (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_special (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA12_transition (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) DFA15_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA15_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA17_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA18_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA19_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA1_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA20_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA21_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA22_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA24_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_accept (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_eof (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_eot (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_max (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_min (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_special (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) DFA25_transition (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) dfs() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) DFT_GRID_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFT_ONLY_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFT_OR_HF_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFT_OTHER (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFT_RECOMMENDED_FUNCS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) DFTComboRadioSelector (class in schrodinger.application.jaguar.gui.tabs.theory_tab) DftType (class in schrodinger.application.matsci.espresso.qeinput) dftu (schrodinger.application.matsci.espresso.qeinput.DftType attribute) DftUType (class in schrodinger.application.matsci.espresso.qeinput) DIAMOND (schrodinger.maestro.markers.Icons attribute) dict_delete_and_decrement_keys() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) dict_to_str() (in module schrodinger.application.matsci.nano.particle) dict_to_xml() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree) dictKeys() (schrodinger.application.canvas.utils.ChmCSVTools method) DictParam (class in schrodinger.models.parameters) dictValues() (schrodinger.application.canvas.utils.ChmCSVTools method) died() (schrodinger.pipeline.pipeline.StageJob method) dielectric (schrodinger.application.jaguar.gui.utils.Solvent attribute) DIELECTRIC (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) dielectric_constant (schrodinger.structutils.minimize.Minimizer attribute) dielectricConstant() (schrodinger.infra.fast3d.Volumizer method) diff() (in module schrodinger.utils.sea) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.jaguar.results.JaguarAtomicResults method) (schrodinger.application.jaguar.results.JaguarResults method) different() (in module schrodinger.application.jaguar.gui.tabs.solvation_tab) DIFFHIGHVAL (schrodinger.application.matsci.rxn_path.ReactionPath attribute) DIFFLOWTHRESH (schrodinger.application.matsci.rxn_path.ReactionPath attribute) dih (schrodinger.application.desmond.torsion_related.TorsionPotential attribute) DIHEDRAL (schrodinger.application.matsci.rxn_path.Coord attribute) DIHEDRALWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) Dimer (class in schrodinger.application.matsci.clusterstruct) DimerSpeciesSelector (class in schrodinger.application.matsci.clusterstructgui) DIPEPTIDE_SASA (schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceAreaByResidue attribute) Dipole (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.application.jaguar.results) DIPOLE (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) dipole_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) dipole_esp_x_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) dipole_esp_y_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) dipole_esp_z_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) dipole_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) dipole_strength_precision (schrodinger.application.jaguar.results.NormalMode attribute) dipole_x_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) dipole_y_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) dipole_z_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) DipoleDirector (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.application.matsci.order_parameter_mod) DIR (schrodinger.application.matsci.desmondutils.MSJStringer attribute) (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) DIRECTION (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) directionChanged() (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) DIRECTIONS (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) Director (class in schrodinger.application.matsci.order_parameter_mod) DirectoryType (class in schrodinger.job.util) dis_solvent_correction() (in module schrodinger.application.desmond.fep_net_charge) disable() (schrodinger.project.Project method) disable_lr_columns (schrodinger.application.livedesign.panel_components.AbstractExportTableModel attribute) disable_mmerr (class in schrodinger.infra.mmerr) disableDuplicatesElimination() (schrodinger.infra.fast3d.Engine method) disableResidue() (schrodinger.ui.residueselector.MutationSelectorFrame method) disableResidues() (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorFrame method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) disableSidechainPacking() (schrodinger.protein.reliability.ProteinCheckParameters method) disableSmartDistribution() (schrodinger.job.queue.JobDJ method) discardTokenType() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) disconnectSlots() (schrodinger.application.bioluminate.actions.factory.SAction method) disp (schrodinger.tasks.jobtasks.JobConfig attribute) dispChanged (schrodinger.tasks.jobtasks.JobConfig attribute) display() (schrodinger.application.jaguar.gui.base_panel.CoordinateDialog method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) display_asl() (schrodinger.application.desmond.maestro.Workspace method) display_only_asl() (schrodinger.application.desmond.maestro.Workspace method) displayedEntryIds() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) displayLocalAtoms() (schrodinger.application.matsci.sliceplot.SlicePlot method) displayRecognitionError() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) dissociate() (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule method) DISSOCIATION_BOND_LENGTH (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) DISSOCIATION_TYPE (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) dist3() (in module schrodinger.application.bindingsite.cavutils) dist_cell_iterator() (in module schrodinger.structutils.measure) Distance (class in schrodinger.application.desmond.packages.analysis) DISTANCE (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) distance (schrodinger.application.qsite.input.HydrogenCap attribute) (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) (schrodinger.structutils.interactions.pi.PiPiInteraction attribute) distance() (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.PhpSite method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) DISTANCE_THRESH (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) DistanceCellIterator (class in schrodinger.structutils.measure) DistanceMatrixPlotDialog (class in schrodinger.application.canvas.clustergui) distEuclidean() (schrodinger.infra.phase.PhpDatabaseFp static method) distHamming() (schrodinger.infra.phase.PhpDatabaseFp static method) distributeCpus() (schrodinger.pipeline.pipeline.Pipeline method) distSoergel() (schrodinger.infra.phase.PhpDatabaseFp static method) DISULFIDE (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) disulfide_bonds (schrodinger.protein.alignment.ProteinAlignment attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.sequence.ProteinSequence attribute) DisulfideBond (class in schrodinger.protein.residue) Divider (class in schrodinger.application.matsci.mswidgets) dlst() (schrodinger.application.macromodel.utils.ComUtil method) do() (schrodinger.utils.pymol.PymolInstance method) do_any_residues_have_missing_side_chains() (in module schrodinger.application.prepwizard) do_GET() (schrodinger.application.glide.http_server.GlideHTTPHandler method) do_POST() (schrodinger.application.glide.http_server.GlideHTTPHandler method) do_rings_share_atoms() (in module schrodinger.structutils.assignbondorders) doApplyClustering() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) doBonding() (schrodinger.application.matsci.nano.xtal.Crystal method) doBondOrders() (schrodinger.application.matsci.nano.tube.NanoTube method) (schrodinger.application.matsci.nano.xtal.Crystal method) doc (schrodinger.project.ProjectRow attribute) Dock (class in schrodinger.application.glide.glide) dock() (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.glide.http_client.HTTPClient method) dock_widget (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) DockedPoses (class in schrodinger.application.livedesign.maestro_data_types) DockingStage (class in schrodinger.pipeline.stages.glide) doCluster() (schrodinger.application.macromodel.utils.CluUtil method) doCommand() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.utils.installation_check.TestJob method) doctype() (schrodinger.application.jaguar.keywordDB.DTDTreeBuilder method) Dodecahedron (class in schrodinger.application.matsci.shapes) (class in schrodinger.graphics3d.polyhedron) does_res_have_missing_side_chains() (in module schrodinger.application.prepwizard) doesTitleExist() (schrodinger.application.combiglide.combenumdock.collectionViewerModel method) doGroup() (schrodinger.utils.pymol.RowProxy method) doIncorporation() (schrodinger.application.matsci.mecp_mod.MECP method) DONE (schrodinger.tasks.tasks.Status attribute) (schrodinger.tasks.tasks_.Status attribute) done_jobs (schrodinger.job.queue.JobDJ attribute) doneReordering() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) doNonLinearFit() (schrodinger.application.matsci.rxn_path.ReactionPath method) DONOR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) DonorConstraint (class in schrodinger.application.glide.glide) doPropertyEvaluation() (schrodinger.application.matsci.nano.xtal.Crystal method) DOS (class in schrodinger.application.matsci.espresso.qeoutput) doStateOptimizations() (schrodinger.application.matsci.mecp_mod.MECP method) DOT (schrodinger.application.matsci.desmondutils.MSJStringer attribute) dot (schrodinger.surface.Style attribute) (schrodinger.surface.Surface.Style attribute) dot() (schrodinger.pipeline.pipeutils.DotPrinter method) dotdot (schrodinger.application.desmond.antlr3.tree.TreeParser attribute) dotdotPattern (schrodinger.application.desmond.antlr3.tree.TreeParser attribute) doTermination() (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.tube.NanoTube method) DotPrinter (class in schrodinger.pipeline.pipeutils) dotprod() (in module schrodinger.application.desmond.cms) doTranslation() (schrodinger.application.matsci.nano.xtal.Crystal method) Double (schrodinger.structure.BondType attribute) DOUBLE_DISPLACEMENT_TYPE (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) DOUBLE_PRECISION (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) doubleClickTable() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) doubleEtc (schrodinger.application.desmond.antlr3.tree.TreeParser attribute) doubleEtcPattern (schrodinger.application.desmond.antlr3.tree.TreeParser attribute) doublequote (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) download_ent() (in module schrodinger.protein.getpdb) download_fasta() (in module schrodinger.protein.getpdb) download_file() (in module schrodinger.protein.getpdb) download_format() (in module schrodinger.protein.getpdb_utility) download_nodelocked_license() (in module schrodinger.application.licensing.licadmin) download_pdb() (in module schrodinger.protein.getpdb) download_server_license() (in module schrodinger.application.licensing.licadmin) download_sf() (in module schrodinger.protein.getpdb) doXCluster() (schrodinger.application.macromodel.utils.CluUtil method) draw() (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.graphics3d.common.Group method) (schrodinger.protein.membrane.Membrane_Model method) draw_1_arrow() (in module schrodinger.application.desmond.maestro) draw_arrow() (in module schrodinger.application.desmond.maestro) draw_html_string() (in module schrodinger.maestro.maestro) draw_string() (in module schrodinger.maestro.maestro) DRAW_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) drawPageNumber() (schrodinger.application.desmond.report_helper.NumberedCanvas method) drawStructure() (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) driv() (schrodinger.application.macromodel.utils.ComUtil method) driverReservesCores() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) DrugLikeSplitStage (class in schrodinger.pipeline.stages.filtering) dsq (schrodinger.application.matsci.clusterstruct.Neighbor attribute) DTDTreeBuilder (class in schrodinger.application.jaguar.keywordDB) dtor() (schrodinger.application.desmond.maestro.NewEntryGroup method) DTR (schrodinger.application.desmond.packages.traj.Fmt attribute) DtrSource (class in schrodinger.application.desmond.packages.traj) DuckFrame (class in schrodinger.application.desmond.packages.topo) dummy() (in module schrodinger.application.desmond.starter.starter) dummy_entry_id (schrodinger.application.livedesign.maestro_data_types.TargetlessBase attribute) dump() (in module schrodinger.models.json) (schrodinger.job.queue.JobDJ method) (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.stage.Stage method) (schrodinger.utils.sea.Sea method) dumpBE() (schrodinger.job.app.App method) dumpFE() (schrodinger.job.app.App method) dumps() (in module schrodinger.models.json) dumpShuffledStructures() (schrodinger.structutils.shuffle.Shuffler method) dup() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method) duplexDataSet() (schrodinger.infra.phase.PhpQSAR method) DUPLICATE (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) duplicate() (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.desmond.packages.msys.Param method) duplicate_entry() (in module schrodinger.application.desmond.maestro) duplicateRings() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) dupNode() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) dupTree() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) duration (schrodinger.application.jaguar.output.JaguarOutput attribute) dval (schrodinger.utils.sea.Atom attribute) (schrodinger.utils.sea.List attribute) (schrodinger.utils.sea.Map attribute) DynamicAslAnalyzer (class in schrodinger.application.desmond.packages.staf) dynamics (schrodinger.application.matsci.espresso.qeinput.IonControlType attribute)

E

E_f (class in schrodinger.application.desmond.simulation_block_test) E_k (class in schrodinger.application.desmond.simulation_block_test) E_x (class in schrodinger.application.desmond.simulation_block_test) EA2DEBYE (schrodinger.application.desmond.packages.analysis.Dipole attribute) EarlyExitException EDA (class in schrodinger.trajectory.prody.pca) Edge (class in schrodinger.application.matsci.shapes) edge (schrodinger.structure._Ring attribute) edges() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) EDGETYPE1 (schrodinger.application.matsci.nano.constants.Constants attribute) EDGETYPE2 (schrodinger.application.matsci.nano.constants.Constants attribute) EDGETYPES (schrodinger.application.matsci.nano.constants.Constants attribute) editableViewerTable (class in schrodinger.application.combiglide.combenumdock) EditDialog (class in schrodinger.application.jaguar.gui.edit_dialog) editingFinished (schrodinger.application.phase.phase_markers.PhaseMarkers attribute) editInput() (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) EDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) ef_precision (schrodinger.analysis.enrichment.Calculator attribute) EFERMI_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) eff_precision (schrodinger.analysis.enrichment.Calculator attribute) efield (schrodinger.application.matsci.espresso.qeoutput.EsmType attribute) efp_precision (schrodinger.analysis.enrichment.Calculator attribute) efs_precision (schrodinger.analysis.enrichment.Calculator attribute) elec (schrodinger.application.desmond.packages.energygroup.EnergyComponent attribute) electron_transfer() (in module schrodinger.application.jaguar.textparser) ElectronControlType (class in schrodinger.application.matsci.espresso.qeinput) electronic_e() (in module schrodinger.application.jaguar.textparser) electrostatic14_energy() (in module schrodinger.application.qsite.output) electrostatic_energy() (in module schrodinger.application.qsite.output) element (schrodinger.structure._StructureAtom attribute) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) ELEMENT1 (schrodinger.application.matsci.nano.constants.Constants attribute) ELEMENT2 (schrodinger.application.matsci.nano.constants.Constants attribute) elemental_generator() (in module schrodinger.application.matsci.mlearn.features) elemental_mutator() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) ElementAlchemist (class in schrodinger.application.matsci.enumeration) ElementalProperties (class in schrodinger.application.matsci.elementalprops) ElementClass (schrodinger.protein.sequence.NucleicAcidSequence attribute) (schrodinger.protein.sequence.ProteinSequence attribute) (schrodinger.protein.sequence.Sequence attribute) ElementEdit (class in schrodinger.application.matsci.atomicsymbolsgui) elements (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) ElementType (class in schrodinger.protein.residue) ElementValidator (class in schrodinger.application.matsci.atomicsymbolsgui) eliminatePairs() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) eliminateSingles() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) elmnt_mult_dict() (in module schrodinger.application.jaguar.utils) elst() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.ComUtilAppSci method) EMAGGLASS (schrodinger.maestro.markers.Icons attribute) EmbeddedSolventWidget (class in schrodinger.application.matsci.mswidgets) embl (schrodinger.utils.fileutils.SeqFormat attribute) EmbraceConfSearch (class in schrodinger.application.macromodel.input) EmbraceMinimization (class in schrodinger.application.macromodel.input) emit() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) emitAddMarker() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) emitAnnTitleChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitCountChanged() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) emitErrorMessage() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) emitRemoveMarker() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) emitSeqNameChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitSeqResChanged() (schrodinger.protein.alignment.AlignmentSignals method) emitSetMarkerHighlighting() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) empty() (schrodinger.application.licensing.flexlm.License method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.infra.phase.PhpStructureBus method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) EmptyIterator (class in schrodinger.project) enable() (schrodinger.project.Project method) enable_lasso (schrodinger.ui.picking.PickMixedToggle attribute) ENABLE_WHEN_NO_STRUC (schrodinger.application.jaguar.gui.basis_selector.BasisSelector attribute) enableAllFeatures() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) enableCustomSeed() (schrodinger.application.desmond.gui.RandVelFrame method) enableExcitedState() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) enableExcitedStatesType() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) enableMaestroSync() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) enableMappingWidgets() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) enablePlatformValidation() (schrodinger.application.desmond.gui.DesmondBasicConfigDialog method) enableRevert() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) enableRows() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) enableSelectedCoordinates() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) enableSidechainPacking() (schrodinger.protein.reliability.ProteinCheckParameters method) enableSimulationGroupBox() (schrodinger.application.desmond.gui.GuiApp method) encode() (schrodinger.application.desmond.packages.restrain.Restraints static method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method) encode_extended() (in module schrodinger.application.desmond.gchart) encode_simple() (in module schrodinger.application.desmond.gchart) encodeForPatternSearch() (schrodinger.protein.sequence.ProteinSequence method) end (schrodinger.protein.annotation.AntibodyCDR attribute) (schrodinger.utils.colorscheme.MMrange attribute) end() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.infra.phase.PhpTextFileReader method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) end_drawing() (in module schrodinger.application.desmond.maestro) end_geometry() (in module schrodinger.application.jaguar.textparser) END_OF_DEF_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) end_scan() (in module schrodinger.application.jaguar.textparser) end_time() (in module schrodinger.application.jaguar.textparser) endBacktrack() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) endGeopt() (schrodinger.application.jaguar.textparser.TextParser method) endGroup() (schrodinger.utils.preferences.Preferences method) endIRC() (schrodinger.application.jaguar.textparser.TextParser method) endpointSelected (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit attribute) EndpointSelectionLineEdit (class in schrodinger.application.livedesign.panel_components) EndpointSelectionModel (class in schrodinger.application.livedesign.panel_components) EndpointSelectionPopup (class in schrodinger.application.livedesign.panel_components) EndpointSelectionPopUpDelegate (class in schrodinger.application.livedesign.panel_components) endResync() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) endScan() (schrodinger.application.jaguar.textparser.TextParser method) eneg (schrodinger.application.matsci.elementalprops.ElementalProperties attribute) eneg_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) Energy (class in schrodinger.application.desmond.packages.energygroup) (class in schrodinger.application.desmond.simulation_block_test) energy (schrodinger.application.jaguar.results.JaguarResults attribute) energy_criterion (schrodinger.structutils.minimize.Minimizer attribute) ENERGY_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) energy_lj_repulsive_only (schrodinger.structutils.minimize.Minimizer attribute) energy_no_electrostatics (schrodinger.structutils.minimize.Minimizer attribute) energy_precision (schrodinger.application.jaguar.results.JaguarResults attribute) (schrodinger.application.qsite.output.QSiteResults attribute) energy_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) ENERGY_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) ENERGY_UNIT_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) EnergyAndGradients (class in schrodinger.application.matsci.mecp_mod) EnergyComponent (class in schrodinger.application.desmond.packages.energygroup) EnergyFacade (class in schrodinger.application.desmond.packages.energygroup) EnergyGroupBase (class in schrodinger.application.desmond.packages.energygroup) EnergyGroupError EnergyListing (class in schrodinger.application.macromodel.input) EnergySurface (class in schrodinger.application.matsci.amorphous) Engine (class in schrodinger.infra.fast3d) engine (schrodinger.application.matsci.espresso.qeinput.DataType attribute) EnhancedChothia (schrodinger.protein.annotation.AntibodyCDRScheme attribute) EnhancedComboBox (class in schrodinger.application.jaguar.gui.utils) ensClassChanged() (schrodinger.application.desmond.gui.EnsembleClassFrame method) Ensemble (class in schrodinger.trajectory.prody.ensemble) ENSEMBLE (schrodinger.application.matsci.desmondutils.MSJStringer attribute) ENSEMBLE_CLASS (schrodinger.application.matsci.desmondutils.MSJStringer attribute) ENSEMBLE_METHOD (schrodinger.application.matsci.desmondutils.MSJStringer attribute) Ensemble_Priority_Queue (class in schrodinger.application.glide.ensemble_selection) EnsembleClassFrame (class in schrodinger.application.desmond.gui) ensembles (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue attribute) EnsembleTab (class in schrodinger.application.desmond.gui) ensure_logger() (in module schrodinger.application.bindingsite.common) ensurePrjzipCreationComplete() (schrodinger.application.livedesign.export_controller.ExportController method) ensureValidCollectionTitles() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) enter_scope() (schrodinger.application.desmond.enhsamp.binding method) enterAlt() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) enterDecision() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) enterRule() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) enterSubRule() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) entropy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) ENTRY (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) entry (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) entry_id (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) (schrodinger.project.ProjectRow attribute) (schrodinger.structure._StructureAtom attribute) ENTRY_NAME_KEY (schrodinger.application.matsci.nano.xtal.CheckInput attribute) (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput attribute) ENTRY_TYPE_NAMES (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) ENTRY_TYPES (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel attribute) entryByName() (schrodinger.utils.installation_check.TestJobDJ method) EntryField (class in schrodinger.application.desmond.cwidget) EntryGroup (class in schrodinger.project) entryIds() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) ENTRYKEY (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) ENTRYNAMEKEY (schrodinger.application.matsci.rxn_path.CheckInput attribute) EntryRestrictor (class in schrodinger.application.desmond.util) EntrySurface (class in schrodinger.project) entryTitles() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) enum_speedup() (in module schrodinger.infra.util) enumerate() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) enumerate_changeable_states() (schrodinger.protein.assignment.ProtAssign method) enumerate_states() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) enumerateChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) enumeration_files_written (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration attribute) EnumParam (class in schrodinger.models.parameters) Env (class in schrodinger.application.desmond.enhsamp) EnvironmentContext (class in schrodinger.utils.env) EOF (schrodinger.application.desmond.antlr3.streams.CharStream attribute) eof() (schrodinger.infra.mmgpgpu.istream method) (schrodinger.infra.mmjob.istream method) (schrodinger.infra.mmsurf.istream method) (schrodinger.utils.colorscheme.istream method) EP (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings attribute) epn() (in module schrodinger.application.jaguar.textparser) epn_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) eq_re (schrodinger.application.jaguar.input.GenOptions attribute) equal() (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) equal_rotations() (in module schrodinger.application.matsci.nano.xtal) equalize_number_waters() (in module schrodinger.application.desmond.gcmc_utils) EQUALS (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property attribute) (schrodinger.maestro.markers.Icons attribute) equals() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) EquilibriumMdBase (class in schrodinger.application.matsci.equilibrium_md)

erase() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) Error (class in schrodinger.job.host_check) error (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) ERROR (schrodinger.application.jaguar.input.GenOptions attribute) (schrodinger.tasks.tasks.Status attribute) error() (in module schrodinger.application.desmond.packages.cui) (schrodinger.application.desmond.antlr3.dfa.DFA method) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.pipeline.stage.Stage method) (schrodinger.tasks.runners.AbstractTaskReporter method) (schrodinger.tasks.runners.CmdlineTaskReporter method) (schrodinger.tasks.runners.PanelTaskReporter method) (schrodinger.tasks.runners.TaskRunner method) (schrodinger.utils.ligfilter.CriterionParser method) (schrodinger.utils.ligfilter.DefinitionParser method) ERROR_BACKGROUND_BRUSH (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) error_dialog() (in module schrodinger.application.desmond.gui) error_pattern (schrodinger.infra.mmcheck.ReturnCode attribute) ERROR_POST (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) ERROR_PRE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) ErrorHandler (class in schrodinger.infra.mmerr) errorHandler() (schrodinger.application.livedesign.ld_base_classes.ImportExportThreadRunner method) errorNode() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) errorRaised (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel attribute) errors (schrodinger.application.desmond.packages.msys.AnnotatedSystem attribute) errors() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) ES_EXCLUDE_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) escape_dollars_for_cmdline() (in module schrodinger.application.matsci.jobutils) escapeNewlines() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) esm (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) ESM_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) EsmType (class in schrodinger.application.matsci.espresso.qeinput) (class in schrodinger.application.matsci.espresso.qeoutput) ESP (schrodinger.application.mopac.results71.MopacResults71 attribute) esp_analysis() (in module schrodinger.application.jaguar.textparser) esp_analysis_precision (schrodinger.application.jaguar.results.JaguarResults attribute) ESP_ATOMS (schrodinger.application.jaguar.results.JaguarOptions attribute) ESP_ATOMS_AND_BOND_MIDPOINTS (schrodinger.application.jaguar.results.JaguarOptions attribute) esp_balance (schrodinger.application.jaguar.results.JaguarResults attribute) esp_charge_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) esp_charges() (in module schrodinger.application.jaguar.textparser) esp_fit_atoms() (in module schrodinger.application.jaguar.textparser) esp_fit_atoms_and_bonds() (in module schrodinger.application.jaguar.textparser) esp_local_polarity (schrodinger.application.jaguar.results.JaguarResults attribute) ESP_NONE (schrodinger.application.jaguar.results.JaguarOptions attribute) esp_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) espmax (schrodinger.application.jaguar.results.JaguarResults attribute) espmean_n (schrodinger.application.jaguar.results.JaguarResults attribute) espmean_p (schrodinger.application.jaguar.results.JaguarResults attribute) espmin (schrodinger.application.jaguar.results.JaguarResults attribute) ESPSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) estate_is_physical() (in module schrodinger.application.jaguar.reactiq_validation) estimate_memory() (in module schrodinger.application.desmond.memory_estimate) estimate_natoms() (in module schrodinger.application.desmond.memory_estimate) eth0_is_missing() (in module schrodinger.application.licensing.licadmin) etot() (in module schrodinger.application.jaguar.textparser) etree_iter_path() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree) etree_node_to_dict() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree) etree_to_dict() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree) ev_to_hartree() (in module schrodinger.application.matsci.mecp_mod) evaluate() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis method) (schrodinger.application.matsci.genetic_optimization.genetic_optimization.StructureGenome method) evaluate_asl() (in module schrodinger.structutils.analyze) evaluate_matched_list() (in module schrodinger.application.desmond.smarts) evaluate_multiple_smarts() (in module schrodinger.structutils.analyze) evaluate_net_smarts() (in module schrodinger.application.desmond.smarts) evaluate_smarts() (in module schrodinger.structutils.analyze) evaluate_smarts_by_molecule() (in module schrodinger.structutils.analyze) evaluate_smarts_canvas() (in module schrodinger.structutils.analyze) evaluate_smarts_ex() (in module schrodinger.application.canvas.r_group) evaluate_substructure() (in module schrodinger.structutils.analyze) evaluateAsl() (schrodinger.structutils.rmsd.ConformerRmsd method) evaluateSpeciesCriterion() (schrodinger.application.matsci.clusterstruct.Dimer method) evaluateURL() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) event (class in schrodinger.application.licensing.lmgrd_log_parser) event() (schrodinger.application.matsci.builderwidgets.StructureLabel method) eventFilter() (schrodinger.application.jaguar.gui.input_tab_widgets.CommitMultipleDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.livedesign.ld_base_classes.SwallowEnterFilter method) (schrodinger.application.matsci.mswidgets.WheelEventFilterer method) ExampleStage (class in schrodinger.pipeline.stages.example) exc_precision (schrodinger.application.jaguar.results.JaguarResults attribute) ExceptionDialog (class in schrodinger.infra.exception_handler_dir.exception_dialog) ExceptionInfo (class in schrodinger.tasks.tasks_) ExceptionRecorder (class in schrodinger.infra.exception_handler) exchange_acceptance_ratio() (schrodinger.application.desmond.bennett.CalcBAR method) EXCITED_STATE_CB_TEXT (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabOptimization attribute) excited_state_changed (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget attribute) EXCITED_STATE_TEXT (schrodinger.application.jaguar.gui.theory_tab_widgets.HFExcitedStateWidget attribute) EXCITED_STATE_TYPES (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabOptimization attribute) ExcitedStateValidatorMixin (class in schrodinger.application.jaguar.gui.base_panel) ExcitedStateWidget (class in schrodinger.application.jaguar.gui.theory_tab_widgets) exclude() (schrodinger.ui.ligfilter.AddDefinitionDialog method) exclude_amino_acids (schrodinger.structutils.analyze.AslLigandSearcher attribute) exclude_ions (schrodinger.structutils.analyze.AslLigandSearcher attribute) excludeCommandParser() (schrodinger.application.ligprep.ionizer.Ionizer method) Excluded (schrodinger.protein.sequence.Inclusion attribute) excluded_residues (schrodinger.structutils.analyze.AslLigandSearcher attribute) ExcludedVolumeGenerator (class in schrodinger.application.phase.create_xvol) excludes() (schrodinger.utils.ligfilter.Definition method) EXEC (schrodinger.job.util.DirectoryType attribute) execute() (schrodinger.application.desmond.antlr3.streams.InsertBeforeOp method) (schrodinger.application.desmond.antlr3.streams.ReplaceOp method) (schrodinger.application.desmond.antlr3.streams.RewriteOperation method) (schrodinger.infra.phase.PhpFeatureFinder method) (schrodinger.infra.phase.PhpMMconfAdaptor method) execute_lictest() (in module schrodinger.application.licensing.licadmin) execute_lmutil() (in module schrodinger.application.licensing.licadmin) EXISTING_RESTRAINT (class in schrodinger.application.desmond.constants) exit() (schrodinger.pipeline.stage.Stage method) exit_status_BAD_INPUT (schrodinger.application.mopac.results71.MopacResults71 attribute) exit_status_FATAL (schrodinger.application.mopac.results71.MopacResults71 attribute) exit_status_OK (schrodinger.application.mopac.results71.MopacResults71 attribute) exitDecision() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) exitRule() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) ExitStatus (schrodinger.job.jobcontrol.Job attribute) exitSubRule() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) expActivity() (schrodinger.infra.phase.PhpProject method) expand() (schrodinger.utils.ligfilter.Definition method) (schrodinger.utils.ligfilter.SmartsCriterion method) expand_ark_string() (in module schrodinger.utils.sea) expand_macro() (in module schrodinger.application.desmond.util) (in module schrodinger.utils.sea) expand_macro_old() (in module schrodinger.utils.sea) expand_sea_string() (in module schrodinger.utils.sea) expand_solutions() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) expandAll() (schrodinger.application.matsci.mswidgets.MultiStageArea method) expandFamily() (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) expComp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) expecter() (schrodinger.application.desmond.enhanced_sampling.FcnTypes.BinaryThreadSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.MetaSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.RMSDSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.SimpleSyntax method) (schrodinger.application.desmond.enhanced_sampling.FcnTypes.ThreadSyntax method) (schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes.BinaryThreadSyntax method) (schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes.MetaSyntax method) (schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes.RMSDSyntax method) (schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes.SimpleSyntax method) (schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes.ThreadSyntax method) expiration_str() (schrodinger.application.licensing.flexlm.Feature method) export() (schrodinger.application.desmond.replica_dE.replica_container method) (schrodinger.application.desmond.replica_dE.replicas_monitor method) (schrodinger.application.desmond.replica_sid_generator.FEPReport method) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) Export3D (class in schrodinger.application.livedesign.maestro_data_types) export_3d (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel attribute) (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) export_dE_data() (schrodinger.application.desmond.replica_dE.replica_container method) EXPORT_TEXT (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) exportAllTables() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) exportBatched() (schrodinger.application.livedesign.export_controller.ExportController method) exportCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) exportCombLibSelectFile() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) exportConstraints() (schrodinger.infra.phase.PhpSiteConstrainer method) ExportController (class in schrodinger.application.livedesign.export_controller) exportCoreSelectFile() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) exportCurrentTable() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) ExportData (class in schrodinger.application.livedesign.data_classes) exportData() (schrodinger.application.livedesign.export_controller.ExportController method) exportFile() (in module schrodinger.infra.propedit) ExportMap (class in schrodinger.application.livedesign.ld_export) ExportMapManager (class in schrodinger.application.livedesign.ld_export) ExportMapTypeError exportModel() (schrodinger.infra.phase.PhpQSAR method) exportModelToStream() (schrodinger.infra.phase.PhpQSAR method) exportPalette() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) exportRLMap() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) ExportRow (class in schrodinger.application.livedesign.panel_components) exportTables() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) ExportTableView (class in schrodinger.application.livedesign.panel_components) ExportThreadRunner (class in schrodinger.application.livedesign.ld_export) exportToFile() (schrodinger.infra.phase.PhpDeltaHypo method) (schrodinger.infra.phase.PhpExclVol method) (schrodinger.infra.phase.PhpFeatureData method) (schrodinger.infra.phase.PhpFeatureRules method) (schrodinger.infra.phase.PhpSiteMask method) exportToMMTableFile() (schrodinger.infra.phase.PhpExclVol method) exportToStream() (schrodinger.infra.phase.PhpDeltaHypo method) (schrodinger.infra.phase.PhpExclVol method) (schrodinger.infra.phase.PhpFeatureData method) (schrodinger.infra.phase.PhpFeatureRules method) (schrodinger.infra.phase.PhpSiteMask method) Exposure (schrodinger.application.glide.xpdes.TermKeywords attribute) exposure_tendency (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) expr() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) expression_error() (schrodinger.utils.ligfilter.CriterionParser method) exprOrBind() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) EXT (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) ext_gcd() (in module schrodinger.application.matsci.nano.plane) extend() (schrodinger.protein.sequence.Sequence method) (schrodinger.structure.Structure method) (schrodinger.structure.StructureWriter method) (schrodinger.utils.sea.List method) extend_connection_colors() (in module schrodinger.application.combiglide.connection_storage) extend_hotregion() (in module schrodinger.application.desmond.r_group_asl) extend_phosphate_states() (in module schrodinger.application.prepwizard) extend_sulfate_states() (in module schrodinger.application.prepwizard) extend_targeted_to_hyds() (schrodinger.protein.assignment.ProtAssign method) extendCoreAtoms() (schrodinger.application.desmond.fep_mapping.AtomMappingData method) extended (schrodinger.surface.MolSurfType attribute) extendToIncludeSideChainAtoms() (schrodinger.protein.pdbname.Substructure method) extendWithSpectator() (schrodinger.application.matsci.rxn_channel.rxn_channel.Products method) extra_keywords (schrodinger.application.mopac.mopac_launchers.MopacLauncher attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher2012 attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher71 attribute) EXTRA_NROOT (schrodinger.application.matsci.mecp_mod.JaguarJobs attribute) EXTRA_OPTIONS (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) extra_validations() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) extract() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) (schrodinger.structure.Structure method) extract_atoms() (in module schrodinger.application.desmond.packages.traj_util) extract_cfg() (in module schrodinger.application.desmond.config) extract_grid_and_radius() (in module schrodinger.application.matsci.freevolume) extract_hypotheses() (in module schrodinger.application.phase.hypothesis) extract_job_data() (in module schrodinger.application.matsci.jobutils) extract_Phob_pack_ligand_indices() (in module schrodinger.application.glide.xpdes) extract_prjzip() (in module schrodinger.application.livedesign.export_controller) extract_properties() (in module schrodinger.pipeline.stages.phase) extract_representative_structure() (in module schrodinger.application.desmond.process_fep_traj) extract_subsystem() (in module schrodinger.application.desmond.packages.topo) (in module schrodinger.application.desmond.packages.traj) extract_trajectories() (schrodinger.application.desmond.title_to_hex.Analysis method) extractConfOptionsArgs() (in module schrodinger.infra.phase) extractData() (schrodinger.application.matsci.cgforcefield.FFIOAngle method) (schrodinger.application.matsci.cgforcefield.FFIOBond method) (schrodinger.application.matsci.cgforcefield.FFIODihedral method) (schrodinger.application.matsci.cgforcefield.FFIOImproper method) (schrodinger.application.matsci.cgforcefield.FFIOParam method) (schrodinger.application.matsci.cgforcefield.FFIOSite method) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) extractInformationFromTreeNodeStream() (schrodinger.application.desmond.antlr3.exceptions.RecognitionException method) extractMoieties() (schrodinger.application.matsci.amorphous.PolymerToFragments method) extractSolventFromSt() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) extractStructure() (schrodinger.structure._AtomCollection method) extractWithMap() (schrodinger.application.matsci.amorphous.PolymerToFragments method) ExtraSectionData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) EYE (schrodinger.maestro.markers.Icons attribute)

F

F1_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) F1F2F3_FORMAT (schrodinger.application.matsci.nano.xtal.Crystal attribute) F1F2F3_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) F2_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) F3_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) Face (class in schrodinger.application.matsci.shapes) faces (schrodinger.graphics3d.polyhedron.Polyhedron attribute) FACIAL (in module schrodinger.application.matsci.buildcomplex) factor() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) Factory (class in schrodinger.application.bioluminate.actions.factory) FAILED (schrodinger.tasks.tasks.Status attribute) (schrodinger.tasks.tasks_.Status attribute) failed() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) failed_files (schrodinger.structure.MultiFileStructureReader attribute) failed_jobs (schrodinger.job.queue.JobDJ attribute) FailedPredicateException Failure (class in schrodinger.application.matsci.genetic_optimization.genetic_optimization) family_name (schrodinger.application.livedesign.data_classes.LDData attribute) FAR_LIG_DIST (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) fasta (schrodinger.utils.fileutils.SeqFormat attribute) fatal() (in module schrodinger.application.desmond.util) fatal_error() (in module schrodinger.application.jaguar.textparser) FatalCoordinateError fcc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) FcnCall (class in schrodinger.application.desmond.enhsamp) fcnCall() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) fe_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) Feature (class in schrodinger.application.glide.glide) (class in schrodinger.application.licensing.flexlm) feature (schrodinger.application.licensing.lmgrd_log_parser.event attribute) feature_coordinates (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) feature_counter (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) FEATURE_DEFINITION_PRESETS (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo attribute) FEATURE_EQUIV_PRESETS (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo attribute) feature_expiring() (in module schrodinger.application.licensing.licadmin) feature_name (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) FEATURE_QCOLORS() (in module schrodinger.application.phase.constants) FEATURE_TYPE (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) feature_type (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) featureExists() (schrodinger.application.phase.phase_markers.PhaseMarkers method) FeatureMatchCombo (class in schrodinger.application.phase.phase_widgets) FeatureModel (class in schrodinger.application.phase.featureselector) FeatureOptionsCombo (class in schrodinger.application.phase.phase_widgets) FeaturePattern (class in schrodinger.application.glide.glide) featureRadii (schrodinger.infra.phase.PhpQSARModel attribute) FeatureRow (class in schrodinger.application.phase.featureselector) FeatureSelector (class in schrodinger.application.phase.featureselector) featureToggled (schrodinger.application.phase.featureselector.FeatureModel attribute) feedback_string_set() (in module schrodinger.maestro.maestro) fep() (schrodinger.application.macromodel.utils.ComUtil method) FEP_TYPES (class in schrodinger.application.desmond.constants) FEPConfigDialog (class in schrodinger.application.desmond.fep_gui) FEPEdgeData (class in schrodinger.application.desmond.fep_edge_data) FEPEdgeReportMaker (class in schrodinger.application.desmond.fep_edge_report_maker) fepio (schrodinger.application.desmond.ffiostructure.FFIOStructure attribute) FEPReport (class in schrodinger.application.desmond.replica_sid_generator) FEPReportMaker (class in schrodinger.application.desmond.fep_reporter) FEPScholarMapper (class in schrodinger.application.desmond.fep_scholar_util) FEPScholarMsjGenerator (class in schrodinger.application.desmond.fep_scholar_msj_generator) FEPSimulationReport (class in schrodinger.application.desmond.replica_sid_generator) FEPStructureObject (class in schrodinger.application.desmond.fep_scholar_util) FEPTorsions (class in schrodinger.application.desmond.fep_edge_data) FEPTorsionsContainer (class in schrodinger.application.desmond.fep_edge_data) fetchPPDB() (schrodinger.application.matsci.espresso.qeinput.StructureType method) ffio (schrodinger.application.desmond.ffiostructure.FFIOStructure attribute) ffio_add_atoms_block() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util) ffio_add_block() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util) ffio_add_header() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util) ffio_add_pseudo_block() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_util) ffio_delete_atoms() (in module schrodinger.application.desmond.gcmc_utils) ffio_extend_ct() (in module schrodinger.application.desmond.gcmc_utils) ffio_refresh() (schrodinger.application.desmond.cms.Cms method) FFIOAngle (class in schrodinger.application.matsci.cgforcefield) FFIOBond (class in schrodinger.application.matsci.cgforcefield) FFIODihedral (class in schrodinger.application.matsci.cgforcefield) FFIOExclusion (class in schrodinger.application.matsci.cgforcefield) FFIOImproper (class in schrodinger.application.matsci.cgforcefield) FFIOParam (class in schrodinger.application.matsci.cgforcefield) FFIOSite (class in schrodinger.application.matsci.cgforcefield) FFIOStructure (class in schrodinger.application.desmond.ffiostructure) FFIOVdwType (class in schrodinger.application.matsci.cgforcefield) FFIOVdwTypesCombined (class in schrodinger.application.matsci.cgforcefield) ffld() (in module schrodinger.application.qsite.output) ffldVersion() (schrodinger.infra.fast3d.Volumizer method) Field (class in schrodinger.application.bindingsite.intfield) fields (schrodinger.protein.analysis.Report.data_set attribute) file_config() (in module schrodinger.utils.log) file_dirname() (in module schrodinger.application.licensing.licadmin) FILE_IMPORT_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) FILE_PICK_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) FileDialogWithExtraCombo (class in schrodinger.application.jaguar.gui.filedialog) FileEntry (class in schrodinger.application.desmond.cwidget) FileFormatError FileLogger (class in schrodinger.application.jaguar.file_logger) filename (schrodinger.analysis.reaction.ReagentSource attribute) filename_extensions (schrodinger.application.desmond.packages.msys.molfile.SeqFile attribute) (schrodinger.application.desmond.packages.msys.molfile.StkFile attribute) FILES (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) files (schrodinger.structure.MultiFileStructureReader attribute) FileStream (in module schrodinger.application.desmond.antlr3.streams) fill() (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.infra.mmbitset.Bitset method) fill_map() (in module schrodinger.application.jaguar.structure_isomorphism) fill_missing_loops() (in module schrodinger.application.prepwizard) fill_missing_side_chains() (in module schrodinger.application.prepwizard) fillBranchPoints() (schrodinger.application.matsci.amorphous.Initiator method) fillBuffer() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) fillFolderTree() (schrodinger.application.livedesign.ld_folder_tree.LDFolderTree method) fillStatusLabel() (schrodinger.application.matsci.builderwidgets.ItemRow method) Filter (class in schrodinger.structutils.filter) filter() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.infra.phase.PhpExclVol method) (schrodinger.structutils.filter.Filter method) filter_data() (schrodinger.application.desmond.bennett.CalcBAR method) filter_missing_entry() (in module schrodinger.application.livedesign.panel_components) filter_reactions() (in module schrodinger.analysis.reaction) filter_undesired_states() (in module schrodinger.application.prepwizard) filterAcceptsColumn() (schrodinger.application.bioluminate.antibody.search_results_table.SplitProxyModel method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesProxyModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesProxyModel method) filterAcceptsIndex() (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterAcceptsParent() (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterAcceptsRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) (schrodinger.application.livedesign.panel_components.ColumnSelectionProxyModel method) (schrodinger.application.livedesign.panel_components.StringSearchFilterProxyModel method) filterFile() (schrodinger.pipeline.stages.filtering.SubSetStage method) filterList() (schrodinger.application.bioluminate.propfilter.SelectingFilteredListWidget method) FilterReporter (class in schrodinger.structutils.smilesfilter) filterRowsByExcitedState() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) filterSelectionChanged() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) filterSmilesFile() (schrodinger.pipeline.stages.filtering.SubSetStage method) final (schrodinger.application.jaguar.scan.Scan attribute) FINAL_VAL (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) finalize() (schrodinger.job.queue.BaseJob method) (schrodinger.structutils.shuffle.Shuffler method) finalize_smap() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) finalizeSideGroup() (schrodinger.application.matsci.amorphous.BaseMoiety method) find() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.application.desmond.packages.msys.HydrogenBondFinder method) (schrodinger.application.desmond.packages.msys.ParamTable method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) (schrodinger.structutils.interactions.salt_bridge.SaltBridgeFinder class method) (schrodinger.utils.mmutil.StringStringMap method) find_all_fragment_pairs() (in module schrodinger.application.desmond.fep_mapping) find_atoms_closest_to_atoms() (in module schrodinger.application.matsci.clusterstruct) find_atoms_near_point() (in module schrodinger.application.matsci.reorder) find_atoms_to_remove() (in module schrodinger.application.matsci.buildcomplex) find_attached_atom_index() (in module schrodinger.application.matsci.amorphous) find_best_core_match() (in module schrodinger.application.canvas.r_group) find_block() (schrodinger.application.desmond.simulation_block_test.Block method) find_buddies_on_other_surf() (in module schrodinger.application.bioluminate.surfcomp) find_closest_rotbond() (in module schrodinger.application.desmond.r_group_asl) find_common (schrodinger.application.phase.input.InputSpecs attribute) find_common_properties() (in module schrodinger.structutils.analyze) find_common_substructure() (in module schrodinger.structutils.analyze) find_component_cts() (in module schrodinger.application.desmond.fep_net_charge) find_dihedrals() (schrodinger.protein.assignment.ProtAssign.water_changeable method) find_equivalent_atoms() (in module schrodinger.application.glide.gui) (in module schrodinger.structutils.analyze) find_equivalent_st() (in module schrodinger.application.desmond.system_builder_util) find_forcefield_invalid_structures() (in module schrodinger.application.matsci.desmondutils) find_frag_from_closest_rotbond() (in module schrodinger.application.desmond.r_group_asl) find_fragment_by_cond() (in module schrodinger.application.desmond.fep_mapping) find_fragment_MCS() (in module schrodinger.application.desmond.fep_mapping) find_generalized_pattern() (in module schrodinger.protein.sequence) find_group_data() (in module schrodinger.application.matsci.smartsutils) find_hbond_hydrogen() (schrodinger.protein.analysis.Report.steric_clash_data_set method) find_head_tail() (in module schrodinger.application.matsci.equilibrium_md) find_hets() (in module schrodinger.protein.findhets) find_index_matches() (in module schrodinger.infra.phase) find_isolated_water_molecules() (in module schrodinger.protein.reliability) find_key_for_value() (in module schrodinger.application.jaguar.gui.utils) find_key_pair() (in module schrodinger.utils.sshconfig) find_license_file() (in module schrodinger.application.licensing.flexlm) find_license_resources() (in module schrodinger.application.licensing.licadmin) find_ligands() (in module schrodinger.structutils.analyze) find_local_pdb() (in module schrodinger.protein.getpdb) find_local_repository() (in module schrodinger.protein.getpdb) find_molecules_closest_to_atoms() (in module schrodinger.application.matsci.clusterstruct) find_n1_atom() (in module schrodinger.protein.pdbname) find_next_residue() (in module schrodinger.application.desmond.cms) find_noncore_fragment() (in module schrodinger.application.desmond.fep_mapping) find_noncore_subfragment() (in module schrodinger.application.desmond.fep_mapping) find_overlapping_atoms() (in module schrodinger.structutils.analyze) find_oxt_atom() (in module schrodinger.protein.pdbname) find_pattern() (in module schrodinger.protein.sequence) find_pi_cation_interactions() (in module schrodinger.structutils.interactions.pi) find_pi_pi_interactions() (in module schrodinger.structutils.interactions.pi) find_ppw_atom() (in module schrodinger.application.prepwizard) find_prev_residue() (in module schrodinger.application.desmond.cms) find_product_package_dir() (in module schrodinger.application.utils) find_production_stage() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator static method) find_protonation_state_changes() (schrodinger.protein.assignment.ProtAssign method) find_recap_bonds() (in module schrodinger.structutils.createfragments) find_residue_atom() (in module schrodinger.application.bioluminate.protein) find_rgroup_from_smarts() (in module schrodinger.structutils.rgroup_enumerate) find_ring_bonds() (in module schrodinger.structutils.analyze) find_rings() (in module schrodinger.structutils.analyze) (schrodinger.structure.Structure method) find_shortest_bond_path() (in module schrodinger.structutils.analyze) find_species() (in module schrodinger.application.matsci.clusterstruct) find_stage() (in module schrodinger.application.desmond.starter.generator.fep_plus) find_stage_number() (in module schrodinger.application.desmond.starter.generator.fep_plus) find_staying_atom() (in module schrodinger.structutils.rgroup_enumerate) FIND_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) find_traj_path() (in module schrodinger.application.desmond.packages.topo) find_traj_path_from_cms_path() (in module schrodinger.application.desmond.packages.topo) findall() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) findAromaticBonders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) findAromaticRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) findAttachedAtomIndex() (schrodinger.application.matsci.amorphous.BaseMoiety method) findAttachmentMarkers() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) findBackbone() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Monomer method) findBackbone2BranchingPoint() (schrodinger.application.matsci.amorphous.BaseMoiety method) findBond() (schrodinger.application.desmond.packages.msys.Atom method) (schrodinger.application.desmond.packages.msys.System method) findBondsToBreak() (schrodinger.application.matsci.amorphous.Monomer method) findChiAtoms() (schrodinger.protein.rotamers.Rotamers method) findColorSchemeByDescription() (schrodinger.utils.colorscheme.ColorSchemeManager method) findColorSchemeByName() (schrodinger.utils.colorscheme.ColorSchemeManager method) findCommonDatanames() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) findContactIds() (schrodinger.application.desmond.packages.msys.System method) findContacts() (schrodinger.application.desmond.packages.msys.SpatialHash method) findCoordinate() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) FindDistinctFragments() (in module schrodinger.application.desmond.packages.msys) findExact() (schrodinger.application.desmond.packages.msys.TermTable method) findFirstDisorderedMolecule() (schrodinger.application.matsci.montecarlo.Metropolizer method) findFirstQSite() (in module schrodinger.infra.phase) findFreeVolume() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) findHead() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Terminator method) findHeadAndTail() (schrodinger.application.matsci.amorphous.PolymerToFragments method) findHeadTailBranch() (schrodinger.application.matsci.amorphous.Monomer method) findHydrogenToReplace() (schrodinger.protein.captermini.CapTermini method) findHydrophobicCenter() (schrodinger.protein.membrane.Membrane_Model method) findInStructure() (schrodinger.ui.picking.ResidueRow method) findLargestTranslat() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) findLocally() (schrodinger.protein.getpdb_utility.Code method) findManageOutfiles() (schrodinger.pipeline.stages.phase.DBExportStage method) findMatches() (schrodinger.application.desmond.packages.msys.SmartsPattern method) findMinVolume() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) findNearest() (schrodinger.application.desmond.packages.msys.SpatialHash method) findNeighborFrags() (schrodinger.application.matsci.amorphous.PolymerToFragments method) findNeighboringCells() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) findNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) findNonlinearAngle() (schrodinger.application.matsci.zmutils.ZMatrix method) findOxygenToReplace() (schrodinger.protein.captermini.CapTermini method) findPath() (schrodinger.application.livedesign.panel_components.PathTreeDict method) findPattern() (schrodinger.protein.alignment.ProteinAlignment method) findPotentialTripleBondAtoms() (schrodinger.structutils.assignbondorders.AssignBondOrders method) findReagentFile() (schrodinger.analysis.reaction.ReagentClass method) (schrodinger.analysis.reaction.ReagentNode method) findResidue() (schrodinger.structure.Structure method) findRings() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) (schrodinger.application.matsci.montecarlo.ClashChecker method) (schrodinger.structutils.assignbondorders.AssignBondOrders method) findRingSideGroup() (schrodinger.application.matsci.amorphous.Monomer method) findRingSpears() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) findRotatableBonds() (schrodinger.application.matsci.amorphous.BaseMoiety method) findRowsMatching() (schrodinger.project.Project method) findSideGroup() (schrodinger.application.matsci.amorphous.BaseMoiety method) findSpears() (schrodinger.structutils.ringspear.SpearRing method) findTextChanged() (schrodinger.application.bioluminate.ssv.toolbars.FindToolBar method) FindToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) findVectorAtoms() (schrodinger.protein.membrane.Membrane_Model method) findViolations() (schrodinger.infra.phase.PhpExclVol method) findWithAll() (schrodinger.application.desmond.packages.msys.TermTable method) findWithAny() (schrodinger.application.desmond.packages.msys.TermTable method) findWithin() (schrodinger.application.desmond.packages.msys.SpatialHash method) findWithOnly() (schrodinger.application.desmond.packages.msys.TermTable method) findXvolSphereIndex() (schrodinger.application.phase.phase_markers.PhaseMarkers method) FINGERPRINT_TYPES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) FingerprintFromFileGenerator (class in schrodinger.analysis.enrichment) finish() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) (schrodinger.application.glide.http_server.GlideHTTPHandler method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.pipeline.pipeline.StageJob method) finish_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) finishGuess() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) finishPolymerFrags() (schrodinger.application.matsci.amorphous.PolymerToFragments method) finishPrevStep() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) finishProcessingJobControlJob() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) first (schrodinger.application.desmond.packages.energygroup.SliceParams attribute) (schrodinger.application.desmond.packages.msys.Bond attribute) (schrodinger.infra.mmgpgpu.SwigIntIntPair attribute) (schrodinger.infra.mmjob.SwigIntIntPair attribute) (schrodinger.infra.mmsurf.SwigIntIntPair attribute) (schrodinger.utils.colorscheme.SwigIntIntPair attribute) first() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) FIRST_CELL (schrodinger.application.matsci.nano.xtal.PBCBonds attribute) first_line_re (schrodinger.application.jaguar.textparser.TextParser attribute) first_property() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) first_quartile (schrodinger.analysis.enrichment.StatisticalSummary attribute) FIRST_SEP (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition attribute) fit() (schrodinger.application.matsci.mlearn.base.BaseFeaturizer method) FIT_ESP_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab attribute) fit_plane_to_points() (in module schrodinger.structutils.measure) fit_plane_to_points_as_list() (in module schrodinger.structutils.measure) fix_cmd() (in module schrodinger.job.jobcontrol) (in module schrodinger.utils.licutils) fix_common_structure_mistakes() (in module schrodinger.application.prepwizard) fix_elements() (schrodinger.protein.assignment.ProtAssign method) fix_filenames() (schrodinger.application.desmond.cms.Cms method) fix_for_prime() (in module schrodinger.application.prime.primefix) fix_formal_charge() (in module schrodinger.application.prime.primefix) fix_free_volume_coordinates() (in module schrodinger.application.matsci.freevolume) fix_linear_angles() (in module schrodinger.application.matsci.coarsegrain) fix_metal_bond_orders() (in module schrodinger.application.matsci.buildcomplex) fix_metal_bonding() (in module schrodinger.application.matsci.nano.xtal) fix_N4s() (schrodinger.structutils.assignbondorders.AssignBondOrders method) fix_sulfur_charges() (in module schrodinger.application.prepwizard) fixAll() (schrodinger.application.prime.primefix.FixForPrime method) fixAtomNames() (schrodinger.protein.pdbname.Substructure method) fixDNACaps() (schrodinger.application.prime.primefix.FixForPrime method) fixFormalCharge() (schrodinger.structutils.assignbondorders.AssignBondOrders method) FixForPrime (class in schrodinger.application.prime.primefix) fixHets() (schrodinger.application.prime.primefix.FixForPrime method) fixHydrogens() (schrodinger.application.matsci.enumeration.ElementAlchemist method) fixKetones() (schrodinger.structutils.assignbondorders.AssignBondOrders method) fixMetals() (schrodinger.application.prime.primefix.FixForPrime method) fixPdbresAndPdbnames() (schrodinger.application.prime.primefix.FixForPrime method) fixResName() (schrodinger.protein.pdbname.Substructure method) fixSolute() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) fixSpecialResidues() (schrodinger.application.prime.primefix.FixForPrime method)

flag_context_manager() (in module schrodinger.infra.util) flags() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) (schrodinger.application.livedesign.panel_components.EndpointSelectionModel method) (schrodinger.application.livedesign.panel_components.LDSelectionModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.PatternModel method) flashRow() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) flatten_list() (in module schrodinger.application.bioluminate.surfcomp) flattenChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions static method) flipTailFirst() (schrodinger.application.matsci.amorphous.Monomer method) FLOATABLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) floatChange() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) FloatParam (class in schrodinger.models.parameters) flush() (schrodinger.infra.mmgpgpu.ostream method) (schrodinger.infra.mmjob.ostream method) (schrodinger.infra.mmsurf.ostream method) (schrodinger.utils.colorscheme.ostream method) Fmt (class in schrodinger.application.desmond.packages.traj) fmt (schrodinger.application.desmond.packages.timer.Timer.Args attribute) fn_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) focusFinder() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) focusInEvent() (schrodinger.application.livedesign.panel_components.AddNewLineEdit method) fod_precision (schrodinger.analysis.enrichment.Calculator attribute) Folder (schrodinger.application.livedesign.panel_components.LRSort attribute) FOLLOW_45_in_static244 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_46_in_decl_output296 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_47_in_decl_meta349 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_48_in_meta_term592 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_48_in_output_term404 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_49_in_meta_term664 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_49_in_output_term476 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_meta_term681 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_meta_term745 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_meta_term809 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_output_term493 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_50_in_output_term557 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_51_in_meta_term724 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_51_in_output_term536 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_52_in_meta_term786 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_53_in_meta_term852 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_54_in_meta_term922 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_55_in_series1392 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_56_in_if_1436 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_57_in_if_1442 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_58_in_if_1448 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_ADDOP_in_signedExpComp1111 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_atom_in_comp1149 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_BCLOSE_in_comp1158 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_bind_in_exprOrBind1017 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_block_in_atom1379 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_block_in_prog160 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_BOPEN_in_comp1152 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_CCLOSE_in_atom1381 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COLON_in_iter1484 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_decl_meta358 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_decl_output305 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_fcnCall1192 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_series1401 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COMMA_in_static251 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_comp_in_expComp1129 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_COPEN_in_atom1376 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_decl_in_header191 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_decl_meta_in_decl222 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_decl_output_in_decl226 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EOF_in_prog162 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_bind1029 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_iter1478 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term600 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term671 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term728 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term792 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term855 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_meta_term927 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_output_term412 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_output_term483 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EQ_in_output_term540 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_EXP_in_expComp1132 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expComp_in_signedExpComp1121 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_atom1354 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_bind1033 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_comp1156 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_exprOrBind1013 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_fcnCall1189 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_fcnCall1195 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_if_1440 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_if_1446 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_if_1452 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_iter1482 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_iter1488 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_expr_in_series1413 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_exprOrBind_in_block980 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_exprOrBind_in_block987 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_factor_in_expr1057 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_factor_in_expr1070 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_fcnCall_in_atom1267 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_header_in_prog158 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_atom1304 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_bind1027 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_fcnCall1182 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_iter1476 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_IDENT_in_varWithType272 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_if__in_atom1248 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_iter_in_series1398 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_iter_in_series1405 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_atom1332 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_meta_term687 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_meta_term751 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_meta_term815 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_meta_term869 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_output_term499 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_output_term563 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_LIT_in_varWithType276 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_meta_term_in_decl_meta355 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_meta_term_in_decl_meta362 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_output_term_in_decl_output302 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_output_term_in_decl_output309 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_atom1356 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_decl_meta366 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_decl_output313 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_fcnCall1201 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_series1409 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_PCLOSE_in_varWithType278 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_atom1351 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_decl_meta351 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_decl_output298 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_fcnCall1185 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_series1394 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_POPEN_in_varWithType274 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SEMI_in_block983 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SEMI_in_block991 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SEMI_in_header193 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_series_in_atom1229 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_set_in_expr1061 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_set_in_factor1086 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_signedExpComp_in_expComp1135 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_signedExpComp_in_factor1081 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_signedExpComp_in_factor1096 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_static_in_decl230 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_STRING_in_atom1286 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_STRING_in_meta_term614 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_STRING_in_meta_term941 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_STRING_in_output_term426 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SUBTROP_in_meta_term675 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SUBTROP_in_output_term487 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_SUBTROP_in_signedExpComp1116 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_varWithType_in_static248 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FOLLOW_varWithType_in_static255 (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) FORBIDDEN_TO_MATCH (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) force_constant_precision (schrodinger.application.jaguar.results.NormalMode attribute) force_field_name_to_file_name() (in module schrodinger.application.matsci.cgforcefield) force_remove() (in module schrodinger.utils.fileutils) force_rename() (in module schrodinger.utils.fileutils) force_rmtree() (in module schrodinger.utils.fileutils) ForceField (class in schrodinger.application.matsci.cgforcefield) forceFieldChanged (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector attribute) forces (schrodinger.application.jaguar.results.JaguarResults attribute) forces() (in module schrodinger.application.jaguar.textparser) forces_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) forEdgeInRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) formal_charge (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.structure.Structure attribute) (schrodinger.structure._StructureAtom attribute) format() (in module schrodinger.application.jaguar.check_headers) (schrodinger.analysis.enrichment.Calculator method) (schrodinger.application.hitexpander.LogFormatter method) (schrodinger.application.matsci.textlogger.GetLogger.MyFormatter method) format_alignment_ids() (in module schrodinger.application.matsci.nano.particle) format_charge() (in module schrodinger.application.ligprep.ionizer) format_numbered_message() (in module schrodinger.application.livedesign.maestro_data_types) format_option_strings() (schrodinger.utils.cmdline.DelegatingIndentedHelpFormatter method) format_protein_label() (in module schrodinger.application.desmond.feputils) format_usage_row() (in module schrodinger.application.licensing.lmgrd_log_parser) FormatError FormatReader (class in schrodinger.structure) FORMATS (schrodinger.application.matsci.textlogger.GetLogger.MyFormatter attribute) FormatSDF() (in module schrodinger.application.desmond.packages.msys) formCommand() (schrodinger.utils.installation_check.TestJob method) formLine() (schrodinger.application.matsci.desmondutils.BrownieMSJStringer method) (schrodinger.application.matsci.desmondutils.MSJStringer method) fortfloat() (in module schrodinger.application.mopac.results2012) FP_CLASSES (schrodinger.application.matsci.cgforcefield.ForceField attribute) FP_OPTIONS_DICT_KEY (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) FP_TEXT_FILE (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) fp_types() (in module schrodinger.application.hitexpander) FPTypeCB() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) FRACT_KEYS (schrodinger.application.matsci.nano.xtal.Crystal attribute) frag_handle (schrodinger.application.combiglide.corehop.SubstCoreDatabase attribute) FragClass (class in schrodinger.application.desmond.fep_gui) fragid (schrodinger.application.desmond.packages.msys.Atom attribute) fragImportFromSketcher() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) FRAGMARK (schrodinger.maestro.markers.Icons attribute) Fragment (class in schrodinger.application.ligprep.ionizer) fragment_mutator() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) FRAGMENT_NAME (schrodinger.application.matsci.nano.constants.Constants attribute) fragment_size_cond() (in module schrodinger.application.desmond.fep_mapping) FragmentCreator (class in schrodinger.structutils.createfragments) FragmentLibrary (class in schrodinger.utils.cgxutils) fragments() (schrodinger.application.matsci.amorphous.PolymerFragment method) fragmentStructure() (schrodinger.structutils.createfragments.FragmentCreator method) fragmentStructureForEA() (schrodinger.structutils.createfragments.FragmentCreator method) fragType (schrodinger.infra.phase.PhpFragPair attribute) Frame (class in schrodinger.application.desmond.packages.traj) frame() (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method) (schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method) FrameIter (class in schrodinger.application.desmond.packages.msys.molfile) frames() (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method) (schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method) FrameworkModel (class in schrodinger.application.bioluminate.antibody.search_results_table) FrameworkTemplate (class in schrodinger.application.bioluminate.antibody.utils) free_energy_costs() (in module schrodinger.application.ligprep.ionizer) freeAll() (schrodinger.application.matsci.zmutils.ZAtom method) freeAtom() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomAngle() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomBond() (schrodinger.application.matsci.zmutils.ZMatrix method) freeAtomDihedral() (schrodinger.application.matsci.zmutils.ZMatrix method) freeCachedEntries() (schrodinger.project.Project method) freeCoord() (schrodinger.application.matsci.zmutils.ZAtom method) FreeEnergy (class in schrodinger.application.jaguar.utils) FreeEnergyContrib (class in schrodinger.application.desmond.fepana) FreePositionsType (class in schrodinger.application.matsci.espresso.qeinput) FreeVolumeDriver (class in schrodinger.application.matsci.freevolume) FreeVolumeException freeze_atom() (in module schrodinger.application.desmond.remd) freeze_atoms() (in module schrodinger.application.desmond.predict_remd_temp) freeze_existing_hydrogens() (schrodinger.protein.assignment.ProtAssign method) frequencies() (in module schrodinger.application.jaguar.textparser) frequencies_old() (in module schrodinger.application.jaguar.textparser) frequency_precision (schrodinger.application.jaguar.results.NormalMode attribute) freshenParentAndChildIndexes() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) from_dict() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) from_initial_population() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) from_list() (schrodinger.infra.mmbitset.Bitset class method) from_maestro() (in module schrodinger.protein.getpdb_utility) from_rdkit() (in module schrodinger.thirdparty.rdkit_adapter) from_string() (schrodinger.application.desmond.measurement.Measurement class method) from_style (schrodinger.structure._StructureBond attribute) fromClustalFile() (schrodinger.protein.alignment.ProteinAlignment static method) fromEtotString() (schrodinger.application.jaguar.results.ScfIteration static method) fromFastaFile() (schrodinger.protein.alignment.ProteinAlignment static method) fromFastaString() (schrodinger.protein.alignment.ProteinAlignment static method) fromFastaStringList() (schrodinger.protein.alignment.ProteinAlignment static method) fromJSON() (schrodinger.job.launchapi.JobSpecification static method) (schrodinger.job.launchapi.TaskSpecification static method) fromJson() (schrodinger.models.json.JsonableClassMixin class method) fromJsonData() (schrodinger.application.matsci.freevolume.JsonObject class method) fromkeys() (schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap class method) fromSmartsError() (schrodinger.application.canvas.r_group.RGroupException class method) FromSmilesString() (in module schrodinger.application.desmond.packages.msys) fromString() (schrodinger.application.jaguar.input.GenOptions static method) (schrodinger.structure.StructureReader static method) fromText() (schrodinger.application.jaguar.gui.input_tab_widgets.Basis class method) front() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) front_transparency (schrodinger.surface.Surface attribute) FROZEN_ATOMS_PROPERTY_NAME (schrodinger.infra.fast3d.Engine attribute) FrozenStep (class in schrodinger.application.matsci.jaguarworkflows) FsysCtAnalysis (class in schrodinger.application.desmond.packages.staf) fukui_indices() (in module schrodinger.application.jaguar.textparser) FukuiIndices (class in schrodinger.application.jaguar.results) FULL_HERMANN_MAUGUIN_SYMBOL (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) FULL_NAME_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) fullCmdList() (schrodinger.tasks.jobtasks.AbstractJobTask method) FullColumns (class in schrodinger.application.bioluminate.antibody.search_results_table) fullname (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo attribute) (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.project.Project attribute) (schrodinger.protein.sequence.Sequence attribute) fullName() (schrodinger.application.desmond.fep_edge_data.ResData method) FullProxyModel (class in schrodinger.application.bioluminate.antibody.search_results_table) fullsystem_ct (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData attribute) FullTable (class in schrodinger.application.bioluminate.antibody.search_results_table) FULLY_ANALYTIC_ACCURACY (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) fully_conserved (schrodinger.protein.annotation.Consensus attribute) FULLY_REL (schrodinger.application.matsci.espresso.utils.UPFParser attribute) FullyVisible (schrodinger.protein.sequence.Inclusion attribute) func (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) func() (in module schrodinger.application.mopac.results2012) FUNCTION (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwType attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) functional() (in module schrodinger.application.jaguar.textparser) FusedRing (class in schrodinger.application.matsci.coarsegrain) fuseIonFragment() (schrodinger.application.ligprep.ionizer.Ionizer method) FVAL_DICT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVAL_KEYS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVAL_VALUES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) FVALINCREMENT (schrodinger.application.matsci.rxn_path.ReactionPath attribute) fxnname() (in module schrodinger.infra.propedit)

G

g (schrodinger.graphics3d.arrow.MaestroArrow attribute) (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.graphics3d.torus.MaestroTorus attribute) GAMMA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) GAMMA_ONLY_KEY (schrodinger.application.matsci.espresso.qeinput.BasisType attribute) GAMMA_PARAM (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) gamma_polar() (in module schrodinger.application.jaguar.textparser) gamma_polar_precision (schrodinger.application.jaguar.results.JaguarResults attribute) Gap (class in schrodinger.protein.residue) gap_char (schrodinger.protein.sequence.Sequence attribute) gap_extend_penalty (schrodinger.protein.align.AbstractAligner attribute) gap_open_penalty (schrodinger.protein.align.AbstractAligner attribute) gap_penalty (schrodinger.structutils.structalign.StructAlign attribute) gapless_index_in_seq (schrodinger.protein.residue.Residue attribute) gapped_index_in_seq (schrodinger.protein.residue.Residue attribute) gas_phase() (in module schrodinger.application.jaguar.textparser) gasPhaseReferenceChanged() (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) gather_rings() (in module schrodinger.structutils.interactions.pi) gaussian_delta() (in module schrodinger.application.matsci.espresso.qeoutput) GaussianFilter (class in schrodinger.application.desmond.gaussian_filter) gcg (schrodinger.utils.fileutils.SeqFormat attribute) GCMC (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) gcmc (schrodinger.application.desmond.config.TAG_SPECS attribute) gen (schrodinger.application.qsite.input.QSiteInput attribute) gen_alpha_helix_restraint() (in module schrodinger.application.desmond.cms) gen_charges() (in module schrodinger.application.jaguar.textparser) gen_dE_files() (in module schrodinger.application.desmond.deltaE) gen_protein_rmsf_image() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) gen_random_color() (in module schrodinger.application.combiglide.connection_storage) gen_range_specification() (in module schrodinger.application.canvas.driverutils) gen_replica() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) gen_temperature_for_solute_tempering() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) gen_test() (in module schrodinger.application.desmond.simulation_block_test) genAllJobs() (schrodinger.job.queue.BaseJob method) genAllPrereqs() (schrodinger.job.queue.BaseJob method) general_superimpose() (in module schrodinger.application.jaguar.autots_rmsd) GENERAL_VEC_1 (schrodinger.application.matsci.nano.xtal.Crystal attribute) GENERAL_VEC_2 (schrodinger.application.matsci.nano.xtal.Crystal attribute) GENERAL_VEC_3 (schrodinger.application.matsci.nano.xtal.Crystal attribute) generalize() (schrodinger.infra.fast3d.Generalizer method) Generalizer (class in schrodinger.infra.fast3d) generate() (in module schrodinger.application.desmond.starter.generator.fep_plus) (schrodinger.application.bioluminate.protein.Mutator method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.desmond.image_generator.ImageGenerator method) generate3dConformation() (schrodinger.structure.Structure method) generate_aligned_2d_ligand_pair() (in module schrodinger.application.desmond.report_helper) generate_all_keywords() (in module schrodinger.application.jaguar.reactiq_keywords) generate_asl() (in module schrodinger.structutils.analyze) generate_complex_msj() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) generate_config() (in module schrodinger.application.desmond.packages.gdesmond_utils) generate_core_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_criterion() (in module schrodinger.utils.ligfilter) generate_crystal_mates() (in module schrodinger.structutils.analyze) generate_curve() (in module schrodinger.application.matsci.spectra) generate_default_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_description() (in module schrodinger.application.jaguar.gui.basis_selector) generate_dummy_atoms() (schrodinger.protein.membrane.Membrane_Model method) generate_eval_string() (in module schrodinger.infra.propedit) generate_eval_string_all() (in module schrodinger.infra.propedit) generate_groups() (in module schrodinger.infra.propedit) generate_hot_atoms_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_job_name() (in module schrodinger.application.jaguar.gui.utils) generate_ligand_2d_image() (in module schrodinger.application.desmond.report_helper) generate_ligand_2d_placeholder() (in module schrodinger.application.desmond.report_helper) generate_mapping_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_master_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) generate_mates() (schrodinger.protein.assignment.ProtAssign method) generate_meta_cfg() (in module schrodinger.application.desmond.meta) generate_method() (in module schrodinger.models.parameters) generate_molecular_formula() (in module schrodinger.structutils.analyze) generate_mutation_pic() (in module schrodinger.application.desmond.fep_scholar_util) generate_reduced_trajectory() (in module schrodinger.application.desmond.process_fep_traj) generate_return_code_dict() (in module schrodinger.infra.mmcheck) generate_scripts() (in module schrodinger.application.desmond.fep_scholar_util) (in module schrodinger.application.desmond.feputils) generate_smarts() (in module schrodinger.structutils.analyze) generate_smarts_canvas() (in module schrodinger.structutils.analyze) generate_smiles() (in module schrodinger.structutils.analyze) generate_solvent_msj() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) generate_special_states() (in module schrodinger.application.prepwizard) generate_subjob_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.ProteinMapperMsjGenerator method) generate_tautomer_code() (in module schrodinger.structutils.analyze) generate_vacuum_msj() (schrodinger.application.desmond.mapper_msj_generator.VacuumMsjGenerator method) generateCfg() (schrodinger.application.desmond.meta.Meta method) generateConformers() (schrodinger.infra.phase.PhpMMconfAdaptor method) generateConfs() (schrodinger.infra.phase.PhpProject method) generateCsvFile() (schrodinger.pipeline.stages.glide.DockingStage method) generateCSVTable() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) generateDM() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) generateFingerprint() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) generateHtml() (schrodinger.application.report2d.Report2D method) generateJaguarStatus() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.StandardStatusMixin method) (schrodinger.application.jaguar.gui.base_panel.TaskStatusMixin method) generateLcsMapFromBaseFeatures() (in module schrodinger.infra.phase) generatePdf() (schrodinger.application.report2d.Report2D method) generatePicture() (schrodinger.application.combiglide.combenumdock.createFragmentDelegate method) (schrodinger.application.combiglide.combenumdock.simpleEnumDockDelegate method) generatePictureHighlight() (schrodinger.application.desmond.fep_scholar_util.ScholarStructureItem method) generatePlotData() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) GeneratePropsStage (class in schrodinger.pipeline.stages.filtering) generateSeqProjectRows() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) generateSeqStructures() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) generateSitesFromBaseFeatures() (in module schrodinger.infra.phase) generateSpecs() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) generateStateCT() (schrodinger.application.ligprep.ionizer.Ionizer method) generateStatus() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) generateSymmetryEquiv() (schrodinger.application.matsci.nano.sheet.SymmetryEquiv method) generateXls() (schrodinger.application.report2d.Report2D method) GeneratorTypes (class in schrodinger.application.desmond.restraint) GenericType (class in schrodinger.application.matsci.espresso.qeinput) GeneticOptimization (class in schrodinger.application.matsci.genetic_optimization.genetic_optimization) genFileName() (schrodinger.pipeline.stage.Stage method) GenOptions (class in schrodinger.application.jaguar.input) genOutputFileName() (schrodinger.pipeline.stage.Stage method) gensym() (schrodinger.application.desmond.enhsamp.Env method) geom() (schrodinger.application.macromodel.utils.ComUtil method) GEOM_AND_SETTINGS (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) GEOM_ONLY (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) GeomAnalyzerBase (class in schrodinger.application.desmond.packages.staf) GeomCalc (class in schrodinger.application.desmond.packages.staf) GeomConstraint (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) geometry_read() (in module schrodinger.application.jaguar.textparser) geometry_scan_step() (in module schrodinger.application.jaguar.textparser) geopt_geometry() (in module schrodinger.application.jaguar.textparser) geopt_stuck1() (in module schrodinger.application.jaguar.textparser) geopt_stuck2() (in module schrodinger.application.jaguar.textparser) get() (in module schrodinger.application.desmond.envir) (in module schrodinger.application.desmond.icon) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.TokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) (schrodinger.application.desmond.packages.energygroup.EnergyFacade method) (schrodinger.application.desmond.packages.msys.Ct method) (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.job.jobcontrol.Job method) (schrodinger.utils.preferences.Preferences method) get14EleEnergy() (schrodinger.structutils.minimize.Minimizer method) get14LJEnergy() (schrodinger.structutils.minimize.Minimizer method) get2dStructure() (schrodinger.structure.SmilesStructure method) get3dStructure() (schrodinger.structure.SmilesStructure method) (schrodinger.structure.Structure method) get_2d_ligand_image() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) get_2d_tors_annotated_lig_pair() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.PRMEdgeReportMaker method) get_2var_plot() (in module schrodinger.application.desmond.mplchart) get_abfep_cross_link() (in module schrodinger.application.desmond.fepana) get_action_obj_name() (in module schrodinger.application.bioluminate.actions.factory) get_active_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_active_fsys_ct_from_frame() (in module schrodinger.application.desmond.packages.topo) get_active_jobs() (in module schrodinger.job.jobcontrol) get_adjustable_atoms() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_aids_with_virtuals() (in module schrodinger.application.desmond.packages.topo) get_alchem_solv() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_aligned_chmmol_from_ct() (in module schrodinger.application.desmond.depictor) get_aligned_coordinates() (in module schrodinger.application.desmond.frag_snap) get_aligned_coordinates_from_fragments() (in module schrodinger.application.desmond.frag_snap) get_aligned_fragment_coords() (in module schrodinger.application.desmond.frag_snap) get_aligned_residues() (in module schrodinger.protein.sequence) get_alignment_matrix() (in module schrodinger.structutils.transform) get_all_atoms_marked_as_neighbors() (in module schrodinger.application.matsci.clusterstruct) get_all_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_all_force_field_paths() (in module schrodinger.application.matsci.cgforcefield) get_allocator() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) get_alt_index_name() (in module schrodinger.infra.phase) get_analysis() (schrodinger.application.desmond.replica_sid_generator.FEPReport method) get_angle_between_vectors() (in module schrodinger.structutils.transform) get_angle_in_degrees() (in module schrodinger.application.matsci.mecp_mod) get_angle_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) get_angle_potential_type() (in module schrodinger.application.matsci.coarsegrain) get_angles() (schrodinger.application.desmond.torsion_related.TorsionPotential method) get_anion() (in module schrodinger.application.matsci.mlearn.features) get_antibody_scheme() (in module schrodinger.application.bioluminate.antibody.utils) get_APBS_potential_grid() (in module schrodinger.application.bioluminate.escomp) get_appdata_dir() (in module schrodinger.utils.fileutils) get_approximate_atomic_sasa() (in module schrodinger.structutils.analyze) get_approximate_sasa() (in module schrodinger.structutils.analyze) get_ark_results() (schrodinger.application.desmond.replica_sid_generator.FEPReport method) get_aromatic_hydrogen_bonds() (in module schrodinger.structutils.interactions.hbond) get_assembled_structure() (in module schrodinger.application.matsci.swap_fragments_utils) get_atom() (schrodinger.application.desmond.maestro.Workspace method) get_atom_chirality() (in module schrodinger.application.canvas.r_group) get_atom_group() (schrodinger.application.desmond.cms.Cms method) get_atom_indices() (schrodinger.protein.analysis.Report.local_residue method) get_atom_info() (in module schrodinger.application.jaguar.gui.utils) get_atom_key() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_atom_layers() (in module schrodinger.application.matsci.freevolume) get_atom_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) get_atom_mapping() (in module schrodinger.application.desmond.fep_mapping) get_atom_mapping_data() (in module schrodinger.application.desmond.fep_mapping) get_atom_marking() (in module schrodinger.application.desmond.fep_mapping) get_atom_name() (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) get_atom_names_for_chi_angle() (in module schrodinger.structure) get_atom_numbering_chirality() (in module schrodinger.application.jaguar.chirality) get_atom_positions() (in module schrodinger.application.bindingsite.cavutils) get_atom_reference_coordinates() (in module schrodinger.application.desmond.struc) get_atom_type() (schrodinger.application.jaguar.structure_isomorphism.AutoTSAtomMapper method) (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) get_atom_type_dict() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) get_atomic_constraints_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_atomic_element_symbols() (in module schrodinger.application.matsci.nano.util) get_atomic_forces_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_atomic_positions_cell_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_atomic_species_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_atoms_close_to_point() (in module schrodinger.structutils.measure) get_atoms_close_to_structure() (in module schrodinger.structutils.measure) get_atoms_close_to_subset() (in module schrodinger.structutils.measure) get_atoms_from_asl() (in module schrodinger.structutils.analyze) get_atoms_from_uid() (in module schrodinger.application.desmond.maestro) get_attach() (schrodinger.application.canvas.r_group.TempAtom method) get_attachment_bonds() (in module schrodinger.application.desmond.r_group_asl) get_attachment_points() (schrodinger.application.canvas.r_group.Data method) get_attribute_alias() (in module schrodinger.application.jaguar.results) get_attribute_default() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) get_attribute_type() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) get_attributes() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) get_average_box_volume() (in module schrodinger.application.desmond.fepana) get_average_structure() (in module schrodinger.structutils.analyze) get_b64decoded_str() (in module schrodinger.application.desmond.cmdline) get_b64encoded_str() (in module schrodinger.application.desmond.cmdline) get_backbone_indices() (schrodinger.protein.analysis.Report.local_residue method) get_backend() (in module schrodinger.application.desmond.meta) (in module schrodinger.job.jobcontrol) get_backend_host_list() (in module schrodinger.job.jobcontrol) get_base_names() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_basename() (in module schrodinger.utils.fileutils) get_bases() (in module schrodinger.application.jaguar.basis) get_basis() (in module schrodinger.application.jaguar.basis) get_basis_by_name() (in module schrodinger.application.jaguar.basis) get_bb_ordered_aids() (in module schrodinger.application.desmond.packages.parch) get_big_fused_rings() (in module schrodinger.application.desmond.r_group_asl) get_bigger_rclone_setting() (in module schrodinger.application.matsci.desmondutils) get_bio_database() (in module schrodinger.application.bioluminate.antibody.utils) get_block_summary() (in module schrodinger.application.desmond.simulation_block_data) get_bond_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) get_bond_type_dict() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) get_bonded_hydrogens() (in module schrodinger.application.ligprep.ionizer) get_bonded_term_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) get_bonding_cell_deltas() (in module schrodinger.application.matsci.nano.xtal) get_bonds_in_molecule() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) get_bonds_in_rings() (schrodinger.application.canvas.r_group.Data method) get_box() (in module schrodinger.application.desmond.cms) get_boxsize() (in module schrodinger.application.desmond.cms) get_boxvolume() (in module schrodinger.application.desmond.cms) get_bridge_atoms() (in module schrodinger.application.desmond.fep_mapping) get_bridging_waters() (in module schrodinger.application.prepwizard) get_bs_spectrum_file_temps_keys() (in module schrodinger.application.matsci.bandshape_utils) get_builtin_directory() (in module schrodinger.application.matsci.builderwidgets) get_canonical_ordering() (in module schrodinger.structutils.assignbondorders) get_carat_map() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_carts_from_anchor_string() (in module schrodinger.application.matsci.nano.xtal) get_cell() (in module schrodinger.application.matsci.nano.xtal) get_cell_dofree() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_cell_pairs() (in module schrodinger.application.matsci.nano.xtal) get_cell_parameters_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_center_gridlen() (in module schrodinger.application.bioluminate.escomp) get_centroid() (in module schrodinger.application.matsci.shapes) (in module schrodinger.structutils.transform) get_cg_cutoff_data() (in module schrodinger.application.matsci.coarsegrain) get_chain_sequences() (in module schrodinger.application.prepwizard) get_charge() (in module schrodinger.application.bioluminate.propka_parse) get_checksum() (in module schrodinger.application.matsci.espresso.ppdb) get_child_like_parent() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_chiral_atoms() (in module schrodinger.structutils.analyze) get_chirality() (in module schrodinger.application.jaguar.chirality) get_chmmol_bonds_from_atoms() (in module schrodinger.application.desmond.fep_scholar_util) get_chorus_from_params() (in module schrodinger.application.matsci.nano.xtal) get_chorus_properties() (in module schrodinger.application.matsci.nano.xtal) get_climbing_images() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_close_atoms() (in module schrodinger.structutils.measure) get_closest_atom() (in module schrodinger.application.matsci.swap_fragments_utils) get_cms() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_coarse_grain_msj_family_header() (in module schrodinger.application.matsci.coarsegrain) get_coarse_grain_msj_header() (in module schrodinger.application.matsci.coarsegrain) get_collapsed_index() (in module schrodinger.application.matsci.nano.xtal) get_color() (in module schrodinger.application.matsci.amorphous) (schrodinger.application.desmond.torsion_related.TorsionPotential method) get_color_list() (in module schrodinger.application.combiglide.connection_storage) get_color_scheme() (in module schrodinger.structutils.color) get_com_and_axes() (in module schrodinger.application.bindingsite.cavutils) get_combined_exclusion_str() (in module schrodinger.application.matsci.coarsegrain) get_command() (in module schrodinger.job.queue) get_command_items() (in module schrodinger.maestro.maestro) get_command_line_host_list() (in module schrodinger.job.jobcontrol) get_command_option() (in module schrodinger.maestro.maestro) get_config_filename() (in module schrodinger.application.jaguar.user_config) get_connected_components() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) get_connected_ring_bonds() (in module schrodinger.application.canvas.r_group) get_connection_color() (in module schrodinger.application.combiglide.connection_storage) get_constraint() (schrodinger.application.desmond.cms.Cms method) get_control_gdir() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_conv_from_vecs() (in module schrodinger.application.matsci.nano.xtal) get_converged() (in module schrodinger.structutils.minimize) get_coords_array_from_list() (in module schrodinger.structutils.transform) get_coords_dict() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_core() (schrodinger.application.canvas.r_group.Data method) get_core_bonds() (schrodinger.application.canvas.r_group.Data method) get_core_map() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_cores() (schrodinger.application.canvas.r_group.Data method) get_cov_lig_info() (in module schrodinger.application.desmond.replica_sid_generator) get_cov_radii() (in module schrodinger.application.matsci.nano.xtal) get_cpu() (in module schrodinger.utils.sysinfo) get_cpu_gpu_info() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_cross() (in module schrodinger.graphics3d.common) get_ct() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) get_ct_offsets() (schrodinger.application.canvas.r_group.Data method) get_current_command_item() (in module schrodinger.maestro.maestro) get_custom_reagent_classes() (in module schrodinger.analysis.reaction) get_cut_bonds() (in module schrodinger.application.matsci.swap_fragments_utils) get_data_frame_from_project() (in module schrodinger.utils.pandasutils) get_database_ids() (in module schrodinger.infra.phase) get_databases() (in module schrodinger.application.bioluminate.antibody.utils) get_default() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method) get_default_box_size() (in module schrodinger.application.glide.glide) get_default_criterion_parser() (in module schrodinger.utils.ligfilter) get_default_far_timestep() (in module schrodinger.application.matsci.desmondutils) get_default_near_timestep() (in module schrodinger.application.matsci.desmondutils) get_default_reactions_filename() (in module schrodinger.analysis.reaction) get_default_reagent_classes_filename() (in module schrodinger.analysis.reaction) get_default_setting() (in module schrodinger.application.desmond.config) get_degrees_of_freedom() (in module schrodinger.application.desmond.remd) (schrodinger.application.desmond.cms.Cms method) get_delta_time() (in module schrodinger.application.desmond.fepana) get_density() (in module schrodinger.application.matsci.amorphous) get_density_from_ene() (in module schrodinger.application.matsci.desmondutils) get_descriptors_from_file() (in module schrodinger.application.matsci.order_parameter_mod) get_desktop_dir() (in module schrodinger.utils.fileutils) get_detailed() (in module schrodinger.application.bioluminate.propka_parse) get_dihedral_atoms() (schrodinger.protein.assignment.ProtAssign.changeable method) get_dimers_in_structure() (in module schrodinger.application.matsci.clusterstruct) get_dimers_with_molecule() (in module schrodinger.application.matsci.clusterstruct) get_directory() (in module schrodinger.maestro.maestro) (in module schrodinger.utils.fileutils) get_directory_path() (in module schrodinger.utils.fileutils) get_dist() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_distance() (in module schrodinger.application.desmond.meta) get_distance_cell() (in module schrodinger.application.matsci.mlearn.features) get_disulfide_bonds() (in module schrodinger.structutils.interactions.ssbond) get_driver_option_parser() (in module schrodinger.application.canvas.driverutils) get_dummy_filter() (in module schrodinger.structutils.rgroup_enumerate) get_edge_normals() (in module schrodinger.structutils.assignbondorders) get_electric_potential_related() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_electrons_efield() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_element() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) get_element_default() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) get_element_histogram() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_element_mutator_dict() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_element_priority() (in module schrodinger.application.matsci.nano.xtal) get_element_tag() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) get_element_type() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) get_encoded_restraints() (in module schrodinger.application.desmond.restraint) get_energies() (in module schrodinger.application.desmond.packages.energygroup) get_energy() (in module schrodinger.application.macromodel.apps) (in module schrodinger.structutils.minimize) get_energy_group_output_filename() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) get_energy_table() (in module schrodinger.application.desmond.fepana) get_enrichment_calculator() (in module schrodinger.application.glide.glideanalysis) get_ensemble() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_ensemble_class_method() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) get_ent() (in module schrodinger.protein.getpdb) get_entry_2d_tooltip() (in module schrodinger.maestro.maestro) get_entry_id() (in module schrodinger.application.desmond.maestro) (in module schrodinger.application.desmond.util) get_entry_structure_image() (in module schrodinger.maestro.maestro) get_entry_title() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_entryname_prefix() (in module schrodinger.application.desmond.maestro) get_environ_log_level() (in module schrodinger.utils.log) get_error_text() (schrodinger.application.mopac.mopac_results.MopacResults method) (schrodinger.application.mopac.results2012.MopacResults2012 method) (schrodinger.application.mopac.results71.MopacResults71 method) get_eta_marker_indexes() (in module schrodinger.application.matsci.builderwidgets) get_exception_handler() (in module schrodinger.infra.exception_handler) get_excluded_columns() (in module schrodinger.application.canvas.driverutils) get_exec() (in module schrodinger.application.desmond.config) get_exec_name() (in module schrodinger.application.desmond.config) get_extracted_and_maps() (in module schrodinger.application.matsci.swap_fragments_utils) get_extracted_atom_index() (in module schrodinger.application.matsci.clusterstruct) get_feature_text() (in module schrodinger.application.phase.constants) get_fep_cts() (in module schrodinger.application.desmond.r_group_asl) (schrodinger.application.desmond.cms.Cms method) get_fep_lambda_schedule() (in module schrodinger.application.desmond.config) get_fep_lambdas() (in module schrodinger.application.desmond.config) get_fep_mapping() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) get_fep_output_filename() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) get_fepio_atom_mapping() (in module schrodinger.application.desmond.fep_mapping) get_fepio_sub_block_std_prop_getter() (in module schrodinger.application.desmond.ffiostructure) get_fepio_sub_block_std_prop_setter() (in module schrodinger.application.desmond.ffiostructure) get_fepio_sub_block_std_prop_short_name() (in module schrodinger.application.desmond.ffiostructure) get_ff() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_ffio_sub_block_std_prop_getter() (in module schrodinger.application.desmond.ffiostructure) get_ffio_sub_block_std_prop_setter() (in module schrodinger.application.desmond.ffiostructure) get_ffio_sub_block_std_prop_short_name() (in module schrodinger.application.desmond.ffiostructure) get_field_from_log() (in module schrodinger.application.desmond.fepana) get_file_data() (in module schrodinger.application.matsci.freevolume) (in module schrodinger.application.matsci.spectra) get_file_url() (in module schrodinger.job.launchapi) get_files_from_folder() (in module schrodinger.utils.fileutils) get_final_state() (in module schrodinger.application.matsci.mecp_mod) get_fingerprint_types() (in module schrodinger.utils.multifpfile) get_fingerprints() (schrodinger.utils.multifpfile.MultiFPFile method) get_first_hostid() (in module schrodinger.application.licensing.licadmin) get_first_hostname() (in module schrodinger.tasks.jobtasks) get_flat_color_list() (in module schrodinger.application.combiglide.connection_storage) get_flexlm_search_path() (in module schrodinger.application.licensing.licadmin) get_fmt() (in module schrodinger.application.desmond.packages.traj) get_font_id() (in module schrodinger.utils.pymol) get_font_names() (in module schrodinger.maestro.maestro) get_force_field_file_path() (in module schrodinger.application.matsci.cgforcefield) get_force_field_name() (in module schrodinger.application.matsci.cgforcefield) get_formula_dict() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) get_formulas_basename() (in module schrodinger.application.matsci.nano.interface_mod) get_fragment() (in module schrodinger.application.desmond.r_group_asl) get_fragment_smiles() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) get_fragment_structure() (in module schrodinger.protein.helix) get_fragments_from_att_points() (in module schrodinger.application.desmond.r_group_asl) get_fragname() (in module schrodinger.application.desmond.struc) (schrodinger.application.desmond.cms.Cms method) get_free_energy() (in module schrodinger.application.bioluminate.propka_parse) get_free_volume_structure() (in module schrodinger.application.matsci.freevolume) get_freezer_structure() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_fullsys_ct_atom_index_range() (schrodinger.application.desmond.cms.Cms method) get_functional_rings() (schrodinger.application.canvas.r_group.Data method) get_gcd_list_ints() (in module schrodinger.application.matsci.nano.xtal) get_generation_log_file_name() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_glibc_version() (in module schrodinger.utils.sysinfo) get_glide_job() (in module schrodinger.application.glide.glide) get_global_quantity() (in module schrodinger.application.desmond.fepana) get_gluepoints() (in module schrodinger.application.desmond.cms) get_grid_data() (schrodinger.application.desmond.cns_io.CNSData method) get_grid_parameters() (in module schrodinger.application.bindingsite.cavutils) get_grid_radius_property_values() (in module schrodinger.application.matsci.freevolume) get_guess() (in module schrodinger.application.matsci.mecp_mod) get_halogen_bonds() (in module schrodinger.structutils.interactions.hbond) get_handlers_for_key() (in module schrodinger.infra.mmkv) get_hbond_direction() (in module schrodinger.application.bindingsite.intfield) get_heavies() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_heavy_atoms() (in module schrodinger.application.desmond.r_group_asl) get_heavy_fragment() (in module schrodinger.application.desmond.fep_mapping) get_het_name() (in module schrodinger.application.prepwizard) get_hill_order() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) get_histogram() (schrodinger.application.desmond.replica_dE.replicas_monitor method) get_hkl() (in module schrodinger.application.matsci.nano.slab) get_home_dir() (in module schrodinger.utils.fileutils) get_homebox() (in module schrodinger.application.desmond.config) get_host() (in module schrodinger.application.livedesign.login) (in module schrodinger.job.jobcontrol) get_host_entries() (in module schrodinger.utils.installation_check) get_hostfile() (in module schrodinger.job.jobcontrol) get_hostid() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.utils.sysinfo) get_hostname() (in module schrodinger.utils.sysinfo) get_hosts() (in module schrodinger.job.jobcontrol) get_hot_atoms() (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_hydrogen_bonds() (in module schrodinger.structutils.interactions.hbond) get_hypo_monitor() (in module schrodinger.application.phase.pt_hypothesis) get_hypothesis_entry_ids() (in module schrodinger.application.phase.pt_hypothesis) get_hypothesis_from_project() (in module schrodinger.application.phase.pt_hypothesis) get_idx() (in module schrodinger.application.desmond.automatic_analysis_generator) get_idx_groups() (in module schrodinger.application.matsci.reaction_workflow_utils) get_idx_groups_str() (in module schrodinger.application.matsci.reaction_workflow_utils) get_idxs() (in module schrodinger.application.matsci.swap_fragments_utils) get_idxs_marked_atoms() (in module schrodinger.application.matsci.reaction_workflow_utils) get_idxs_str() (in module schrodinger.application.matsci.swap_fragments_utils) get_image() (in module schrodinger.application.desmond.report_helper) get_image_coords() (in module schrodinger.application.matsci.nano.xtal) get_in_cms_from_cpt() (in module schrodinger.application.desmond.gui) get_included_entries() (in module schrodinger.maestro.maestro) get_included_entry() (in module schrodinger.maestro.maestro) get_included_entry_ids() (in module schrodinger.maestro.maestro) get_index() (schrodinger.application.canvas.r_group.TempAtom method) get_indices() (in module schrodinger.application.desmond.util) get_input_files() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) get_input_path() (schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument method) (schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method) (schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument method) (schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method) (schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument method) (schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument method) get_installed_hostfiles() (in module schrodinger.job.jobcontrol) get_int_tuples_from_str_property() (in module schrodinger.application.matsci.reaction_workflow_utils) get_interaction_sites() (in module schrodinger.application.bindingsite.intfield) get_interface_kwargs() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_inversion_index() (in module schrodinger.application.matsci.nano.util) get_isoelectronic_mutator_indicies() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_jaguar_keywords_list() (in module schrodinger.application.matsci.reaction_workflow_utils) get_jaguar_max_atoms() (in module schrodinger.application.matsci.jaguarworkflows) get_jaguar_out_mae() (in module schrodinger.application.matsci.jaguarworkflows) get_jaguar_output() (in module schrodinger.application.matsci.jaguarworkflows) get_jaguar_output_structure() (in module schrodinger.application.matsci.jaguarworkflows) get_job_command_in_startup() (in module schrodinger.application.desmond.cmdline) get_job_details() (in module schrodinger.application.desmond.simulation_block_test) get_job_spec() (schrodinger.application.desmond.packages.cui.CommandLine method) get_job_status_color() (in module schrodinger.maestro.maestro) get_job_status_loop() (in module schrodinger.tasks.jobtasks) get_job_type() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_jobname() (in module schrodinger.application.jaguar.utils) (in module schrodinger.application.matsci.jobutils) (in module schrodinger.utils.fileutils) get_jobs() (in module schrodinger.maestro.maestro) get_jobs_by_program() (in module schrodinger.job.jobcontrol) get_k_points_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_keep_idxs() (in module schrodinger.application.matsci.swap_fragments_utils) get_kernel_version() (in module schrodinger.utils.sysinfo) get_keyword() (in module schrodinger.application.glide.glide) get_keywords_dicts() (in module schrodinger.application.glide.glide) get_keywords_set() (in module schrodinger.application.glide.glide) get_knime_workflows_url() (in module schrodinger.utils.config) get_lambda_atom_indices() (schrodinger.application.desmond.cms.Cms method) get_last_20_lines() (in module schrodinger.pipeline.pipeutils) get_last_EZ_property_index() (in module schrodinger.structutils.rgroup_enumerate) get_lattice_param_properties() (in module schrodinger.application.matsci.nano.xtal) get_lattice_properties() (in module schrodinger.application.matsci.nano.particle) get_lattice_vectors() (in module schrodinger.application.matsci.nano.xtal) get_ld_client_and_models() (in module schrodinger.application.livedesign.login) get_ld_data_from_data_names() (in module schrodinger.application.livedesign.maestro_data_types) get_LD_version() (in module schrodinger.application.livedesign.login) get_lead_confs() (in module schrodinger.application.macromodel.apps) get_legal_name() (schrodinger.utils.pymol.PymolInstance method) get_lengths() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method) get_libpath() (in module schrodinger.analysis.reaction) get_license() (in module schrodinger.application.canvas.utils) get_license_request_info() (in module schrodinger.application.licensing.netsuiteapi) get_ligand1_atom_dict() (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) get_ligand2_atom_dict() (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) get_ligand_asl() (in module schrodinger.maestro.maestro) (in module schrodinger.structutils.sitealign) get_ligand_fragments() (in module schrodinger.application.desmond.packages.analysis) get_ligands() (in module schrodinger.application.desmond.feputils) get_ligands_asl() (in module schrodinger.application.desmond.process_fep_traj) get_linked_path() (in module schrodinger.application.licensing.flexlm) (in module schrodinger.utils.licutils) get_listof_props_ene() (in module schrodinger.application.desmond.simulation_block_data) get_local_appdata_dir() (in module schrodinger.utils.fileutils) get_local_server() (in module schrodinger.application.licensing.licadmin) get_local_symmetry() (in module schrodinger.application.desmond.meta) get_log_props() (in module schrodinger.application.desmond.simulation_block_data) get_loggable_float() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_logger() (in module schrodinger.utils.log) get_long_family_name() (in module schrodinger.application.livedesign.data_classes) get_low_energy_conformers() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_machid_output() (in module schrodinger.application.licensing.licadmin) get_macro() (in module schrodinger.application.jaguar.user_config) (schrodinger.application.jaguar.keywordDB.Keyword method) (schrodinger.application.jaguar.keywordDB.Setting method) get_maestro() (in module schrodinger) get_maestro_groupname() (in module schrodinger.application.combiglide.combenumdock) get_maestro_scripts_path() (in module schrodinger.utils.maestro_scripts_path) get_maestro_toplevel_window() (in module schrodinger.maestro.maestro) get_mag_hubbu() (in module schrodinger.application.matsci.espresso.utils) get_main_window() (in module schrodinger.maestro.maestro) get_marker_atom_indexes_from_structure() (in module schrodinger.application.matsci.builderwidgets) get_martini_antifreeze_type_from_type() (in module schrodinger.application.matsci.coarsegrain) get_martini_bond_force_constant() (in module schrodinger.application.matsci.coarsegrain) get_martini_epsilon() (in module schrodinger.application.matsci.coarsegrain) get_martini_eq_length() (in module schrodinger.application.matsci.coarsegrain) get_martini_ring_type_from_type() (in module schrodinger.application.matsci.coarsegrain) get_martini_sigma() (in module schrodinger.application.matsci.coarsegrain) get_martini_subtypes() (in module schrodinger.application.matsci.coarsegrain) get_martini_type_from_super_type() (in module schrodinger.application.matsci.coarsegrain) get_matrix_value() (in module schrodinger.protein.residue) get_matsci_user_data_dir() (in module schrodinger.application.matsci.jobutils) get_max_and_rms_and_len() (in module schrodinger.application.matsci.mecp_mod) get_max_occurs() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method) get_maximum_vdw_radius() (in module schrodinger.application.matsci.amorphous) get_md_results() (in module schrodinger.application.matsci.equilibrium_md) get_mean() (in module schrodinger.application.desmond.fepana) get_measurement_items() (in module schrodinger.utils.pymol) get_meta_cfg_filename() (in module schrodinger.application.desmond.meta) get_min_occurs() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDGroup method) get_mmlewis_bonding() (in module schrodinger.application.jaguar.autots_bonding) get_mmshare_common_dir() (in module schrodinger.utils.fileutils) get_mmshare_data_dir() (in module schrodinger.utils.fileutils) get_mmshare_dir() (in module schrodinger.utils.fileutils) get_mmshare_listing() (in module schrodinger.application.licensing.licadmin) get_mmshare_scripts_dir() (in module schrodinger.utils.fileutils) get_mmshare_version() (in module schrodinger) get_model_coordinates() (in module schrodinger.maestro.maestro) get_model_ff_name() (in module schrodinger.application.matsci.desmondutils) get_model_from_pt_row() (in module schrodinger.application.desmond.gui) get_model_system_type() (in module schrodinger.application.desmond.cms) get_mol_formula() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_mol_ids() (schrodinger.utils.multifpfile.MultiFPFile method) get_mol_reader() (in module schrodinger.analysis.reaction) get_mopac_launcher() (in module schrodinger.application.mopac.mopac_launchers) get_mopac_results_instance() (in module schrodinger.application.mopac.mopac_launchers) get_mpircores_from_environ() (in module schrodinger.application.matsci.espresso.utils) get_mpl_backend_name() (in module schrodinger) get_multisim_command() (in module schrodinger.application.matsci.desmondutils) get_mutation_atoms_and_bonds() (in module schrodinger.application.desmond.fep_scholar_util) get_mydocuments_dir() (in module schrodinger.utils.fileutils) get_mynetworkplaces_dir() (in module schrodinger.utils.fileutils) get_name() (schrodinger.infra.mmcheck.ReturnCode method) get_name_file() (in module schrodinger.application.jaguar.input) get_name_filter() (in module schrodinger.utils.fileutils) get_natom_btw_two_cells() (in module schrodinger.application.matsci.nano.xtal) get_natoms() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_neb_atomic_forces_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_neb_cell_parameters_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_neb_images_positions_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_neighbor_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) get_neighbors() (in module schrodinger.structutils.assignbondorders) get_netsuite_license() (in module schrodinger.application.licensing.licadmin) get_network_info() (in module schrodinger.application.licensing.licadmin) get_new_file_name() (in module schrodinger.application.livedesign.export_controller) get_new_index() (schrodinger.protein.assignment.ProtAssign.changeable method) get_next_filename() (in module schrodinger.utils.fileutils) get_next_filename_prefix() (in module schrodinger.utils.fileutils) get_next_partition() (in module schrodinger.application.desmond.autopartition) get_next_subgroup_id() (in module schrodinger.application.livedesign.ld_import) get_nmr() (in module schrodinger.application.jaguar.textparser) get_nonbond_potential_type() (in module schrodinger.application.matsci.coarsegrain) get_nonduplicated_atom() (in module schrodinger.application.desmond.remd) get_normal_surf_from_HKL() (in module schrodinger.application.matsci.nano.xtal) get_normalized() (in module schrodinger.graphics3d.common) get_normalized_spanning_vectors() (in module schrodinger.application.matsci.nano.xtal) get_normalized_vector() (in module schrodinger.structutils.transform) get_nrep() (schrodinger.application.desmond.replica_dE.replica_container method) (schrodinger.application.desmond.replica_dE.replicas_monitor method) get_num_constraint() (in module schrodinger.application.desmond.remd) (schrodinger.application.desmond.cms.Cms method) get_num_nonwateratom() (in module schrodinger.application.desmond.remd) get_num_rotatable_bonds() (in module schrodinger.structutils.analyze) get_num_simple_bonds() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_num_wateratom() (in module schrodinger.application.desmond.remd) get_number_atoms() (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) get_number_density_from_cms() (in module schrodinger.application.desmond.fepana) get_number_electrons() (in module schrodinger.application.jaguar.utils) get_nwaters() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_obj_param_value() (in module schrodinger.models.parameters) get_obj_param_values() (in module schrodinger.models.parameters) get_obj_params() (in module schrodinger.models.parameters) get_old2new() (in module schrodinger.application.desmond.torsion_related) get_one_step_route() (in module schrodinger.analysis.reaction) get_op_positions() (in module schrodinger.infra.propedit) get_opacity() (in module schrodinger.application.desmond.fep_edge_report_maker) get_open_file_name() (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog static method) get_open_file_names() (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog static method) get_opls_dir_setting() (in module schrodinger.application.desmond.feputils) get_optimal_atom_mapping() (in module schrodinger.structutils.rmsd) get_option() (in module schrodinger.application.matsci.jobutils) (schrodinger.utils.cmdline.SingleDashOptionParser method) get_osname() (in module schrodinger.utils.sysinfo) get_other_item() (in module schrodinger.application.matsci.amorphous) get_output_file_name() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_output_logger() (in module schrodinger.utils.log) get_output_logger_handler() (in module schrodinger.utils.log) get_pairwise_sequence_similarity() (in module schrodinger.protein.sequence) get_parallelepiped_vertices() (in module schrodinger.application.matsci.shapes) get_param_signal() (in module schrodinger.models.parameters) get_param_string() (in module schrodinger.application.matsci.textlogger) get_params_from_chorus() (in module schrodinger.application.matsci.nano.xtal) get_params_from_vectors() (in module schrodinger.application.matsci.nano.xtal) get_pargph() (in module schrodinger.application.desmond.report_helper) get_pathway() (in module schrodinger.application.desmond.fepana) get_pbc() (in module schrodinger.structutils.pbc_tools) get_pbc_bonds_dict() (in module schrodinger.application.matsci.nano.xtal) get_pdb() (in module schrodinger.protein.getpdb) get_pdb_id() (in module schrodinger.application.prepwizard) get_penalty() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_periodic_fix_msj_header() (in module schrodinger.application.matsci.desmondutils) get_phase_file_format() (in module schrodinger.infra.phase) get_phase_markers() (in module schrodinger.application.phase.phase_markers) get_pkeywords() (in module schrodinger.application.matsci.espresso.utils) get_polygon_area() (in module schrodinger.application.matsci.shapes) get_potential() (schrodinger.application.desmond.torsion_related.TorsionPotential method) get_ppdb() (in module schrodinger.application.matsci.espresso.ppdb) get_prime_factors() (in module schrodinger.application.desmond.autopartition) get_print_simbox_data() (in module schrodinger.application.desmond.simulation_block_data) get_product_info() (in module schrodinger.application.desmond.util) get_project_name() (in module schrodinger.tasks.jobtasks) get_prop() (in module schrodinger.application.glide.xpdes) (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader method) (schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader method) get_prop_dicts_from_export_data() (in module schrodinger.application.livedesign.ld_utils) get_prop_idx() (in module schrodinger.application.glide.xpdes) get_prop_list() (schrodinger.application.canvas.r_group.Data method) get_prop_value() (schrodinger.application.desmond.simulation_block_data.Array_Prop method) get_prop_values() (schrodinger.application.canvas.r_group.Data method) get_proper_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) get_property_keys_from_keywords() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) get_property_name() (in module schrodinger.structutils.smiles) get_protein() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) get_protein_asl() (in module schrodinger.application.desmond.process_fep_traj) get_protein_label_string() (in module schrodinger.application.desmond.feputils) get_protein_residues_sequence_tags() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData method) get_protein_rmsf() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) get_proteins() (in module schrodinger.application.desmond.feputils) get_pseudo_terms() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) get_pyatom_from_cppatom() (in module schrodinger.structure) get_pymol_cmd() (in module schrodinger.utils.fileutils) get_qcolor() (in module schrodinger.application.desmond.report_helper) get_qe_input() (schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter method) (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method) (schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter method) (schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument method) (schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method) get_qpoints_card() (in module schrodinger.application.matsci.qexsd.qespresso.cards) get_r_group_for_atom() (schrodinger.application.canvas.r_group.Data method) get_r_groups() (schrodinger.application.canvas.r_group.Data method) get_r_groups_per_atom() (schrodinger.application.canvas.r_group.Data method) get_random_csearch_seed() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_random_nonzero_to_one() (in module schrodinger.application.matsci.amorphous) get_random_structure() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_range_specification() (in module schrodinger.application.canvas.driverutils) get_rank() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method) get_rb_potential() (in module schrodinger.application.desmond.torsion_related) get_rb_torsions_potential() (in module schrodinger.application.desmond.torsion_related) get_rdkit_atoms() (in module schrodinger.application.matsci.smartsutils) get_reader() (in module schrodinger.pipeline.pipeutils) get_reagent_sources() (in module schrodinger.analysis.reaction) get_recep_structure_from_grid() (in module schrodinger.application.glide.utils) get_reciprocal_lattice_vectors() (in module schrodinger.application.matsci.nano.xtal) get_reference_ct() (in module schrodinger.application.desmond.struc) get_reference_data() (in module schrodinger.application.matsci.shapes) get_release_name() (in module schrodinger) get_rep_confs() (in module schrodinger.application.macromodel.apps) get_replica_setting() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) get_residue_asl() (in module schrodinger.application.bioluminate.protein) (in module schrodinger.structutils.sitealign) get_residue_label() (in module schrodinger.application.desmond.fep_edge_report_maker) get_residue_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) get_residue_name() (schrodinger.protein.analysis.Report method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) get_residue_sitename() (in module schrodinger.application.desmond.struc) get_residues() (schrodinger.application.desmond.replica_sid_generator.ProteinReport method) get_residues_asl() (in module schrodinger.application.bioluminate.protein) get_residues_by_connectivity() (in module schrodinger.structure) get_residues_for_asl() (in module schrodinger.application.bioluminate.protein_protein_docking_shared) get_residues_unsorted() (in module schrodinger.structure) get_residues_within() (in module schrodinger.application.bioluminate.protein) get_resname() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_rest_density_img() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) get_rest_density_plot() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) get_rest_density_text (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) get_rest_input() (in module schrodinger.application.desmond.rest_inp) get_rest_params() (in module schrodinger.application.desmond.remd) get_rest_region() (in module schrodinger.application.desmond.rest_inp) get_rest_replica() (in module schrodinger.application.desmond.config) get_restart_id_filename() (in module schrodinger.application.matsci.jobutils) get_restart_options() (in module schrodinger.application.matsci.jobutils) get_restrain() (schrodinger.application.desmond.cms.Cms method) get_restrain_angle_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_restrain_atom_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_restrain_dihedral_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_restrain_distance_idxs() (in module schrodinger.application.matsci.reaction_workflow_utils) get_rev_dict() (in module schrodinger.application.matsci.cgforcefield) get_rg_ct() (schrodinger.application.canvas.r_group.Data method) get_rgb_from_color_index() (in module schrodinger.structutils.color) get_rgroup_DEE() (in module schrodinger.application.canvas.r_group) get_rgroup_MCS() (in module schrodinger.application.canvas.r_group) get_rgroup_SMARTS() (in module schrodinger.application.canvas.r_group) get_ring_atom_coords() (in module schrodinger.structutils.assignbondorders) get_rings() (schrodinger.application.canvas.r_group.Data method) get_rings_in_group() (in module schrodinger.structutils.assignbondorders) get_rms_gradient() (in module schrodinger.structutils.minimize) get_rotable_bonds() (in module schrodinger.application.desmond.r_group_asl) get_rotatable_bonds() (in module schrodinger.application.desmond.automatic_analysis_generator) get_rotated_vector() (in module schrodinger.application.matsci.nano.util) get_rotation_matrix() (in module schrodinger.structutils.transform) get_rotation_matrix_from_eulers() (in module schrodinger.structutils.transform) get_rsh_exec() (in module schrodinger.job.remote_command) get_runtime_path() (in module schrodinger.job.jobcontrol) get_salt_bridges() (in module schrodinger.structutils.interactions.salt_bridge) get_sbt_tests() (in module schrodinger.application.desmond.simulation_block_test) get_schrodinger_temp_dir() (in module schrodinger.utils.fileutils) get_script_center_url() (in module schrodinger.utils.config) get_selected_st() (schrodinger.trajectory.prody.ensemble.Ensemble method) get_sequence_file_format() (in module schrodinger.utils.fileutils) get_server_processes() (in module schrodinger.application.licensing.licadmin) get_set() (schrodinger.protein.analysis.Report method) get_shape_object_by_name() (in module schrodinger.application.matsci.shapes) get_shared_file_listing() (in module schrodinger.application.licensing.licadmin) get_shell_runner() (in module schrodinger.application.matsci.espresso.utils) get_shortest_distance() (in module schrodinger.structutils.measure) get_sidebar_dict() (in module schrodinger.application.combiglide.combenumdock) get_sidechain_att_atom() (in module schrodinger.application.desmond.struc) get_sidechain_indices() (schrodinger.protein.analysis.Report.local_residue method) get_sim_time_ns() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_simbox_output_filename() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) get_simple_supercell() (in module schrodinger.application.matsci.nano.xtal) get_simple_supercell_matrix() (in module schrodinger.application.matsci.nano.xtal) get_single_bond_length() (in module schrodinger.structutils.assignbondorders) get_smiles() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method) (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) get_solute_st() (schrodinger.trajectory.prody.ensemble.Ensemble method) get_solvent_cts() (schrodinger.application.desmond.cms.Cms method) get_sorted_atomic_smarts() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) get_source_path() (in module schrodinger.application.matsci.jobutils) get_sources_from_r_labels() (in module schrodinger.structutils.rgroup_enumerate) get_spec_dict() (in module schrodinger.application.combiglide.utils) get_specie_related_values() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_spg_from_spglib() (in module schrodinger.application.matsci.nano.xtal) get_starting_magnetization() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_state_sites() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_static_data_directory() (in module schrodinger.application.ffbuilder.utils) GET_STD_CELL (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) get_std_cell_from_spglib_dataset() (in module schrodinger.application.matsci.nano.xtal) get_stoichiometry_string() (in module schrodinger.application.jaguar.utils) get_stripped_defaults() (in module schrodinger.application.matsci.jobutils) get_struct_from_CIF() (in module schrodinger.application.matsci.nano.xtal) get_structure_data_names() (in module schrodinger.application.livedesign.maestro_data_types) get_structure_entry_IDs() (in module schrodinger.application.livedesign.maestro_data_types) get_structure_file_format() (in module schrodinger.utils.fileutils) get_structure_item() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) get_structure_score() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) get_structure_sequences() (in module schrodinger.protein.sequence) get_structure_with_contiguous_molecules() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) get_subst_from_mapping() (in module schrodinger.application.desmond.fep_mapping) get_subst_score() (schrodinger.application.combiglide.corehop.SubstCoreDatabase method) get_summary() (in module schrodinger.application.bioluminate.propka_parse) get_super_transformation_matrix() (in module schrodinger.structutils.rmsd) get_superposition_idxs() (in module schrodinger.application.matsci.swap_fragments_utils) get_surface_kwargs() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_surfnet_gaps() (in module schrodinger.application.bindingsite.cavutils) get_symmops_from_spglib() (in module schrodinger.application.matsci.nano.xtal) get_system_eamp() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_system_edir() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_system_nspin() (in module schrodinger.application.matsci.qexsd.qespresso.options) get_temp_from_bs_spectrum_file_key() (in module schrodinger.application.matsci.bandshape_utils) get_temp_location() (in module schrodinger.maestro.maestro) get_temperature() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) get_template_vars() (in module schrodinger.application.livedesign.upload_utils) get_tg_props() (in module schrodinger.application.matsci.property_names) get_time() (in module schrodinger.pipeline.stage) get_title() (in module schrodinger.analysis.reaction) get_top_level_props() (in module schrodinger.application.desmond.simulation_block_data) get_torsions_plot() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) get_total_charge() (in module schrodinger.application.jaguar.utils) get_total_proc() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) get_trait() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.SysType method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) get_transformation_matrix() (in module schrodinger.application.matsci.nano.xtal) get_translation_matrix() (in module schrodinger.structutils.transform) get_trj_dir_name() (in module schrodinger.application.matsci.parserutils) get_trj_from_cms_file() (in module schrodinger.application.matsci.order_parameter_mod) get_type() (in module schrodinger.infra.propedit) (schrodinger.application.canvas.r_group.TempAtom method) (schrodinger.application.desmond.enhsamp.Bind method) (schrodinger.application.desmond.enhsamp.FcnCall method) (schrodinger.application.desmond.enhsamp.If method) (schrodinger.application.desmond.enhsamp.Iter method) (schrodinger.application.desmond.enhsamp.Let method) (schrodinger.application.desmond.enhsamp.Lit method) (schrodinger.application.desmond.enhsamp.Node method) (schrodinger.application.desmond.enhsamp.Series method) (schrodinger.application.desmond.enhsamp.String method) (schrodinger.application.desmond.enhsamp.Var method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method) get_type_dict_from_ff_file() (in module schrodinger.application.matsci.cgforcefield) get_type_dict_from_st() (in module schrodinger.application.matsci.coarsegrain) get_type_name() (in module schrodinger.application.matsci.cgforcefield) get_typenames() (schrodinger.utils.multifpfile.MultiFPFile method) get_umbrella_mode_command_line() (in module schrodinger.application.desmond.fep_util) get_uname() (in module schrodinger.utils.sysinfo) get_unique_ligands() (in module schrodinger.application.livedesign.maestro_data_types) get_unique_title() (in module schrodinger.application.combiglide.combenumdock) get_unit_cell_formula() (in module schrodinger.application.matsci.nano.xtal) get_unit_lattice_vector_info() (in module schrodinger.application.matsci.nano.xtal) get_unused_name() (schrodinger.utils.pymol.PymolInstance method) get_update_delay() (in module schrodinger.job.queue) get_userdata_dir() (in module schrodinger.utils.fileutils) get_username() (in module schrodinger.application.livedesign.login) get_val() (in module schrodinger.utils.sea) get_value() (schrodinger.utils.sea.Map method) get_vdw() (schrodinger.application.desmond.cms.Cms method) get_vdw_radius() (schrodinger.protein.analysis.Report method) get_vdw_type_name() (in module schrodinger.application.matsci.cgforcefield) get_vector_atoms_from_internal_coords() (schrodinger.protein.membrane.Membrane_Model method) get_vector_magnitude() (in module schrodinger.structutils.transform) get_vectors_from_chorus() (in module schrodinger.application.matsci.nano.xtal) get_version() (schrodinger.models.json.JsonableClassMixin method) get_vetted_vec_index() (in module schrodinger.application.jaguar.textparser) get_view_atoms() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method) get_voids_data() (in module schrodinger.application.matsci.freevolume) get_volume_data() (in module schrodinger.application.matsci.freevolume) get_volume_from_params() (in module schrodinger.application.matsci.nano.xtal) get_volume_from_vecs() (in module schrodinger.application.matsci.nano.xtal) get_warning_pixmap() (in module schrodinger.application.desmond.feputils) get_water_gids_to_keep() (in module schrodinger.application.desmond.packages.topo) get_word_list_from_file() (in module schrodinger.application.matsci.nano.surfaces_interfaces_mod) get_working_resources() (in module schrodinger.application.licensing.licadmin) get_x() (schrodinger.application.canvas.r_group.TempAtom method) get_xlink_type_atoms() (in module schrodinger.application.matsci.freevolume) get_xy_plot() (in module schrodinger.application.desmond.mplchart) get_xy_plot_widget() (in module schrodinger.application.desmond.mplchart) get_xy_url() (in module schrodinger.application.desmond.gchart) get_y() (schrodinger.application.canvas.r_group.TempAtom method) get_z() (schrodinger.application.canvas.r_group.TempAtom method) getAbsolutePath() (schrodinger.infra.phase.PhpProject method) getAccuracyAndInitialGuessKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getAction() (schrodinger.application.bioluminate.actions.factory.Factory method) getActiveFitnessOpt() (schrodinger.infra.phase.PhpHypoOptimizer method) getActiveFitnessStart() (schrodinger.infra.phase.PhpHypoOptimizer method) getActiveProcCounts() (schrodinger.job.queue.JobDJ method) getActiveRankCsvRows() (schrodinger.analysis.enrichment.Calculator method) getActivities() (schrodinger.infra.phase.PhpQSAR method) getActivity() (schrodinger.infra.phase.PhpProject method) getActivityMissing() (schrodinger.infra.phase.PhpProject method) getAddCtCount() (schrodinger.infra.phase.PhpHypoAdaptor method) getAddCts() (schrodinger.infra.phase.PhpHypoAdaptor method) getAdditionalDataDir() (schrodinger.project.Project method) getAdjustedNJobs() (schrodinger.pipeline.stage.Stage method) getAlignCutoff() (schrodinger.infra.phase.PhpMatchOptions method) getAlignedB() (schrodinger.infra.phase.PhpAlignCore method) getAlignedBlocks() (schrodinger.protein.alignment.BaseAlignment method) getAlignedMobileStructures() (schrodinger.structutils.sitealign.BindingSiteAligner method) getAlignmentScore() (schrodinger.protein.align.PairwiseAligner method) getAlignmentVector() (schrodinger.application.matsci.nano.particle.Nanoparticle method) getAlignPenalty() (schrodinger.infra.phase.PhpMatchOptions method) getAlignWeight() (schrodinger.infra.phase.PhpMatchOptions method) getAllAngles() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllArrayCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAllAtomicBases() (schrodinger.application.jaguar.input.JaguarInput method) getAllAtomPairs() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) getAllExcludes() (schrodinger.infra.phase.PhpFeatureDefinition method) getAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) (schrodinger.infra.phase.PhpFeatureFinder method) getAllHypoIDs() (schrodinger.application.phase.phase_widgets.HypothesisModel method) getAllHypotheses() (schrodinger.application.phase.phase_widgets.HypothesisModel method) getAllIDs() (schrodinger.infra.phase.PhpDatabaseFp method) getAllIncludes() (schrodinger.infra.phase.PhpFeatureDefinition method) getAllMoietyNames() (schrodinger.application.matsci.amorphous.Moieties method) getAllowedRange() (schrodinger.application.glide.glide.GlideJob method) getAllowedRows() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabIGO method) getAllPotentialAtomChargeProperties() (schrodinger.application.matsci.chargegui.ChargePropertySelector static method) getAllPreferences() (schrodinger.utils.preferences.Preferences method) getAllSpaceGroups() (schrodinger.application.matsci.nano.xtal.SpaceGroups method) getAllTorsions() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getAllWorldCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAlpha() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getAlphaCarbon() (schrodinger.structure._Residue method) getAlphaParameter() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getAnalysis() (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) getAncestor() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) getAncestors() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) getAnchorAtoms() (schrodinger.application.desmond.fep_mapping.AtomMappingData method) getAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method) getAngleType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getAnnotation() (schrodinger.protein.sequence.Sequence method) getAntibodyCDR() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAntibodyCDRs() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getAppendConfs() (schrodinger.infra.phase.PhpConfOptions method) getApplicationHeaderFields() (schrodinger.job.jobcontrol.Job method) getApplicationHeaderString() (schrodinger.job.jobcontrol.Job method) getApplyGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getArgs() (schrodinger.infra.phase.PhpOptionsParser method) getArray() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getArrayNx3() (schrodinger.trajectory.prody.mode.VectorBase method) getAsl() (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.structure._Residue method) getASL() (schrodinger.utils.colorscheme.MM_CSchemeRule method) getASLExcludingLigand() (in module schrodinger.application.desmond.automatic_analysis_generator) getASLName() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) getAssayFolderPath() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) getAssociationChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) getAsymmetricUnit() (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) getAtArrayCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtArrayCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtomBondTypingSchemeDescription() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getAtomByPdbName() (schrodinger.structure._Residue method) getAtomClassDescription() (schrodinger.infra.phase.PhpAtomClassDescriptions method) (schrodinger.infra.phase.PhpQSAR method) getAtomClasses() (schrodinger.infra.phase.PhpQSAR method) getAtomColorList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getAtomCount() (schrodinger.application.jaguar.input.JaguarInput method) getAtomEntry() (schrodinger.application.desmond.maestro.NewEntryGroup method) getAtomGroups() (schrodinger.application.desmond.gui.AtomGroupFrame method) getAtomicBasis() (schrodinger.application.jaguar.input.JaguarInput method) getAtomicNonPolarSASAGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getAtomicPolarSASAGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getAtomicSpecies() (schrodinger.application.matsci.espresso.qeinput.StructureType method) getAtomicStructure() (schrodinger.application.matsci.espresso.qeinput.StructureType method) getAtomIndices() (schrodinger.application.matsci.coarsegrain.FusedRing method) (schrodinger.structure.Structure method) (schrodinger.structure._AtomCollection method) getAtomList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.infra.phase.PhpFeaturePattern method) (schrodinger.structure._AtomCollection method) getAtomName() (schrodinger.application.matsci.zmutils.ZAtom method) getAtomNums() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) getAtoms() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) getAtomsAndWeight() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) getAtomsRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getAtomsToTerminate() (schrodinger.application.matsci.nano.sheet.Grow method) getAtomText() (schrodinger.application.matsci.reordergui.ComparisonListWidget method) (schrodinger.application.matsci.reordergui.ReferenceListWidget method) getAtomTotal() (schrodinger.application.jaguar.results.JaguarResults method) getAttachmentPoints() (schrodinger.application.desmond.fep_mapping.AtomMappingData method) getAtWorldCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAtWorldCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) getAvailableMappings() (schrodinger.application.livedesign.ld_export.ExportMapManager method) getAvailableProperties() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) getAverageDistanceFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getAxisExtreme() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) getAxisNum() (schrodinger.application.matsci.sliceplot.SlicePlot method) getBackboneNitrogen() (schrodinger.structure._Residue method) getBackboneOxygen() (schrodinger.structure._Residue method) getBacktrackingLevel() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getBandGap() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) getBaroMethod() (schrodinger.application.desmond.gui.EnsembleTab method) getBaseName() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getBasis() (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesBasisMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.matsci.chargegui.BasisSetSelector method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) getBasisForEid() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) getBasisSetSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getBatches() (schrodinger.application.livedesign.data_classes.ReceptorLigandMap method) (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) getBending() (schrodinger.structutils.minimize.Minimizer method) getBendingEnergy() (schrodinger.structutils.minimize.Minimizer method) getBestDoubleBond() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getBestMatch() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) getBestNumberOfClusters() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getBeta() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getBetaCarbon() (schrodinger.structure._Residue method) getBFGSObject() (schrodinger.application.matsci.mecp_mod.MECP method) getBinarySimilarity() (schrodinger.protein.residue.Residue method) getBindingModes() (schrodinger.infra.phase.PhpProject method) getBond() (schrodinger.structure.Structure method) getBondColorList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondedEnergies() (schrodinger.structutils.minimize.Minimizer method) getBondedEnergyComponents() (schrodinger.structutils.minimize.Minimizer method) getBondedInteractionEnergy() (schrodinger.structutils.minimize.Minimizer method) getBondingInfo() (schrodinger.application.matsci.nano.sheet.Grow method) getBondLength() (schrodinger.application.matsci.amorphous.BaseMoiety method) getBondList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondListWithIgnored() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getBondXYIntersection() (schrodinger.structutils.ringspear.SpearRing method) getBoxVectors() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) getBridgeAtoms() (schrodinger.application.desmond.fep_mapping.AtomMappingData method) getBuildingBlock() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getBuildingBlocks() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getBuriedNode() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getBuriedXYZ() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getButtons() (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getCalculationGUI() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) getCapperTerminator() (schrodinger.application.matsci.amorphous.PolymerToFragments method) getCarbonColorSchemeByRGB() (schrodinger.utils.colorscheme.ColorSchemeManager method) getCarbonylCarbon() (schrodinger.structure._Residue method) getCartesianCoords() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getCascadeGenerations() (schrodinger.application.matsci.amorphous.Moieties method) getCbmVbm() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getCell() (schrodinger.application.desmond.packages.msys.System method) getCenterOrientationOfAtoms() (schrodinger.protein.membrane.Membrane_Model method) getCentroid() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.infra.phase.PhpDeNovoPharm method) getCentroidHypo() (schrodinger.infra.phase.PhpDeNovoPharm method) getCfgParams() (schrodinger.application.desmond.packages.energygroup.Bulk method) getChain() (schrodinger.structure._StructureAtom method) getChainAtoms() (schrodinger.structure.Structure method) getChannel() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) getCharErrorDisplay() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) getCharge() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) getChargeConstraintSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getCharIndex() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) getCharPositionInLine() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) getCheckedColumns() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) getCheckedData() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) getCheckedRowNumbers() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) getChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getChildCount() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getChildIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getChildItems() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) getChildren() (schrodinger.application.desmond.antlr3.tree.BaseTree method) getChiralAngle() (schrodinger.application.matsci.nano.tube.NanoTube method) getChoiceSpectrum() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing static method) getChorusPBC() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) (schrodinger.application.matsci.nano.tube.NanoTube method) getCircumRadius() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Tetrahedron method) getClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) getClashPenalty() (schrodinger.application.matsci.montecarlo.Metropolizer method) getClassFraction() (schrodinger.infra.phase.PhpQSAR method) getClassKwargsPropertySubOption() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property static method) getCleanupRequested() (schrodinger.pipeline.stage.Stage method) getClosest() (schrodinger.application.bioluminate.protein.Consensus method) getClosestApproach() (schrodinger.application.matsci.montecarlo.Metropolizer method) getClusterCenters() (schrodinger.analysis.cluster.ClusterValues method) getClusterContents() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterCutPoints() (schrodinger.infra.phase.PhpHiCluster method) getClusteredValues() (schrodinger.analysis.cluster.ClusterValues method) getClusterGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getClusteringMap() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusteringStatistics() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getClusterMemberships() (schrodinger.analysis.cluster.ClusterValues method) getClusterOrderMap() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusters() (schrodinger.infra.phase.PhpHiCluster method) getClusterSizes() (schrodinger.infra.phase.PhpHiCluster method) getClustersMerged() (schrodinger.infra.phase.PhpHiCluster method) getClusterStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getClusterTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getClusterVariance() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getCnst() (schrodinger.infra.phase.PhpHypoAdaptor method) getCode() (schrodinger.structure._Residue method) getCollectionFilename() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) getColor() (schrodinger.utils.colorscheme.MM_CSchemeRule method) getColorIndices() (schrodinger.utils.colorscheme.MM_ColorRamp method) (schrodinger.utils.colorscheme.MM_ColorRampHolder method) getColorName() (schrodinger.utils.colorscheme.MM_CSchemeRule method) getColorSchemeName() (schrodinger.utils.colorscheme.ColorSchemeManager method) getColorsForPatchVertices() (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) getColumn() (schrodinger.protein.alignment.BaseAlignment method) getColumnIndex() (schrodinger.infra.table.Table method) getColumnNames() (schrodinger.infra.table.Table method) getColumnTotal() (schrodinger.infra.table.Table method) getCommand() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.queue.JobControlJob method) getCommandArgs() (schrodinger.job.launcher.Launcher method) getCommandDir() (schrodinger.job.queue.BaseJob method) getCommandLineArgs() (schrodinger.application.matsci.mswidgets.SaveDesmondFilesWidget method) getCommandLineFlag() (schrodinger.application.matsci.mswidgets.RandomSeedWidget method) getCommandTemplate() (schrodinger.job.launchapi.TaskSpecification method) getCommonBasis() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getCommonCount() (schrodinger.infra.phase.PhpDatabaseFp static method) getCompleteBondList() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConfCount() (schrodinger.infra.phase.PhpScreener method) getConfigDialog() (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) getConfOptions() (schrodinger.infra.phase.PhpScreener method) getConformationHandle() (schrodinger.infra.phase.PhpMMconfAdaptor method) getConformer() (schrodinger.infra.phase.PhpProject method) getConformerCount() (schrodinger.infra.phase.PhpProject method) getConformers() (schrodinger.infra.phase.PhpProject method) getConnectionColor() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionFile() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionMaxLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionMinLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionName() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConnectionSize() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getConservation() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.Sequence method) getConstraint() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.infra.phase.PhpSiteConstrainer method) getConstraints() (schrodinger.infra.phase.PhpSiteConstrainer method) getConstraintValue() (schrodinger.infra.phase.PhpSiteConstrainer method) getConvergenceCriteriaKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getConvergenceKeywords() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) getConvergenceMethodsKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getCoordinates() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) (schrodinger.infra.phase.PhpSite method) getCoordName() (schrodinger.application.matsci.zmutils.ZAtom method) getCoords() (schrodinger.application.matsci.espresso.qeoutput.KPoint method) (schrodinger.trajectory.prody.ensemble.Ensemble method) getCoordsStr() (schrodinger.application.matsci.espresso.qeoutput.KPoint method) getCore() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) getCoreAtoms() (schrodinger.application.desmond.fep_mapping.AtomMappingData method) getCoreCBChanged() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) getCoreRmsd() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) getCount() (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) getCouplerAndGrower() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getCouplerElement() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getCovariance() (schrodinger.trajectory.prody.nma.NMA method) getCrystalSystem() (schrodinger.application.matsci.nano.xtal.CrystalSystems method) getCsvRows() (schrodinger.analysis.enrichment.Calculator method) getCt() (schrodinger.infra.phase.PhpDatabaseFp method) (schrodinger.infra.phase.PhpStructureBus method) getCtCopy() (schrodinger.infra.phase.PhpStructureBus method) getCts() (schrodinger.infra.phase.PhpDatabaseFp method) getCtTitle() (in module schrodinger.infra.phase) getCtVector() (schrodinger.infra.phase.PhpStructureBus method) getCtVectorCopy() (schrodinger.infra.phase.PhpStructureBus method) getCumulativeMatches() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) getCurrentAtomBondTyping() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getCurrentButton() (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getCurrentColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) getCurrentColorSchemeName() (schrodinger.utils.colorscheme.ColorSchemeManager method) getCurrentInputSymbol() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getCurrentJobDir() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) getCurrentLinkage() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getCurrentSchemeDescription() (schrodinger.utils.colorscheme.ColorSchemeManager method) getCurrentSetting() (schrodinger.application.matsci.qualityslider.QualitySlider method) getCurrentSymbol() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) getCurrentType() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getCustom() (schrodinger.application.desmond.packages.staf.GeomCalc method) getData() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile static method) (schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType method) getDatabaseData() (schrodinger.application.matsci.cgforcefield.ForceField method) getDataColumn() (schrodinger.infra.phase.PhpFeatureData method) getDataModelClass() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) getDataRow() (schrodinger.infra.phase.PhpFeatureData method) getDataValue() (schrodinger.infra.phase.PhpFeatureData method) getDbCount() (schrodinger.infra.phase.PhpSubsetSplitter method) getDbID() (schrodinger.infra.phase.PhpProject method) getDbPaths() (schrodinger.infra.phase.PhpSubsetSplitter method) getDebugLevel() (schrodinger.job.launchparams.LaunchParameters method) getDebugListener() (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) getDecoyFitnessOpt() (schrodinger.infra.phase.PhpHypoOptimizer method) getDecoyFitnessStart() (schrodinger.infra.phase.PhpHypoOptimizer method) getDefault() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getDefaultAtomTypingScheme() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getDefaultCustomTemplateDir() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getDefaultFdFile() (schrodinger.infra.phase.PhpProject method) getDefaultFdFileBaseName() (in module schrodinger.infra.phase) getDefaultFdFilePath() (in module schrodinger.infra.phase) getDefaultFeatureDef() (schrodinger.infra.phase.PhpProject method) getDefaultFeatureEquiv() (schrodinger.infra.phase.PhpProject method) getDefaultFeatureFreq() (schrodinger.infra.phase.PhpProject method) getDefaultFeatureRadii() (schrodinger.infra.phase.PhpProject method) getDefaultFeatureTol() (schrodinger.infra.phase.PhpProject method) getDefaultKeywords() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) getDefaultMap() (schrodinger.utils.colorscheme.MM_ColormapGL static method) getDefaultSiteMasks() (schrodinger.infra.phase.PhpProject method) getDefaultSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getDefaultStderr() (schrodinger.job.launchapi.JobSpecification method) getDefaultStdout() (schrodinger.job.launchapi.JobSpecification method) getDefinition() (schrodinger.ui.ligfilter.AddDefinitionDialog method) getDelNextResnumByAtomID() (schrodinger.application.matsci.amorphous.PolymerToFragments method) getDelNextResnumByResnum() (schrodinger.application.matsci.amorphous.PolymerToFragments method) getDeltaDist() (schrodinger.infra.phase.PhpMatchOptions method) getDeltaXYZ() (schrodinger.infra.phase.PhpDeltaHypo method) getDendrogramData() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getDensities() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getDescription() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.application.desmond.antlr3.dfa.DFA method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.utils.colorscheme.MM_CScheme method) (schrodinger.utils.colorscheme.MM_CSchemeRule method) getDescriptor() (schrodinger.application.matsci.order_parameter_mod.Descriptor method) getDesiredVolume() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getDesolvationPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method)

getDeviations() (schrodinger.trajectory.prody.ensemble.Ensemble method) getDihedralAtoms() (schrodinger.structure._Residue method) getDihedralType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getDiheValues() (schrodinger.application.matsci.amorphous.PolymerFragment method) getDirective() (schrodinger.application.jaguar.input.JaguarInput method) getDirectives() (schrodinger.application.jaguar.input.JaguarInput method) getDirector() (schrodinger.application.matsci.order_parameter_mod.OrderParameter static method) getDiscontinuousSubalignment() (schrodinger.protein.alignment.BaseAlignment method) getDisplayName() (schrodinger.infra.phase.PhpSite method) getDissociationChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) getDistance() (schrodinger.application.desmond.packages.staf.GeomCalc method) getDistanceCellDistance() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) getDistanceMatrixFile() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getDistanceToCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getDmatrix() (schrodinger.application.matsci.rxn_path.InternalCoords method) getDOS() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getDoubleDisplacementChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) getDuration() (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.job.jobcontrol.Job method) getEdgeLength() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Tetrahedron method) getEdges() (schrodinger.application.matsci.shapes.Face method) getEditStatus() (schrodinger.infra.phase.PhpFeaturePattern method) getEids() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) getEigval() (schrodinger.trajectory.prody.mode.Mode method) getEigvals() (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getEigvec() (schrodinger.trajectory.prody.mode.Mode method) getEigvecs() (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getEleEnergy() (schrodinger.structutils.minimize.Minimizer method) getElement() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getEnableOptimization() (schrodinger.infra.phase.PhpMMconfAdaptor method) getEncoded() (schrodinger.application.desmond.restraint.RestraintBuilder method) getEndpointForCurrentAssay() (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) getEnergy() (schrodinger.application.matsci.montecarlo.Metropolizer method) (schrodinger.application.prime.residue_interaction.InteractionReader method) (schrodinger.structutils.minimize.Minimizer method) getEnergyAndGradients() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) getEnergyAndGradientsObject() (schrodinger.application.matsci.mecp_mod.MECP method) getEnergyConvergencePlot() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getEnergyProp() (schrodinger.infra.phase.PhpProject method) getEnergyWindow() (schrodinger.infra.phase.PhpConfOptions method) getEntries() (schrodinger.analysis.transformations.TransformsRepository method) getEntropy() (schrodinger.protein.alignment.BaseAlignment method) getErrMesg() (schrodinger.infra.phase.PhpComplex method) getErrorHandler() (schrodinger.structure.FormatReader method) (schrodinger.structure.MaestroReader method) (schrodinger.structure.Mol2Reader method) (schrodinger.structure.PDBReader method) (schrodinger.structure.SDReader method) getErrorHeader() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getErrorMessage() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getEwaldRealSpaceFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getExcitedState() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) getExcludedAtomList() (schrodinger.structutils.minimize.Minimizer method) getExcludedVolume() (schrodinger.application.matsci.amorphous.Scaffold method) getExcludePattern() (schrodinger.infra.phase.PhpFeatureDefinition method) getExhaustiveMatching() (schrodinger.infra.phase.PhpMatchOptions method) getExportData() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) getExportDataNoData() (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) getExportGlobal() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) getExtendDistance() (schrodinger.infra.phase.PhpFeatureDefinition method) (schrodinger.infra.phase.PhpFeaturePattern method) getExtentsAndStrainedLength() (schrodinger.application.matsci.nano.interface_mod.Interface method) getExtracyclicAtom() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getFaces() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) getFcnSigs() (in module schrodinger.application.desmond.enhanced_sampling.FcnTypes) (in module schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) getFd() (schrodinger.infra.phase.PhpHypoAdaptor method) getFdFile() (schrodinger.infra.phase.PhpProject method) getFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeatureCheckbox() (schrodinger.application.phase.featureselector.FeatureSelector method) getFeatureClassDescription() (schrodinger.infra.phase.PhpFeatureClassDescriptions method) getFeatureComment() (schrodinger.infra.phase.PhpFeatureDefinition method) getFeatureDef() (schrodinger.infra.phase.PhpProject method) getFeatureDefFromProj() (schrodinger.infra.phase.PhpProject method) getFeatureEquiv() (schrodinger.infra.phase.PhpProject method) getFeatureFreq() (schrodinger.infra.phase.PhpProject method) getFeatureFromId() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeatureName() (schrodinger.infra.licensing.License static method) (schrodinger.infra.phase.PhpFeatureDefinition method) getFeatureNames() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getFeatureNumber() (schrodinger.infra.phase.PhpFeatureDefinition method) getFeatureRadii() (schrodinger.infra.phase.PhpProject method) getFeatureTol() (schrodinger.infra.phase.PhpProject method) getFeatureType() (schrodinger.infra.phase.PhpFeatureDefinition method) getFEPTorsionKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getFFIOParam() (schrodinger.application.matsci.cgforcefield.ForceField method) getFHistogram() (schrodinger.application.desmond.replica_dE.replica_energy method) getFileCountIn() (schrodinger.infra.phase.PhpStructureSplitter method) getFileCountOut() (schrodinger.infra.phase.PhpStructureSplitter method) getFileFormat() (schrodinger.infra.phase.PhpStructureSplitter method) getFilename() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) getFileName() (schrodinger.application.matsci.order_parameter_mod.Descriptor method) (schrodinger.utils.colorscheme.MM_CScheme method) (schrodinger.utils.colorscheme.MM_ColorRamp method) getFileNames() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getFileNamesIn() (schrodinger.infra.phase.PhpStructureSplitter method) getFileNamesOut() (schrodinger.infra.phase.PhpStructureSplitter method) getFiles() (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) (schrodinger.structure.MultiFileStructureWriter method) getFilterText() (schrodinger.ui.ligfilter.LigfilterFrame method) getFinalForcesHartreePerAngstrom() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFinalStructure() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFinalTotalEnergy() (schrodinger.application.matsci.mecp_mod.JaguarJob method) getFingerprintDescription() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getFingerprintString() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getFirstChildWithType() (schrodinger.application.desmond.antlr3.tree.BaseTree method) getFirstSelectedRow() (schrodinger.infra.table.Table method) getFixedColumnsCount() (schrodinger.project.Project method) getFlags() (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.infra.phase.PhpOptionsParser method) getFMax() (schrodinger.application.desmond.replica_dE.replica_energy method) getFMean() (schrodinger.application.desmond.replica_dE.replica_energy method) getFMin() (schrodinger.application.desmond.replica_dE.replica_energy method) getForceField() (schrodinger.infra.phase.PhpConfOptions method) (schrodinger.infra.phase.PhpMMconfAdaptor method) getForceFieldCommonName() (schrodinger.infra.phase.PhpConfOptions static method) getForceFieldDisplayName() (schrodinger.infra.phase.PhpConfOptions static method) getFormattedSummaryLine() (schrodinger.application.matsci.mecp_mod.MECPStep method) getFp() (schrodinger.infra.phase.PhpDatabaseFp method) getFpOptions() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS static method) getFps() (schrodinger.infra.phase.PhpDatabaseFp method) getFpTypesStored() (schrodinger.infra.phase.PhpDatabaseFp method) getFragAtomID() (in module schrodinger.infra.phase) getFragAtoms() (in module schrodinger.infra.phase) getFragCentroid() (schrodinger.application.matsci.amorphous.PolymerToFragments method) getFragType() (schrodinger.infra.phase.PhpSite method) getFrequencies() (schrodinger.protein.alignment.BaseAlignment method) getFunctional() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) getFusedRingNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) getFusedRings() (schrodinger.application.matsci.coarsegrain.FusedRing static method) getGap() (schrodinger.application.matsci.espresso.qeoutput.DOS method) getGapCount() (schrodinger.protein.sequence.Sequence method) getGapIndicesByKeyFunc() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) getGaplessLength() (schrodinger.protein.sequence.ProteinSequence method) getGapOnlyColumns() (schrodinger.protein.alignment.BaseAlignment method) getGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) getGapsByKeyFunc() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) getGeometry() (schrodinger.infra.phase.PhpFeaturePattern method) getGlobalAnnotationData() (schrodinger.protein.alignment.BaseAlignment method) getGoodFFTDim() (schrodinger.application.matsci.espresso.utils.MemoryEstimator method) getGrammarFileName() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getGravityEnergy() (schrodinger.application.matsci.montecarlo.Metropolizer method) getGroup() (schrodinger.infra.phase.PhpProject method) (schrodinger.utils.preferences.Preferences method) getGroupCount() (schrodinger.infra.phase.PhpProject method) getGroupNumber() (schrodinger.infra.phase.PhpSiteMaskGroup method) getGroupTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getGrowParams() (schrodinger.application.matsci.nano.tube.NanoSheet method) getGrowVectors() (schrodinger.application.matsci.nano.sheet.Grow method) getGuessGeometry() (schrodinger.application.matsci.mecp_mod.MECP method) getGUI() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) getHamiltonian() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) getHeader() (schrodinger.application.canvas.utils.ChmCSVTools method) getHiddenSeqCount() (schrodinger.protein.alignment.BaseAlignment method) getHKLIndices() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getHost() (schrodinger.job.jobcontrol.Host method) (schrodinger.job.launchapi.JobSpecification method) getHostList() (schrodinger.pipeline.stage.Stage method) getHostname() (schrodinger.job.launchparams.LaunchParameters method) getHosts() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) getHostStr() (schrodinger.job.app.App method) (schrodinger.pipeline.stage.Stage method) getHostType() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) getHotAtoms() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) getHSliderMax() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getHSliderMin() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getHydropathyGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getHypo() (schrodinger.infra.phase.PhpProject method) getHypoAlignments() (schrodinger.infra.phase.PhpProject method) getHypoCt() (schrodinger.infra.phase.PhpHypoAdaptor method) getHypoDrift() (schrodinger.infra.phase.PhpHypoOptimizer method) getHypoFmt() (schrodinger.infra.phase.PhpProject method) getHypoID() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.infra.phase.PhpHypoAdaptor method) getHypoIDs() (schrodinger.infra.phase.PhpProject method) getHypoMatches() (schrodinger.infra.phase.PhpProject method) getHypoOpt() (schrodinger.infra.phase.PhpHypoOptimizer method) getHypoScores() (schrodinger.infra.phase.PhpProject method) getHypoSites() (schrodinger.infra.phase.PhpHypoAdaptor method) (schrodinger.infra.phase.PhpProject method) getHypoSitesStrings() (schrodinger.infra.phase.PhpProject method) getHypotheses() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) getIdentities() (schrodinger.protein.alignment.BaseAlignment method) getIdentity() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.Sequence method) getIdStr() (schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo method) getIdxs() (schrodinger.application.matsci.coarsegrain.Internals method) getIgnoredSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getImportantRotatableBonds() (in module schrodinger.application.desmond.r_group_asl) getImpTorsion() (schrodinger.structutils.minimize.Minimizer method) getImpTorsionEnergy() (schrodinger.structutils.minimize.Minimizer method) getInactiveAlignments() (schrodinger.infra.phase.PhpProject method) getIncludedVolumeCutoff() (schrodinger.infra.phase.PhpMatchOptions method) getIncludedVolumeWeight() (schrodinger.infra.phase.PhpMatchOptions method) getIncludePattern() (schrodinger.infra.phase.PhpFeatureDefinition method) getIndex() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.utils.colorscheme.MM_Colormap method) getIndices() (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.graphics3d.polyhedron.MaestroCube method) (schrodinger.graphics3d.polyhedron.MaestroDodecahedron method) (schrodinger.graphics3d.polyhedron.MaestroIcosahedron method) (schrodinger.graphics3d.polyhedron.MaestroOctahedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) (schrodinger.graphics3d.polyhedron.MaestroTetrahedron method) (schrodinger.trajectory.prody.modeset.ModeSet method) getInFileType() (schrodinger.infra.phase.PhpProject method) getInfraStructure() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) getIniFragPosition() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getInitialGuess() (schrodinger.application.matsci.rxn_path.ReactionPath method) getInitialInvHessian() (schrodinger.application.matsci.mecp_mod.BFGS method) getInitiatorSubBackbone() (schrodinger.application.matsci.amorphous.PolymerToFragments method) getInPlaceRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getInput() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.pipeline.stage.Stage method) getInputFiles() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.launchapi.JobSpecification method) getInputKeys() (schrodinger.job.launchapi.TaskSpecification method) getInputNames() (schrodinger.pipeline.stage.Stage method) getInputStream() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) getInputText() (schrodinger.application.jaguar.input.JaguarInput method) getInTemplate() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getInteractionEnergy() (schrodinger.structutils.minimize.Minimizer method) getInteractionEnergyGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getInteractionMatrix() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getInteractionPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getInterface() (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) getInterfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) getInternalEnergyGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getInterPlanarSeparation() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getInterpolatedStructure() (schrodinger.application.matsci.rxn_path.ReactionPath method) getIrcStep() (schrodinger.application.jaguar.output.JaguarOutput method) getIsFarthestFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getIsNearestToCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getIvol() (schrodinger.infra.phase.PhpHypoAdaptor method) getJaguarNonDefault() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getJaguarRestartFileName() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) getJaguarValue() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getJob() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.job.queue.JobControlJob method) getJobCount() (schrodinger.application.matsci.guibase.MultiDesmondJobApp method) (schrodinger.application.matsci.guibase.MultiJobApp method) getJobDJ() (schrodinger.job.queue.BaseJob method) (schrodinger.pipeline.stage.Stage method) getJobName() (schrodinger.job.app.App method) getJobname() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchparams.LaunchParameters method) getJobnameSource() (schrodinger.job.launchapi.TaskSpecification method) getJobSpec() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.JobSpecificationBuilder method) getJson() (schrodinger.application.desmond.restraint.RestraintBuilder method) getKelleyPenaltyList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getkey() (schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method) getKeyData() (schrodinger.application.matsci.cgforcefield.ForceField method) getKeystring() (schrodinger.application.matsci.mswidgets.CompactSolventSelector method) getKeyType() (schrodinger.utils.preferences.Preferences method) getKeywordDict() (schrodinger.application.matsci.qualityslider.KeywordEdit method) (schrodinger.application.matsci.qualityslider.QualitySlider method) getKeywords() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) getKeywordString() (schrodinger.application.matsci.qualityslider.KeywordEdit method) (schrodinger.application.matsci.qualityslider.QualitySlider method) getKindOfOps() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) getKptFromCfg() (schrodinger.application.matsci.espresso.qeoutput.KPoint static method) getKwargs() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property static method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) getLargestSpan() (schrodinger.application.matsci.amorphous.Box method) getLargestVoid() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) getLastCustomFeatureNum() (schrodinger.application.phase.featureselector.FeatureModel method) getLastRewriteTokenIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) getLatticeParameters() (schrodinger.application.matsci.nano.xtal.Crystal method) getLatticeProperties() (schrodinger.application.matsci.nano.slab.Surface method) getLatticeVectors() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) getLaunchCommand() (schrodinger.application.macromodel.utils.ComUtil method) getLaunchDirectory() (schrodinger.job.launchparams.LaunchParameters method) getLaunchSubDir() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) getLDInputType() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) getLength() (schrodinger.application.matsci.shapes.Edge method) getLicenseFileList() (in module schrodinger.application.licensing.licadmin) getLicenses() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) getLigand() (in module schrodinger.application.desmond.automatic_analysis_generator) (schrodinger.infra.phase.PhpProject method) (schrodinger.infra.phase.PhpStructureBus method) getLigandColorSchemeByRGB() (schrodinger.utils.colorscheme.ColorSchemeManager method) getLigandCopy() (schrodinger.infra.phase.PhpStructureBus method) getLigandCount() (schrodinger.infra.phase.PhpProject method) getLigandFragments() (schrodinger.application.desmond.replica_sid_generator.SmallMoleculeReport method) getLigandHypo() (schrodinger.infra.phase.PhpDeNovoPharm method) getLigandID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getLigandIDs() (schrodinger.infra.phase.PhpProject method) getLigandImage() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getLigandPropsKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getLigandTitle() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getLimits() (schrodinger.infra.phase.PhpComplex method) getLinDepPlaneVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getLine() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) getline() (schrodinger.infra.mmgpgpu.istream method) (schrodinger.infra.mmjob.istream method) (schrodinger.infra.mmsurf.istream method) getLine() (schrodinger.infra.phase.PhpTextFileReader method) getline() (schrodinger.utils.colorscheme.istream method) getLinkageDescription() (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method) getLinkageGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getListOfBondedAtoms() (in module schrodinger.infra.phase) getLJEnergy() (schrodinger.structutils.minimize.Minimizer method) getLocal() (schrodinger.pipeline.stage.Stage method) GetLogger (class in schrodinger.application.matsci.textlogger) GetLogger.MyFormatter (class in schrodinger.application.matsci.textlogger) getlogin() (in module schrodinger.application.desmond.util) getLongLine() (in module schrodinger.infra.phase) getLongName() (schrodinger.utils.colorscheme.MM_ColorRamp method) (schrodinger.utils.colorscheme.MM_CScheme method) getLoopMutation() (schrodinger.application.bioluminate.protein.Mutator method) getLRDependentColumns() (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) getLRName() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) getMaefilename() (schrodinger.application.jaguar.input.JaguarInput method) getMaestroProjectDisposition() (schrodinger.job.launchparams.LaunchParameters method) getMaestroProjectDispositionString() (schrodinger.job.launchparams.LaunchParameters method) getMaestroProjectName() (schrodinger.job.launchparams.LaunchParameters method) getMaestroViewname() (schrodinger.job.launchparams.LaunchParameters method) getMaeStructure() (schrodinger.application.matsci.jaguarworkflows.Results method) getMag() (schrodinger.application.matsci.espresso.qeinput.MagSpecies method) getMapFilePath() (schrodinger.application.livedesign.ld_export.ExportMapManager method) getMappableRows() (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) getMappings() (schrodinger.infra.phase.PhpAlignCore method) getMask() (schrodinger.infra.phase.PhpHypoAdaptor method) getMaskValue() (schrodinger.infra.phase.PhpSite method) (schrodinger.infra.phase.PhpSiteMaskData method) getMatchCount() (schrodinger.infra.phase.PhpScreener method) getMatchedSites() (schrodinger.infra.phase.PhpProject method) getMatchedSitesStrings() (schrodinger.infra.phase.PhpProject method) getMatches() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) (schrodinger.application.ligprep.ionizer.Spec method) (schrodinger.protein.pdbname.Substructure method) getMatchingAtomMap() (schrodinger.structutils.sitealign.SiteMatchLookup method) getMatchLimits() (schrodinger.infra.phase.PhpSiteMask static method) getMatchOptions() (schrodinger.infra.phase.PhpScreener method) getMatrixTime() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMaxConfs() (schrodinger.infra.phase.PhpConfOptions method) getMaxDistanceFromCentroid() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMaxReport() (schrodinger.infra.phase.PhpMatchOptions method) getMaxRes() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getMaxRetries() (schrodinger.pipeline.stage.Stage method) getMaxSimDecoyByActiveId() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) getMaxSize() (schrodinger.infra.phase.PhpSortCapperDoubleDecreasing method) (schrodinger.infra.phase.PhpSortCapperDoubleIncreasing method) getMCSMatches() (in module schrodinger.application.canvas.r_group) getMDStepStruct() (schrodinger.application.matsci.espresso.qeoutput.Output method) getMeanMaxActiveActiveSim() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) getMeanMaxActiveDecoySim() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) getMeanMaxDecoyDecoySim() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) getMeanSimDecoyByActiveId() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) getMenu() (schrodinger.application.bioluminate.actions.factory.Factory method) getMenuBar() (schrodinger.application.bioluminate.actions.factory.Factory method) getMergeDistanceList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getMessage() (schrodinger.application.desmond.antlr3.tree.RewriteCardinalityException method) getMethod() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) getMetric() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getMetricStyle() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) getMExpr() (schrodinger.application.desmond.meta.CV method) (schrodinger.application.desmond.meta.CVAngle method) (schrodinger.application.desmond.meta.CVDihedral method) (schrodinger.application.desmond.meta.CVDist method) (schrodinger.application.desmond.meta.CVrgyr method) (schrodinger.application.desmond.meta.CVrgyr_mass method) (schrodinger.application.desmond.meta.CVrmsd method) (schrodinger.application.desmond.meta.CVrmsd_symm method) (schrodinger.application.desmond.meta.CVwhim method) (schrodinger.application.desmond.meta.CVzdist method) (schrodinger.application.desmond.meta.CVzdist0 method) getMinMatch() (schrodinger.infra.phase.PhpSiteMaskGroup method) getMinMax() (schrodinger.application.matsci.amorphous.Box method) getMinRes() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getMinSimDecoyByActiveId() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) getMinSites() (schrodinger.infra.phase.PhpMatchOptions method) getMissingSymbol() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getMissingType() (schrodinger.application.desmond.antlr3.exceptions.MissingTokenException method) getMmJagKeywords() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MullikenSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MultipoleSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.RamanSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabIGO method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) getMobileStRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getModel() (schrodinger.application.matsci.guibase.MultiDesmondJobApp method) (schrodinger.infra.phase.PhpQSAR method) (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getModelType() (schrodinger.infra.phase.PhpQSAR method) getMoiety() (schrodinger.application.matsci.amorphous.Moieties method) getMolecularFormula() (schrodinger.application.matsci.builderwidgets.ItemRow method) getMolecule() (schrodinger.structure._StructureAtom method) getMoleculeAtoms() (schrodinger.structure.Structure method) getMolecules() (schrodinger.infra.phase.PhpQSAR method) getMoleculeType() (schrodinger.infra.phase.PhpQSAR method) getMolModel() (schrodinger.infra.phase.PhpQSAR method) getMolSites() (schrodinger.infra.phase.PhpProject method) getMolSitesAtoms() (schrodinger.infra.phase.PhpProject method) getMolSitesStrings() (schrodinger.infra.phase.PhpProject method) getMonomer() (schrodinger.application.matsci.amorphous.Moieties method) getMovingAtoms() (schrodinger.structure.Structure method) getMustMatch() (schrodinger.infra.phase.PhpProject method) getMutationFromChanges() (schrodinger.application.bioluminate.protein.Mutator method) getMutations() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) getName() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.pipeline.stage.Stage method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.utils.colorscheme.MM_Color method) (schrodinger.utils.colorscheme.MM_Colormap method) getNames() (schrodinger.application.matsci.coarsegrain.Internals method) getNanoSheet() (schrodinger.application.matsci.nano.tube.NanoSheet method) getNatomsInTerm() (schrodinger.application.desmond.packages.restrain.Restraints static method) getNB14Pairs() (schrodinger.structutils.minimize.Minimizer method) getNBEnergyComponents() (schrodinger.structutils.minimize.Minimizer method) getNBEnergyForTwoAtomLists() (schrodinger.structutils.minimize.Minimizer method) getNCpus() (schrodinger.pipeline.stage.Stage method) getNeedRebuildColorSchemes() (schrodinger.utils.colorscheme.ColorSchemeManager method) getNeighborCoordVal() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) getNeighboringRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNeighborPBCBond() (schrodinger.application.matsci.nano.xtal.PBCBond method) getNeighbors() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNeighborsObj() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNeighborTypes() (schrodinger.application.matsci.nano.sheet.Grow method) getNewAngles() (schrodinger.application.matsci.coarsegrain.Internals method) getNewAssay() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) getNewCell() (schrodinger.application.matsci.amorphous.Scaffold method) getNewCellStructure() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getNewDihedrals() (schrodinger.application.matsci.coarsegrain.Internals method) getNewImpropers() (schrodinger.application.matsci.coarsegrain.Internals method) getNewResidueName() (schrodinger.application.matsci.amorphous.Monomer method) getNewSolution() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) getNextConfig() (schrodinger.tasks.runners.JobTaskRunner method) getNextEntryId() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) getNextResidue() (schrodinger.protein.sequence.Sequence method) getNextResidueIndex() (schrodinger.protein.sequence.Sequence method) getNextResidueIndices() (schrodinger.protein.sequence.Sequence method) getNextStructure() (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getNJobs() (schrodinger.pipeline.stage.Stage method) getNKpts() (schrodinger.application.matsci.espresso.qeinput.KpointsType method) getNodeIndex() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) getNodeXYZ() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) (schrodinger.application.matsci.freevolume.VoidInfo method) getNonBondedEnergies() (schrodinger.structutils.minimize.Minimizer method) getNonBondType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getNonDefault() (schrodinger.application.jaguar.input.JaguarInput method) getNonDefaultJaguarKeys() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getNonDefaultKeys() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getNonPeriodicPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getNonQCount() (in module schrodinger.infra.phase) getNormal() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getNormalOrdering() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getNormalsAndRadius() (schrodinger.structutils.ringspear.SpearRing method) getNormed() (schrodinger.trajectory.prody.mode.Vector method) getNSpin() (schrodinger.application.matsci.espresso.qeinput.SpinType method) getNumber() (schrodinger.application.desmond.replica_dE.replica_energy method) getNumberOfClustersList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getNumberOfColorSchemes() (schrodinger.utils.colorscheme.ColorSchemeManager method) getNumberOfProcessorsManyNodes() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfProcessorsOneNode() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfQueueSlots() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfSubColorSchemes() (schrodinger.utils.colorscheme.ColorSchemeManager method) getNumberOfSubjobs() (schrodinger.job.launchparams.LaunchParameters method) getNumberOfSyntaxErrors() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getNumberOfType() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) getNumBondOrders() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNumClashes() (schrodinger.application.matsci.montecarlo.Metropolizer method) getNumColors() (schrodinger.utils.colorscheme.MM_ColorRamp method) (schrodinger.utils.colorscheme.MM_ColorRampHolder method) getNumExcludes() (schrodinger.infra.phase.PhpFeatureDefinition method) getNumIncludes() (schrodinger.infra.phase.PhpFeatureDefinition method) getNumMappings() (schrodinger.infra.phase.PhpAlignCore method) getNumMarkers() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) getNumNeighbors() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getNumPlanes() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getNumRamps() (schrodinger.utils.colorscheme.MM_ColorRampHolder method) getNumResidues() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) (schrodinger.protein.sequence.Sequence method) getNumStructures() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.InputTabJobMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.structure.MultiFileStructureWriter method) getNumUnitCells() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getNumUsedCoordSites() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) getObject() (schrodinger.application.matsci.cgforcefield.FFIOAngle method) (schrodinger.application.matsci.cgforcefield.FFIOBond method) (schrodinger.application.matsci.cgforcefield.FFIODihedral method) (schrodinger.application.matsci.cgforcefield.FFIOExclusion method) (schrodinger.application.matsci.cgforcefield.FFIOParam method) (schrodinger.application.matsci.cgforcefield.FFIOSite method) (schrodinger.application.matsci.cgforcefield.FFIOVdwType method) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getOffsetPBCBonds() (schrodinger.application.matsci.nano.xtal.PBCBonds method) getOnBits() (schrodinger.infra.phase.PhpQSAR method) getOneLetterCodes() (schrodinger.application.matsci.amorphous.Moieties method) getOpcdArgs() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.SbcUtil method) getOpenFileName() (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog method) getOpenRingAtoms() (schrodinger.infra.phase.PhpOpenRingFinder method) getOpenRingCount() (schrodinger.infra.phase.PhpOpenRingFinder method) getOptimizationCmd() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) getOptionDesc() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) getOptions() (schrodinger.structutils.minimize.Minimizer method) getOptKwargs() (schrodinger.application.matsci.mecp_mod.MECP method) getOrAddColumn() (schrodinger.infra.table.Table method) getOrbitalsKeywords() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) getOrderedIntersections() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getOrigin() (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.protein.sequence.Sequence method) getOriginalName() (schrodinger.utils.colorscheme.MM_CScheme method) getOuterChiralIndicies() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getOuterTubeVectors() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getOutput() (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.pipeline.stage.Stage method) getOutputFile() (schrodinger.job.launchapi.JobSpecification method) getOutputFiles() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.launchapi.JobSpecification method) getOutputKeys() (schrodinger.job.launchapi.TaskSpecification method) getOutputName() (schrodinger.pipeline.stage.Stage method) getOutputNames() (schrodinger.pipeline.stage.Stage method) getOverlap() (schrodinger.application.desmond.replica_dE.replica_container method) getOverlapEnergyPlot() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getOverride() (schrodinger.application.desmond.packages.msys.TermTable method) getPairFromRow() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getPairs() (schrodinger.infra.phase.PhpOptionsParser method) getPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getPanel() (schrodinger.tasks.runners.PanelTaskReporter method) getParallelepipedLineSegments() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getParallelepipedVertices() (schrodinger.application.matsci.shapes.Parallelepiped method) getParamOpt() (schrodinger.infra.phase.PhpHypoOptimizer method) getParamSlot() (schrodinger.models.mappers.TargetParamMapper method) getParent() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getParticipants() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) getPatchColorRamp() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) getPath() (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) getPattern() (schrodinger.infra.phase.PhpFeaturePattern method) getPatternID() (schrodinger.infra.phase.PhpFeaturePattern method) getPatternMatches() (schrodinger.infra.phase.PhpProject method) getPatternString() (schrodinger.structutils.createfragments.FragmentCreator method) getPattyHandle() (schrodinger.infra.phase.PhpFeaturePattern method) getPBCMinMaxes() (schrodinger.application.matsci.amorphous.Scaffold method) getPBCSide() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) getPDBName() (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Initiator method) (schrodinger.application.matsci.amorphous.Monomer method) (schrodinger.application.matsci.amorphous.Terminator method) getPDOS() (schrodinger.application.matsci.espresso.qeoutput.PDOS method) getPercentScreenCurvePoints() (schrodinger.analysis.enrichment.Calculator method) getPeriodicPairStructure() (schrodinger.application.matsci.clusterstruct.Dimer method) getPermitted() (schrodinger.infra.phase.PhpSite method) getPermittedFeatures() (schrodinger.infra.phase.PhpFeatureRules method) getPharmSet() (schrodinger.infra.phase.PhpProject method) getPhpFunction() (in module schrodinger.infra.phase) getPiperDict() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method) getPkaAtom() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getPlanarAngle() (schrodinger.application.desmond.packages.staf.GeomCalc method) getPlaneBoxIntersections() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getPLISKWList() (in module schrodinger.application.desmond.automatic_analysis_generator) getPointInBox() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) (schrodinger.application.matsci.amorphous.Scaffold method) getPointsFromCalc() (schrodinger.analysis.enrichment.PercentScreenPlotter method) (schrodinger.analysis.enrichment.Plotter method) getPosArgs() (schrodinger.infra.phase.PhpOptionsParser method) getPosition() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) getPositions() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method) (schrodinger.application.desmond.packages.msys.System method) getPotentialDoubleBondAtoms() (schrodinger.structutils.assignbondorders.AssignBondOrders method) getPotentialEnergyGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getPotentialType() (schrodinger.application.matsci.cgforcefield.ForceField static method) getPPIKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getPrecision() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) getPrereqs() (schrodinger.job.queue.BaseJob method) getPreviousResidue() (schrodinger.protein.sequence.Sequence method) getPreviousResidueIndex() (schrodinger.protein.sequence.Sequence method) getPreviousResidueIndices() (schrodinger.protein.sequence.Sequence method) getPrimeEnergyByResidues() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getProductComplex() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getProducts() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) getProgramName() (schrodinger.infra.phase.PhpOptionsParser method) (schrodinger.job.app.App method) (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) getProgressAsPercentage() (schrodinger.job.jobcontrol.Job method) getProgressAsSteps() (schrodinger.job.jobcontrol.Job method) getProgressAsString() (schrodinger.job.jobcontrol.Job method) getProhibited() (schrodinger.infra.phase.PhpSite method) getProhibitedFeatures() (schrodinger.infra.phase.PhpFeatureRules method) getProjCoords() (schrodinger.infra.phase.PhpSite method) getProjectedOnly() (schrodinger.infra.phase.PhpSite method) getProjectedType() (schrodinger.infra.phase.PhpFeatureDefinition method) (schrodinger.infra.phase.PhpFeaturePattern method) getProjectPath() (schrodinger.infra.phase.PhpProject method) getProp() (schrodinger.infra.phase.PhpHypoAdaptor method) getPropDict() (schrodinger.application.livedesign.data_classes.ExportData method) getPropertyMinMax() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) getPropertyNames() (schrodinger.project.Project method) (schrodinger.structutils.filter.PropFilter method) getPropertyNamesForSelectedRows() (schrodinger.project.Project method) getPropertyPrecision() (schrodinger.project.Project method) getPropertyStrings() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property static method) getPropertyValue() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS method) getProtFilename() (schrodinger.application.desmond.gui.RelaxFrame method) getProtLigInterKW() (in module schrodinger.application.desmond.automatic_analysis_generator) getPTGroupnameCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) getPTGroupnamePalette() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) getQProp() (schrodinger.application.matsci.chargegui.NeighborTreatment method) getQsar() (schrodinger.infra.phase.PhpHypoAdaptor method) getQsarAlignments() (schrodinger.infra.phase.PhpProject method) getQsarCount() (schrodinger.infra.phase.PhpProject method) getQsarHypoIDs() (schrodinger.infra.phase.PhpProject method) getQsarIDs() (schrodinger.infra.phase.PhpProject method) getQsarModel() (schrodinger.infra.phase.PhpProject method) getQsarModelClassDescription() (schrodinger.infra.phase.PhpProject method) getQsarModelClasses() (schrodinger.infra.phase.PhpProject method) getQsarModelClassFraction() (schrodinger.infra.phase.PhpProject method) getQsarModelCoeff() (schrodinger.infra.phase.PhpProject method) getQsarModelCoeffRange() (schrodinger.infra.phase.PhpProject method) getQsarModelFactorCount() (schrodinger.infra.phase.PhpProject method) getQsarModelGridLimits() (schrodinger.infra.phase.PhpProject method) getQsarModelGridSpacing() (schrodinger.infra.phase.PhpProject method) getQsarModelRegF() (schrodinger.infra.phase.PhpProject method) getQsarModelRegP() (schrodinger.infra.phase.PhpProject method) getQsarModelRegRsqr() (schrodinger.infra.phase.PhpProject method) getQsarModelRegRsqrCv() (schrodinger.infra.phase.PhpProject method) getQsarModelRegRsqrScramble() (schrodinger.infra.phase.PhpProject method) getQsarModelRegSD() (schrodinger.infra.phase.PhpProject method) getQsarModelRegStability() (schrodinger.infra.phase.PhpProject method) getQsarModelStyle() (schrodinger.infra.phase.PhpProject method) getQsarModelVolBitCount() (schrodinger.infra.phase.PhpProject method) getQsarModelVolClasses() (schrodinger.infra.phase.PhpProject method) getQsarModelVolCoords() (schrodinger.infra.phase.PhpProject method) getQsarModelVolOnBits() (schrodinger.infra.phase.PhpProject method) getQsarProps() (schrodinger.infra.phase.PhpProject method) getQsarSet() (schrodinger.infra.phase.PhpProject method) getQsarStats() (schrodinger.infra.phase.PhpProject method) getRad() (schrodinger.infra.phase.PhpHypoAdaptor method) (schrodinger.infra.phase.PhpSite method) getRampNames() (schrodinger.utils.colorscheme.MM_ColorRampHolder method) getRange() (schrodinger.utils.colorscheme.MM_Colormap method) getReactantComplex() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getReactants() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getReactionInternals() (schrodinger.application.matsci.rxn_path.ReactionCoords method) getReactionSet() (schrodinger.analysis.reaction.RouteNode method) getReactiveAtoms() (schrodinger.application.matsci.rxn_path.ReactionPath method) getReadErrors() (schrodinger.structure.FormatReader method) (schrodinger.structure.StructureReader method) getRecentTemplatePath() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getRecentTemplatesList() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getReceptorHypo() (schrodinger.infra.phase.PhpDeNovoPharm method) getReceptorID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getReceptorLigandMap() (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) getReciprocals() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getRecord() (schrodinger.infra.phase.PhpStructureBus method) getRecordCopy() (schrodinger.infra.phase.PhpStructureBus method) getRecordCount() (schrodinger.infra.phase.PhpSubsetSplitter method) getRedundantAtoms() (schrodinger.application.matsci.nano.sheet.Grow method) getRedundantSequences() (schrodinger.protein.alignment.BaseAlignment method) getRefCt() (schrodinger.infra.phase.PhpHypoAdaptor method) getReferenceEdges() (schrodinger.application.matsci.shapes.Face method) getReferenceEntryId() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) getReferenceFaces() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) getReferenceProductComplex() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getReferenceReactantComplex() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) getReferenceSeq() (schrodinger.protein.alignment.BaseAlignment method) getReferenceStructure() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) getRefSites() (schrodinger.infra.phase.PhpHypoAdaptor method) getRegF() (schrodinger.infra.phase.PhpQSAR method) getRegP() (schrodinger.infra.phase.PhpQSAR method) getRegRsqr() (schrodinger.infra.phase.PhpQSAR method) getRegRsqrCv() (schrodinger.infra.phase.PhpQSAR method) getRegRsqrScramble() (schrodinger.infra.phase.PhpQSAR method) getRegSD() (schrodinger.infra.phase.PhpQSAR method) getRegStability() (schrodinger.infra.phase.PhpQSAR method) getReorderedStructure() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) getReplica() (schrodinger.application.desmond.replica_dE.replica_container method) getRepresentativeStructure() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) getResidualPotential() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidualPotentialByAtom() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidualPotentialByResidue() (schrodinger.application.bioluminate.escomp.ResidualPotential method) getResidue() (schrodinger.structure._StructureAtom method) getResidueAtomicNonPolarSASA() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResidueAtomicPolarSASA() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResidueAtoms() (schrodinger.structure.Structure method) getResidueCheckbox() (schrodinger.ui.residueselector.MutationSelectorFrame method) getResidueGroups() (schrodinger.ui.residueselector.MutationSelectorFrame method) getResidueHydropathy() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResidueID() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getResidueIndices() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) getResidueInteractionEnergy() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResidueInternalEnergy() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResiduepKa() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResiduePotentialEnergy() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResidueRotatableBonds() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResidueSASA() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResiduesCenter() (schrodinger.ui.picking.PickResiduesChangedMixin method) getResiduesList() (schrodinger.ui.picking.PickResiduesChangedMixin method) getResidueSurfComp() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getResidueType() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) getRESTDensityPlot() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getRestrGroup() (schrodinger.application.desmond.gui.RestraintsTab method) getResult() (schrodinger.application.desmond.packages.energygroup.Bulk method) (schrodinger.application.desmond.packages.energygroup.Energy method) (schrodinger.application.desmond.packages.energygroup.EnergyGroupBase method) (schrodinger.application.desmond.packages.energygroup.InteractionEnergy method) getResultsGUI() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) getResultWithThisEnergy() (schrodinger.application.matsci.jaguarworkflows.Results method) getReversedSequenceOrdering() (schrodinger.protein.alignment.BaseAlignment static method) getRGB() (schrodinger.structutils.color.ColorRamp method) getRGBA() (schrodinger.utils.colorscheme.MM_Color method) (schrodinger.utils.colorscheme.MM_Colormap method) getRHistogram() (schrodinger.application.desmond.replica_dE.replica_energy method) getRingCentroid() (schrodinger.structutils.ringspear.SpearRing method) GetRingSystems() (in module schrodinger.application.desmond.packages.msys) getRLEntryIDs() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) getRMax() (schrodinger.application.desmond.replica_dE.replica_energy method) getRMean() (schrodinger.application.desmond.replica_dE.replica_energy method) getRMin() (schrodinger.application.desmond.replica_dE.replica_energy method) getRMSD() (in module schrodinger.trajectory.prody.ensemble) getRmsdDataname() (schrodinger.structutils.rmsd.ConformerRmsd method) getRMSDKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getRMSDLigandKW() (in module schrodinger.application.desmond.automatic_analysis_generator) getRMSFLigandKW() (in module schrodinger.application.desmond.automatic_analysis_generator) getRMSFProtKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getROCAreaRomberg() (schrodinger.analysis.enrichment.Calculator method) getROCCurvePoints() (schrodinger.analysis.enrichment.Calculator method) getroot() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) getRotatableBondsGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getRotationMatrix() (schrodinger.structutils.ringspear.SpearRing method) getRotationToZ() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getRotEnergy() (schrodinger.application.desmond.torsion_related.BondRotator method) getRoutes() (schrodinger.analysis.reaction.RetroSynthesisNode method) getRow() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.project.Project method) getRowCriteria() (schrodinger.ui.ligfilter.CriteriaListModel method) getRowName() (schrodinger.application.desmond.fep_gui.StrucListModel method) getRowTarget() (schrodinger.application.desmond.fep_gui.StrucListModel method) getRowText() (schrodinger.ui.ligfilter.PatternModel method) getRSquaredList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getRuleInvocationStack() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getRuleMemoization() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getRules() (schrodinger.infra.phase.PhpHypoAdaptor method) (schrodinger.utils.colorscheme.MM_CScheme method) getRuntimeName() (schrodinger.infra.phase.PhpProject method) getRuntimePath() (schrodinger.pipeline.stage.Stage method) getRxAtoms() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getSamplePoints() (schrodinger.application.matsci.rxn_path.ReactionPath method) getSampleStructure() (schrodinger.application.matsci.clusterstruct.SpeciesData method) getSamplingMethod() (schrodinger.infra.phase.PhpConfOptions method) getSamplingMethodDisplayName() (schrodinger.infra.phase.PhpConfOptions static method) getSASAGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getSASANonPolarGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getSASAPolarGenerator() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getSasOptions() (schrodinger.infra.phase.PhpFeatureDefinition method) getScaledEwaldConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getScanCoordinate() (schrodinger.application.jaguar.input.JaguarInput method) getScanStep() (schrodinger.application.jaguar.output.JaguarOutput method) getSchrodingerRun() (schrodinger.tasks.jobtasks.AbstractJobTask method) getScoreInPlace() (schrodinger.infra.phase.PhpMatchOptions method) getSeed() (schrodinger.application.matsci.mswidgets.RandomSeedWidget method) getSegmentPlaneIntersections() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) getSelected() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) getSelectedDataTitles() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) getSelectedExcludedVolumes() (schrodinger.application.phase.featureselector.FeatureModel method) getSelectedFeatureEquivalencies() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) getSelectedFeatures() (schrodinger.application.phase.featureselector.FeatureModel method) (schrodinger.application.phase.featureselector.FeatureSelector method) getSelectedIndexes() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getSelectedLigand() (schrodinger.ui.chooseligand.ChooseLigandDialog method) getSelectedLocationType() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedMutations() (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) getSelectedName() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedPath() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) getSelectedPatternName() (schrodinger.ui.ligfilter.LigfilterFrame method) getSelectedProp() (schrodinger.application.matsci.chargegui.ChargePropertySelector method) getSelectedResult() (schrodinger.application.bioluminate.antibody.search_results_table.FullTable method) (schrodinger.application.bioluminate.antibody.search_results_table.TableView method) getSelectedResults() (schrodinger.application.bioluminate.antibody.search_results_table.SplitTable method) getSelectedRows() (schrodinger.infra.table.Table method) getSelectedRowTotal() (schrodinger.infra.table.Table method) (schrodinger.project.Project method) getSelectedX() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getSelectedXY() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getSelfEnergy() (schrodinger.structutils.minimize.Minimizer method) getSemiPartialRSquaredList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getSeparationRatioList() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) getSeqIndex() (schrodinger.protein.alignment.BaseAlignment method) getSeqStructure() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) getSequenceViewerImage() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getSettings() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) getSettingsAffectedBySpinTreatment() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) getShiftedCoulombFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getShiftedLennardJonesFFIOConstants() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getShortName() (schrodinger.utils.colorscheme.MM_ColorRamp method) (schrodinger.utils.colorscheme.MM_CScheme method) getSignalsAndSlots() (schrodinger.models.mappers.AbstractParamMapper method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.models.mappers.SettingsParamMapper method) (schrodinger.models.mappers.TargetParamMapper method) getSimHistogramByActiveId() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) getSimilarity() (schrodinger.protein.residue.Residue method) (schrodinger.protein.sequence.Sequence method) getSimilarityMetricDescription() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method) getSimilarityScore() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) getSimpleSlabVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSingleDisplacementChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) getSite() (schrodinger.infra.phase.PhpHypoAdaptor method) getSiteByDisplayName() (schrodinger.infra.phase.PhpHypoAdaptor method) getSiteCount() (schrodinger.infra.phase.PhpDeNovoPharm method) (schrodinger.infra.phase.PhpHypoAdaptor method) getSiteData() (schrodinger.infra.phase.PhpDeltaHypo method) getSiteDescription() (schrodinger.infra.phase.PhpSite method) getSiteIndexFromDisplayName() (schrodinger.infra.phase.PhpHypoAdaptor method) getSiteIndices() (schrodinger.infra.phase.PhpSiteConstraint method) (schrodinger.infra.phase.PhpSiteMaskGroup method) getSiteMappings() (schrodinger.infra.phase.PhpProject method) getSiteMaskData() (schrodinger.infra.phase.PhpSiteMask method) getSiteMaskGroups() (schrodinger.infra.phase.PhpSiteMask method) getSiteMasks() (schrodinger.infra.phase.PhpProject method) getSiteMaskValue() (schrodinger.infra.phase.PhpSiteMask method) getSiteMaskVector() (schrodinger.infra.phase.PhpSiteMask method) getSiteName() (schrodinger.infra.phase.PhpSite method) getSiteNumber() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) (schrodinger.infra.phase.PhpDeltaHypo method) (schrodinger.infra.phase.PhpFeatureRules method) (schrodinger.infra.phase.PhpSite method) (schrodinger.infra.phase.PhpSiteMask method) (schrodinger.infra.phase.PhpSiteMaskData method) getSitePairs() (schrodinger.infra.phase.PhpDeNovoPharm method) getSites() (schrodinger.application.phase.phase_markers.PhaseMarkers method) getSitesConformer() (schrodinger.infra.phase.PhpProject method) getSitesConformers() (schrodinger.infra.phase.PhpProject method) getSiteSimilarity() (schrodinger.infra.phase.PhpSite method) getSiteStatus() (schrodinger.infra.phase.PhpSite method) getSiteType() (schrodinger.application.matsci.cgforcefield.ForceField static method) (schrodinger.infra.phase.PhpDeltaHypo method) (schrodinger.infra.phase.PhpSite method) (schrodinger.infra.phase.PhpSiteMask method) (schrodinger.infra.phase.PhpSiteMaskData method) getSiteTypeChar() (schrodinger.infra.phase.PhpSite method) getSiteTypes() (schrodinger.infra.phase.PhpHypoAdaptor method) (schrodinger.infra.phase.PhpSiteConstraint method) getSize() (schrodinger.utils.colorscheme.MM_Colormap method) getSketcherStructure() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getSlabUnitCell() (schrodinger.application.matsci.nano.slab.Surface method) getSlabVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSlash() (schrodinger.infra.phase.PhpProject method) getSlots() (schrodinger.application.matsci.siteselector.siteselector.Ligand method) (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) getSmarts() (schrodinger.analysis.transformations.TransformsRepository method) getSMARTSFromSelection() (schrodinger.ui.ligfilter.AddDefinitionDialog method) getSMARTSFromWS() (in module schrodinger.application.matsci.smartsutilsgui) getSmiles() (schrodinger.structutils.smiles.SmilesGenerator method) getSmilesAndMap() (schrodinger.structutils.smiles.SmilesGenerator method) getSolventName() (schrodinger.application.matsci.mswidgets.CompactSolventSelector method) getSourceName() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.streams.ANTLRFileStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) getSpanningVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSparseRescodes() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getSpecialProperties() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabIGO method) getSpecsString() (schrodinger.application.inputconfig.InputConfig method) getSpgObjByName() (schrodinger.application.matsci.nano.xtal.SpaceGroups method) getSphere() (schrodinger.infra.phase.PhpExclVol method) getSphereRadius() (schrodinger.infra.phase.PhpExclVol method) getSpheres() (schrodinger.infra.phase.PhpExclVol method) getSphereXYZ() (schrodinger.infra.phase.PhpExclVol method) getSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getSpinTreatment() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) getSquareVertices() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getSSBondPartner() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) getSSEProtKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) GetSSSR() (in module schrodinger.application.desmond.packages.msys) getStageByJobid() (schrodinger.pipeline.pipeline.Pipeline method) getStageDirectory() (schrodinger.pipeline.stage.Stage method) getStageIndex() (schrodinger.application.matsci.mswidgets.MultiStageArea method) getStandardizedSmiles() (schrodinger.structutils.smiles.SmilesGenerator method) getStandardName() (schrodinger.tasks.runners.TaskRunner method) getStart() (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method) (schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method) (schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method) getStartingNodes() (schrodinger.analysis.reaction.RouteNode method) getStatusStrings() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) getStderr() (schrodinger.job.launchapi.JobSpecification method) getStdout() (schrodinger.job.launchapi.JobSpecification method) getStdSimDecoyByActiveId() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) getStep() (schrodinger.infra.phase.PhpProject method) getSteps() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSWorkFlow method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) getStop() (schrodinger.application.desmond.antlr3.recognizers.ParserRuleReturnScope method) (schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method) getstr() (in module schrodinger.application.matsci.msutils) getStrainedAdsorptionLayer() (schrodinger.application.matsci.nano.interface_mod.Interface method) getStrainedAngle() (schrodinger.application.matsci.nano.interface_mod.Interface method) getStretch() (schrodinger.structutils.minimize.Minimizer method) getStretchEnergy() (schrodinger.structutils.minimize.Minimizer method) getStrucChargeAndSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) getStructFromPtEntry() (schrodinger.application.matsci.guibase.MultiDesmondJobApp method) getStructure() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabRow method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.jaguar.results.JaguarResults method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Results method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) (schrodinger.project.ProjectRow method) (schrodinger.protein.sequence.Sequence method) (schrodinger.structutils.minimize.Minimizer method) getStructureCount() (schrodinger.application.combiglide.combenumdock.collectionViewerModel method) getStructureCountIn() (schrodinger.infra.phase.PhpStructureSplitter method) getStructureCountsIn() (schrodinger.infra.phase.PhpStructureSplitter method) getStructureCountsOut() (schrodinger.infra.phase.PhpStructureSplitter method) getStructureFile() (schrodinger.application.qsite.input.QSiteInput method) getStructureForCoupling() (schrodinger.application.matsci.amorphous.BaseMoiety method) getStructureFormat() (schrodinger.infra.phase.PhpStructureBus method) getStructureOutput() (schrodinger.pipeline.pipeline.Pipeline method) getStructures() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.output.JaguarOutput method) getStructureSize() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) getStructureTitleForJobname() (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) getStructureWithJagNames() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) getSubalignment() (schrodinger.protein.alignment.BaseAlignment method) getSubColorSchemeName() (schrodinger.utils.colorscheme.ColorSchemeManager method) getSubColorSchemeNamesList() (schrodinger.utils.colorscheme.ColorSchemeManager method) getSubColorSchemes() (schrodinger.utils.colorscheme.ColorSchemeManager method) getSubjobCount() (schrodinger.infra.phase.PhpSubsetSplitter method) getSubsequence() (schrodinger.protein.sequence.Sequence method) getSubsetEnergy() (schrodinger.structutils.minimize.Minimizer method) getSubsetFiles() (schrodinger.infra.phase.PhpSubsetSplitter method) getSubTab() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) getSummary() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) (schrodinger.application.livedesign.maestro_data_types.Complexes method) (schrodinger.application.livedesign.maestro_data_types.DockedPoses method) (schrodinger.application.livedesign.maestro_data_types.Ligands method) (schrodinger.application.livedesign.maestro_data_types.OrganometallicCompounds method) (schrodinger.infra.phase.PhpFeaturePattern method) (schrodinger.infra.phase.PhpHypoAdaptor method) (schrodinger.protein.sequence.Sequence method) getSuperimposedRMSD() (schrodinger.structutils.sitealign.SiteMatchLookup method) getSupportedFormats() (schrodinger.application.desmond.image_generator.ImageGenerator method) getSurface() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getSurfaceArea() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.application.matsci.shapes.Cylinder method) (schrodinger.application.matsci.shapes.Sphere method) getSurfaceNodes() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) (schrodinger.application.matsci.freevolume.Void method) getSurfacePotential() (schrodinger.application.bioluminate.escomp.PotGrid method) getSurfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getSymbolicLine() (schrodinger.application.matsci.zmutils.ZAtom method) getTab() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) getTable() (schrodinger.application.desmond.packages.msys.System method) getTableSchema() (schrodinger.application.desmond.packages.restrain.Restraints static method) getTabParentAndLayout() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) getTargetEntryID() (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData method) (schrodinger.application.livedesign.maestro_data_types.Complexes method) (schrodinger.application.livedesign.maestro_data_types.DockedPoses method) (schrodinger.application.livedesign.maestro_data_types.TargetlessBase method) getTargetMolecule() (schrodinger.application.matsci.montecarlo.Metropolizer method) getTargetSlot() (schrodinger.models.mappers.TargetParamMapper method) getTaskByName() (schrodinger.tasks.tasks_.TaskManager method) getTaskSpec() (schrodinger.job.launchapi.TaskSpecificationBuilder method) getTempImageFilename() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) getTemplate() (schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method) getter (schrodinger.models.mappers.AccessType attribute) getTerminalGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) getTerminatingAtoms() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) getTestRCorr() (schrodinger.infra.phase.PhpQSAR method) getText() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getTextSummary() (schrodinger.protein.reliability.Results method) getTheoryLevel() (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) getThermoMethod() (schrodinger.application.desmond.gui.EnsembleTab method) getTimeLimit() (schrodinger.infra.phase.PhpMatchOptions method) getTitle() (schrodinger.application.matsci.desmondutils.BrownieMSJStringer method) (schrodinger.application.matsci.desmondutils.MDMSJStringer method) (schrodinger.application.matsci.desmondutils.MSAnalysisMSJStringer method) (schrodinger.application.matsci.desmondutils.MSJStringer method) (schrodinger.application.matsci.desmondutils.MinimizeMSJStringer method) (schrodinger.infra.phase.PhpProject method) (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getTitles() (schrodinger.infra.phase.PhpQSAR method) getToken() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getTokenErrorDisplay() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) getTokenIndex() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) getTokens() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) getTokenSource() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.TokenStream method) getTokenStartIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getTokenStopIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getTokenStream() (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) getTokenType() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) getTol() (schrodinger.infra.phase.PhpHypoAdaptor method) (schrodinger.infra.phase.PhpSite method) (schrodinger.infra.phase.PhpSiteConstraint method) getToolBar() (schrodinger.application.bioluminate.actions.factory.Factory method) getTopoDistanceMatrix() (in module schrodinger.infra.phase) getTorsion() (schrodinger.application.desmond.packages.staf.GeomCalc method) (schrodinger.structutils.minimize.Minimizer method) getTorsionEnergy() (schrodinger.structutils.minimize.Minimizer method) getTorsionKeywords() (in module schrodinger.application.desmond.automatic_analysis_generator) getTorsionValueInRange() (schrodinger.application.matsci.amorphous.TorsionAngler method) getTotal14Pair() (schrodinger.structutils.minimize.Minimizer method) getTotalAggregation() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalAtom() (schrodinger.structutils.minimize.Minimizer method) getTotalBending() (schrodinger.structutils.minimize.Minimizer method) getTotalComplementarity() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalEnergy() (schrodinger.structutils.minimize.Minimizer method) getTotalHydropathy() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalImpTorsion() (schrodinger.structutils.minimize.Minimizer method) getTotalpKa() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalPotentialEnergy() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalPrimeEnergy() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalRotatableBonds() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalSASA() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalSASANonPolar() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalSASAPolar() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalSolubility() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalStretch() (schrodinger.structutils.minimize.Minimizer method) getTotalSubColorSchemes() (schrodinger.utils.colorscheme.ColorSchemeManager method) getTotalSurfComp() (schrodinger.application.bioluminate.protein.PropertyCalculator method) getTotalTorsion() (schrodinger.structutils.minimize.Minimizer method) getTotalTypes() (schrodinger.graphics3d.common.Group method) getTPP() (schrodinger.job.launchparams.LaunchParameters method) getTranslationToBox() (schrodinger.application.matsci.amorphous.Box method) getTreatHydrogens() (schrodinger.infra.phase.PhpExclVol method) getTree() (schrodinger.application.desmond.antlr3.recognizers.RuleReturnScope method) (schrodinger.application.desmond.antlr3.tree.TreeRuleReturnScope method) getTreeAdaptor() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) getTreeData() (schrodinger.analysis.reaction.RouteNode method) getTreeNodeStream() (schrodinger.application.desmond.antlr3.tree.TreeParser method) getTreeSource() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) getTrimmedTable() (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile static method) getTubeSpacings() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) getTubeVectors() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) getTvalue() (schrodinger.infra.phase.PhpQSAR method) getType() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.infra.phase.PhpFeaturePattern method) getTypeSimilarity() (schrodinger.infra.phase.PhpFeaturePattern method) getUnexpectedToken() (schrodinger.application.desmond.antlr3.exceptions.UnwantedTokenException method) getUnexpectedType() (schrodinger.application.desmond.antlr3.exceptions.RecognitionException method) getUniqueID() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) getUniqueOrder() (schrodinger.structutils.smiles.SmilesGenerator method) getUniqueTitle() (schrodinger.application.combiglide.combenumdock.collectionViewerModel method) getUnitNormalToDeltaForces() (schrodinger.application.matsci.mecp_mod.MECPStep method) getUnknownKeywords() (schrodinger.application.jaguar.input.JaguarInput method) getUnusedHostList() (schrodinger.pipeline.pipeline.StageJob method) getUpdatedCParams() (schrodinger.application.matsci.nano.interface_mod.Interface method) getUseAtomTypes() (schrodinger.infra.phase.PhpMatchOptions method) getUsedHosts() (schrodinger.pipeline.pipeline.Pipeline method) getUsedStatus() (schrodinger.infra.phase.PhpFeaturePattern method) getUseHardAlignCutoff() (schrodinger.infra.phase.PhpMatchOptions method) getUseNDDOForCharges() (schrodinger.infra.phase.PhpMMconfAdaptor method) getUserOutputFiles() (schrodinger.pipeline.pipeline.Pipeline method) getUserOutputs() (schrodinger.pipeline.pipeline.Pipeline method) getUserTemplateList() (schrodinger.application.matsci.builderwidgets.SketcherBox method) getUserURL() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) getValidCanvasKPLSModelFiles() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS static method) getValidFlags() (schrodinger.infra.phase.PhpOptionsParser method) getValidPairs() (schrodinger.infra.phase.PhpOptionsParser method) getValue() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) (schrodinger.application.mopac.structure_launchers.StructureLauncher method) (schrodinger.infra.phase.PhpSiteConstraint method) (schrodinger.models.mappers.AttrTarget method) (schrodinger.models.mappers.ParamTarget method) (schrodinger.models.mappers.Target method) getvalue() (schrodinger.utils.ligfilter.AslCriterion method) (schrodinger.utils.ligfilter.Criterion method) (schrodinger.utils.ligfilter.PredefinedCriterion method) (schrodinger.utils.ligfilter.PropertyCriterion method) (schrodinger.utils.ligfilter.SmartsCriterion method) getValueForKey() (schrodinger.infra.phase.PhpOptionsParser method) getValueFromItem() (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) getValues() (schrodinger.infra.phase.PhpSortCapperDoubleDecreasing method) (schrodinger.infra.phase.PhpSortCapperDoubleIncreasing method) getVariableLines() (schrodinger.application.matsci.zmutils.ZAtom method) getVariance() (schrodinger.trajectory.prody.mode.Mode method) getVariances() (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) getVariant() (schrodinger.infra.phase.PhpFeatureRules method) getVbmCbm() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) getVector() (schrodinger.application.desmond.packages.staf.GeomCalc method) getVectorCutoff() (schrodinger.infra.phase.PhpMatchOptions method) getVectorWeight() (schrodinger.infra.phase.PhpMatchOptions method) getVectSubset() (schrodinger.infra.phase.PhpQSAR method) getVelocities() (schrodinger.application.desmond.packages.msys.System method) getVerbosity() (schrodinger.pipeline.stage.Stage method) getVertices() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.graphics3d.polyhedron.MaestroCube method) (schrodinger.graphics3d.polyhedron.MaestroDodecahedron method) (schrodinger.graphics3d.polyhedron.MaestroIcosahedron method) (schrodinger.graphics3d.polyhedron.MaestroOctahedron method) (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) (schrodinger.graphics3d.polyhedron.MaestroTetrahedron method) getVerticesOfAllPlanes() (schrodinger.application.matsci.nano.plane.CrystalPlane method) getVisibleColumnIndex() (schrodinger.infra.table.Table method) getVisibleColumnTotal() (schrodinger.infra.table.Table method) getVisiblePropertyNames() (schrodinger.project.Project method) getVisibleRowIndex() (schrodinger.infra.table.Table method) getVisibleRowTotal() (schrodinger.infra.table.Table method) getVisibleSeqCount() (schrodinger.protein.alignment.BaseAlignment method) getVoidVolumes() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) getVolAtomClasses() (schrodinger.infra.phase.PhpQSAR method) getVolCoords() (schrodinger.infra.phase.PhpQSAR method) getVolOccBits() (schrodinger.infra.phase.PhpQSAR method) getVolRegCoeffs() (schrodinger.infra.phase.PhpQSAR method) getVolume() (schrodinger.application.matsci.shapes.Cube method) (schrodinger.application.matsci.shapes.Cubeoctahedron method) (schrodinger.application.matsci.shapes.Cylinder method) (schrodinger.application.matsci.shapes.Dodecahedron method) (schrodinger.application.matsci.shapes.Icosahedron method) (schrodinger.application.matsci.shapes.Octahedron method) (schrodinger.application.matsci.shapes.Parallelepiped method) (schrodinger.application.matsci.shapes.Sphere method) (schrodinger.application.matsci.shapes.Tetrahedron method) getVolumeCutoff() (schrodinger.infra.phase.PhpMatchOptions method) getVolumeWeight() (schrodinger.infra.phase.PhpMatchOptions method) getVSliderMax() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getVSliderMin() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) getWeights() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector.ChargeSelectorLineEdit method) (schrodinger.trajectory.prody.ensemble.Ensemble method) getWidthParameter() (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined method) getWorkspaceEntry() (schrodinger.application.desmond.maestro.NewEntryGroup method) getWriteFilename() (schrodinger.tasks.jobtasks.AbstractJobTask method) getXCoord() (schrodinger.infra.phase.PhpSite method) getXP() (schrodinger.infra.phase.PhpSite method) getXtalCell() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) getXvol() (schrodinger.infra.phase.PhpHypoAdaptor method) getXYZ() (schrodinger.structure.Structure method) getYCoord() (schrodinger.infra.phase.PhpSite method) getZCoord() (schrodinger.infra.phase.PhpSite method) getZmatrix() (schrodinger.application.matsci.rxn_path.InternalCoords method) getZmatText() (schrodinger.application.jaguar.input.JaguarInput method) GhostAtomIndexError gibbs (schrodinger.application.jaguar.utils.FreeEnergy attribute) gibbs_energy_property_string() (in module schrodinger.application.jaguar.utils) gid() (schrodinger.application.desmond.cms.Cms method) gid_refresh() (schrodinger.application.desmond.cms.Cms method) gids() (schrodinger.application.desmond.packages.staf.Positer method) glibc() (in module schrodinger.application.jaguar.textparser) glide_finish() (schrodinger.application.glide.http_server.GlideHTTPHandler method) glide_send_response() (schrodinger.application.glide.http_server.GlideHTTPHandler method) glide_shutdown_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) GlideHTTPHandler (class in schrodinger.application.glide.http_server) GlideHTTPServer (class in schrodinger.application.glide.http_server) GlideJob (class in schrodinger.application.glide.glide) glidePrecisionDialog (class in schrodinger.application.combiglide.combenumdock) GlideServerManager (class in schrodinger.application.glide.http_client) GlideSortStage (class in schrodinger.pipeline.stages.glide) GlideWorkspaceMarkers (class in schrodinger.application.glide.gui) global_annotations (schrodinger.protein.alignment.BaseAlignment attribute) (schrodinger.protein.alignment.ProteinAlignment attribute) GLOW_COLOR (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) glue() (in module schrodinger.application.desmond.packages.topo) (schrodinger.application.desmond.packages.msys.System method) glue_cms() (in module schrodinger.application.desmond.packages.topo) glued_topology (schrodinger.application.desmond.packages.msys.System attribute) GMAGGLASS (schrodinger.maestro.markers.Icons attribute) GPU_UNIT_LABEL (schrodinger.application.matsci.guibase.PerStrucConfigDialog attribute) (schrodinger.application.matsci.guibase.PerStrucSingleGpuConfigDialog attribute) GPUAndCPURESTFEPConfigDialog (class in schrodinger.application.desmond.fep_gui) grab() (schrodinger.application.desmond.maestro.Workspace method) gradient_criterion (schrodinger.structutils.minimize.Minimizer attribute) grammarFileName (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) Graph (class in schrodinger.application.desmond.packages.msys) GREATER_THAN (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property attribute) Grid (class in schrodinger.application.bindingsite.cavutils) (class in schrodinger.application.desmond.packages.msys.molfile) (class in schrodinger.pipeline.pipeio) grid (schrodinger.application.matsci.freevolume.GridRadius attribute) GRID_DENSITY (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) GRID_DENSITY_REV (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) grid_property (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) GridBox (class in schrodinger.graphics3d.gridbox) gridBrowse() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) Gridgen (class in schrodinger.application.glide.glide) GridgenStage (class in schrodinger.pipeline.stages.glide) gridNeighbors() (schrodinger.application.matsci.amorphous.XYZVolumeGraph static method) GridRadius (class in schrodinger.application.matsci.freevolume) gridSpacing (schrodinger.infra.phase.PhpQSARModel attribute) Group (class in schrodinger.graphics3d.common) group (schrodinger.project.ProjectRow attribute) group() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) group_by_connectivity() (in module schrodinger.structutils.analyze) group_items() (in module schrodinger.application.jaguar.utils) GROUP_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) group_subtuples_by_key_and_value() (in module schrodinger.application.matsci.nano.particle) groupAromaticRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) groupHidden() (schrodinger.graphics3d.common.Primitive method) groupNumber (schrodinger.infra.phase.PhpSiteMaskGroup attribute) groups (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) (schrodinger.project.Project attribute) groupShown() (schrodinger.graphics3d.common.Primitive method) Grow (class in schrodinger.application.matsci.nano.sheet) grow_fragment() (in module schrodinger.protein.helix) grow_marker (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) grow_mult() (in module schrodinger.structutils.build) grower (schrodinger.application.matsci.amorphous.AttachmentAtoms attribute) growFluoro() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) growFragmentCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) growFragmentForward() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) GROWINDICIES (schrodinger.application.matsci.nano.sheet.Grow attribute) growMethyl() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) growname (schrodinger.structure._StructureAtom attribute) guardedRunMain() (schrodinger.tasks.tasks.ThreadFunctionTask method) guess_filetype() (in module schrodinger.application.desmond.packages.msys.molfile) guess_value_type() (schrodinger.utils.sea.Atom static method) guessAccepted() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) guessBonds() (schrodinger.application.desmond.packages.msys.System method) GUESSCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) guessMode() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) guessOrder() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) guessRejected() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) gui() (schrodinger.job.app.App method) GuiApp (class in schrodinger.application.desmond.gui) gvblmp2() (in module schrodinger.application.jaguar.textparser) GXG_DATA (schrodinger.application.bioluminate.protein.Mutator attribute) GXG_DATA_PRIME (schrodinger.application.bioluminate.protein.Mutator attribute) Gyradius (class in schrodinger.application.desmond.packages.analysis) gzip_it() (schrodinger.application.desmond.title_to_hex.Analysis method) gzip_open() (in module schrodinger.trajectory.prody.writenmd)

H

H1 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H2 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H3 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) H_BOND (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) H_bonds (schrodinger.application.glide.xpdes.TermKeywords attribute) Ha2Ry() (in module schrodinger.application.matsci.qexsd.qespresso.options) hack_for_multiprocessing() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) HALFREVOLUTION (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) HAMILTONIAN (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabNoSoZora attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTabWithSoZora attribute) hamiltonianChanged (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) Handle (class in schrodinger.application.desmond.packages.msys) handle_check_action() (in module schrodinger.application.licensing.licadmin) handle_diag_action() (in module schrodinger.application.licensing.licadmin) handle_generic_action() (in module schrodinger.application.licensing.licadmin) handle_info_action() (in module schrodinger.application.licensing.licadmin) handle_install_action() (in module schrodinger.application.licensing.licadmin) handle_list_action() (in module schrodinger.application.licensing.licadmin) handle_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) handle_start_action() (in module schrodinger.application.licensing.licadmin) handle_stat_action() (in module schrodinger.application.licensing.licadmin) handle_stop_action() (in module schrodinger.application.licensing.licadmin) handle_timeout() (schrodinger.application.glide.http_server.GlideHTTPServer method) handle_ver_action() (in module schrodinger.application.licensing.licadmin) handle_verify_action() (in module schrodinger.application.licensing.licadmin) HandledError handleFinalGeometry() (schrodinger.application.matsci.mecp_mod.MECPStep method) handleFiniteDifferences() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) handleManyToOne() (schrodinger.application.matsci.nano.particle.Nanoparticle method) handleMetalBonding() (schrodinger.application.matsci.rxn_channel.rxn_channel.Products method) handleObsolete() (schrodinger.protein.getpdb_utility.Code method) handleOneToMany() (schrodinger.application.matsci.nano.particle.Nanoparticle method) handleProps() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) (schrodinger.application.matsci.nano.tube.NanoTube method) handleRingExclusions() (schrodinger.application.matsci.coarsegrain.Internals method) handleSettings() (schrodinger.application.matsci.nano.xtal.Crystal method) handleStageMessages() (schrodinger.pipeline.pipeline.Pipeline method) handleStructure() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) handshake() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) hardness_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) hartree_to_kcal_per_mol() (in module schrodinger.application.matsci.mecp_mod) has3dCoords() (schrodinger.structure.Structure method) has_alt_index() (in module schrodinger.infra.phase) has_chorus_box_props() (in module schrodinger.application.matsci.desmondutils) has_fepio() (in module schrodinger.application.desmond.cms) has_ffio() (in module schrodinger.application.desmond.cms) has_key() (schrodinger.project.PropertyDictionary method) (schrodinger.utils.mmutil.StringStringMap method) (schrodinger.utils.scollections.IdentityDict method) (schrodinger.utils.sea.Map method) has_license_file_suffix() (in module schrodinger.application.licensing.licadmin) has_option() (schrodinger.utils.cmdline.SingleDashOptionParser method) has_orthorhombic_pbc() (in module schrodinger.application.matsci.desmondutils) has_plugin() (in module schrodinger.application.desmond.config) has_rule() (schrodinger.application.desmond.systype.DesmondTyper static method) (schrodinger.application.desmond.systype.McproTyper static method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) has_space_group_pbc_props() (in module schrodinger.application.matsci.desmondutils) has_tag() (schrodinger.utils.sea.Sea method) has_undefined_stereo() (in module schrodinger.utils.cgxutils) has_vertex_colors (schrodinger.surface.Surface attribute) hasAcceptableInput() (schrodinger.application.desmond.cwidget.EntryField method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) hasAddCts() (schrodinger.infra.phase.PhpHypoAdaptor method) hasAncestor() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) hasBrancher() (schrodinger.application.matsci.amorphous.Moieties method) hasCascader() (schrodinger.application.matsci.amorphous.Moieties method) hasChanged() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) hasChirality() (schrodinger.application.matsci.amorphous.Monomer method) hasClashes() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) hasCnst() (schrodinger.infra.phase.PhpHypoAdaptor method) hasCompleted() (schrodinger.pipeline.stage.Stage method) hasData() (schrodinger.application.prime.residue_interaction.InteractionReader class method) hasEntryID() (schrodinger.protein.sequence.Sequence method) hasFepio() (schrodinger.application.desmond.ffiostructure.FFIOStructure method) hasFfio() (schrodinger.application.desmond.ffiostructure.FFIOStructure method) hasFlag() (schrodinger.infra.phase.PhpOptionsParser method) hash() (schrodinger.application.desmond.packages.msys.Graph method) hash_of_list() (in module schrodinger.application.jaguar.structure_isomorphism) hasIvol() (schrodinger.infra.phase.PhpHypoAdaptor method) hasKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) hasLicenseFeature() (schrodinger.infra.phase.PhpLicenseGeneric method) hasMask() (schrodinger.infra.phase.PhpHypoAdaptor method) hasMissingAtoms() (schrodinger.structure._Residue method) hasMixedFeatures() (schrodinger.infra.phase.PhpFeatureRules method) hasNext() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) hasProjectedSites() (schrodinger.infra.phase.PhpSiteConstrainer method) hasQsar() (schrodinger.infra.phase.PhpHypoAdaptor method) hasRad() (schrodinger.infra.phase.PhpHypoAdaptor method) hasRefCt() (schrodinger.infra.phase.PhpHypoAdaptor method) hasRefCtMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hasRings() (schrodinger.application.matsci.amorphous.Moieties method) hasRules() (schrodinger.infra.phase.PhpHypoAdaptor method) hasSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) hasStarted() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobDJ method) (schrodinger.pipeline.stage.Stage method) hasStructure() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.protein.sequence.Sequence method) hasTerm() (schrodinger.application.desmond.packages.msys.TermTable method) hasTol() (schrodinger.infra.phase.PhpHypoAdaptor method) hasTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hasUniqueNavigationNodes() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) hasValidBasis() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.PerAtomBasisRow method) hasXP() (schrodinger.infra.phase.PhpSite method) hasXvol() (schrodinger.infra.phase.PhpHypoAdaptor method) hasXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) haveMasterDiffs() (schrodinger.infra.phase.PhpProject method) hbond_energy() (in module schrodinger.application.qsite.output) hbond_heavy_max_angle (schrodinger.protein.assignment.ProtAssign.changeable attribute) hbond_heavy_min_angle (schrodinger.protein.assignment.ProtAssign.changeable attribute) hbond_iterator() (in module schrodinger.structutils.analyze) hbond_min_angle (schrodinger.protein.assignment.ProtAssign.changeable attribute) hcount() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method) header (schrodinger.application.jaguar.results.ScfIteration attribute) header() (in module schrodinger.application.desmond.report_helper) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) (schrodinger.application.qsite.input.Cut method) (schrodinger.application.qsite.input.HydrogenCap method) headerData() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.desmond.fep_gui.PathModel method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.PatternModel method) HEADERS (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) headerToEnv() (in module schrodinger.application.desmond.enhsamp) health() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) healthier() (in module schrodinger.application.licensing.licadmin) HEAVY (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) heavy_atom_num_cond() (in module schrodinger.application.desmond.fep_mapping) heavy_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method)

HEAVY_FR_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) HEAVY_FR_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) HEAVY_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) HEAVY_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) height() (schrodinger.application.desmond.reorder_atom.Node method) HELIX (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute) HELIX_BREAKING (schrodinger.protein.residue.HELIX_PROPENSITY attribute) HELIX_COLOR (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) HELIX_ENDING (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) HELIX_PROPENSITY (class in schrodinger.protein.residue) helix_propensity (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) HELIX_STARTING (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) HELIX_TERMINATION_TENDENCY (class in schrodinger.protein.residue) helix_termination_tendency (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) helmholtz_free_energy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) help() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.matsci.mswidgets.SolventDialog method) HELP_TOPIC (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) HelpLabel (class in schrodinger.application.desmond.fep_gui) helpNC() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) helpPressed() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) helpRequested() (schrodinger.infra.phase.PhpOptionsParser method) hex() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) Hex_pairs (schrodinger.application.glide.xpdes.TermKeywords attribute) Hex_sp (schrodinger.application.glide.xpdes.TermKeywords attribute) hex_string (schrodinger.structutils.color.Color attribute) (schrodinger.surface.Surface.Color attribute) HEXAGONAL_NAME (schrodinger.application.matsci.nano.xtal.CrystalSystems attribute) HFExcitedStateWidget (class in schrodinger.application.jaguar.gui.theory_tab_widgets) HIDDEN (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) hide() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.gridbox.GridBox method) (schrodinger.maestro.markers.Marker method) (schrodinger.surface.Surface method) hide_object() (in module schrodinger.maestro.maestro) hide_phase_hover_markers() (in module schrodinger.application.phase.phase_markers) hide_workspace_phase_markers() (in module schrodinger.application.phase.phase_markers) hideAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hideAllFeaturesForEntry() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hideColumns() (schrodinger.application.livedesign.panel_components.ExportTableView method) hideCoreImportWidgets() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) hideDialog() (schrodinger.application.desmond.gui.AdvOptionsFrame method) hideEvent() (schrodinger.application.matsci.sliceplot.SlicePlot method) hideFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) hideLabels() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) hideScheme() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) hideSlab() (schrodinger.application.matsci.sliceplot.SlicePlot method) highlightAtom() (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.application.matsci.reordergui.StructurePic method) highlightCompAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) highlightMapPair() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) highlightRefAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) HighSymmetryKPath (class in schrodinger.application.matsci.espresso.utils) hijackPos() (schrodinger.application.desmond.packages.traj.Frame method) histogram (schrodinger.analysis.enrichment.StatisticalSummary attribute) HOH_angle (schrodinger.protein.assignment.ProtAssign.changeable attribute) HOME (schrodinger.application.desmond.envir.CONST attribute) home_atom (schrodinger.application.matsci.clusterstruct.Neighbor attribute) homo() (in module schrodinger.application.jaguar.textparser) homo_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) HoneycombBilayers (class in schrodinger.application.matsci.nano.sheet) HoneycombCell (class in schrodinger.application.matsci.nano.sheet) HoneycombLattice (class in schrodinger.application.matsci.nano.sheet) HoneycombUnitCell (class in schrodinger.application.matsci.nano.sheet) HorizontalBar (class in schrodinger.application.desmond.fep_gui) (class in schrodinger.application.desmond.gui) Host (class in schrodinger.job.jobcontrol) host (schrodinger.application.licensing.lmgrd_log_parser.event attribute) (schrodinger.job.jobcontrol.Host attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) (schrodinger.tasks.jobtasks.JobOptions attribute) host_check() (in module schrodinger.job.host_check) host_is_local() (in module schrodinger.utils.licutils) host_list_to_str() (in module schrodinger.job.jobcontrol) host_str_to_list() (in module schrodinger.job.jobcontrol) host_text (schrodinger.tasks.jobtasks.JobConfig attribute) host_textChanged (schrodinger.tasks.jobtasks.JobConfig attribute) hostChanged (schrodinger.tasks.jobtasks.JobConfig attribute) (schrodinger.tasks.jobtasks.JobOptions attribute) hostfile_is_empty() (in module schrodinger.job.jobcontrol) hostfile_is_valid() (in module schrodinger.job.jobcontrol) hostid_is_local() (in module schrodinger.application.licensing.licadmin) hostid_order() (in module schrodinger.application.licensing.flexlm) hostname() (schrodinger.application.licensing.flexlm.Server method) hostname_in_registry() (in module schrodinger.utils.sshconfig) hostname_is_local() (in module schrodinger.application.licensing.licadmin) hostport() (schrodinger.application.licensing.flexlm.Server method) hover_callback_add() (in module schrodinger.maestro.maestro) hover_callback_remove() (in module schrodinger.maestro.maestro) hoverMoveEvent() (schrodinger.application.matsci.reordergui.StructurePic method) html_embed_image() (in module schrodinger.application.desmond.util) HTTPClient (class in schrodinger.application.glide.http_client) hunt() (in module schrodinger.job.hunt_stub) (in module schrodinger.job.util) hybrid (schrodinger.application.matsci.espresso.qeinput.DftType attribute) hybridization() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method) HybridType (class in schrodinger.application.matsci.espresso.qeinput) Hydrogen (class in schrodinger.utils.sea) HYDROGEN_BOND_ACCEPTOR (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROGEN_BOND_DONOR (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROGEN_BOND_ORDER (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule attribute) hydrogen_neighbors() (in module schrodinger.application.prepwizard) HYDROGEN_SYM (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule attribute) HydrogenBondFinder (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.application.desmond.packages.msys) HydrogenCap (class in schrodinger.application.qsite.input) hydrogens_present() (in module schrodinger.structutils.analyze) hydrophilicity (schrodinger.protein.residue.Residue attribute) hydrophobic (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute) HYDROPHOBIC_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROPHOBIC_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HYDROPHOBIC_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) HydrophobicConstraint (class in schrodinger.application.glide.glide) HydrophobicInter (class in schrodinger.application.desmond.packages.analysis) hydrophobicity (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) hydrophobicity_window_padding (schrodinger.protein.sequence.ProteinSequence attribute) HypothesesListWidget (class in schrodinger.application.phase.phase_widgets) hypothesisChanged (schrodinger.application.phase.pt_hypothesis.PhaseHypothesisMonitor attribute) HypothesisModel (class in schrodinger.application.phase.phase_widgets) HypothesisRow (class in schrodinger.application.phase.phase_widgets)

I

i1 (schrodinger.infra.phase.PhpFastShapePair attribute) i2 (schrodinger.infra.phase.PhpFastShapePair attribute) Icons (class in schrodinger.maestro.markers) icons (schrodinger.application.matsci.mswidgets.StageFrame attribute) Icosahedron (class in schrodinger.application.matsci.shapes) (class in schrodinger.graphics3d.polyhedron) id (schrodinger.application.desmond.packages.msys.Handle attribute) (schrodinger.application.desmond.packages.msys.Param attribute) (schrodinger.application.desmond.packages.msys.Term attribute) (schrodinger.application.desmond.packages.traj.Source attribute) ID (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) id() (schrodinger.application.desmond.fep_struc.Struc method) ID_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) ident() (schrodinger.application.licensing.licadmin.LicenseResource method) identifier (schrodinger.analysis.enrichment.StatisticalSummary attribute) identify_all_hbonders() (schrodinger.protein.assignment.ProtAssign method) identify_species() (schrodinger.protein.assignment.ProtAssign method) identifyGroups() (schrodinger.structutils.assignbondorders.AssignBondOrders method) IdentityDict (class in schrodinger.utils.scollections) ids (schrodinger.application.desmond.packages.msys.atomsel.Atomsel attribute) If (class in schrodinger.application.desmond.enhsamp) if_() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) ifstream (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) IGNORE (schrodinger.application.desmond.constants.EXISTING_RESTRAINT attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) ignore_cleanup_window() (in module schrodinger.application.livedesign.export_controller) ignore_project_close() (in module schrodinger.maestro.maestro) ignore_project_update() (in module schrodinger.maestro.maestro) ignore_workspace_changed() (in module schrodinger.maestro.maestro) ignoreCheckboxChanged() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) IgnoreProjectClose (class in schrodinger.maestro.maestro) IgnoreProjectUpdate (class in schrodinger.maestro.maestro) IgnoreWorkspaceChanged (class in schrodinger.maestro.maestro) IMAG_TOL (schrodinger.application.matsci.mecp_mod.BFGS attribute) IMAGE_FILE (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) ImageGenerator (class in schrodinger.application.desmond.image_generator) IMAGGLASS (schrodinger.maestro.markers.Icons attribute) IMGT (schrodinger.protein.annotation.AntibodyCDRScheme attribute) IMINO_ACID (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) import3DColumns() (schrodinger.application.livedesign.import_controller.ImportController method) import_canvas() (in module schrodinger.application.canvas.r_group) import_module_from_file() (in module schrodinger.utils.imputils) import_pt_entries() (in module schrodinger.application.desmond.feputils) import_pv_file() (in module schrodinger.application.desmond.feputils) IMPORT_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) importActivities() (schrodinger.infra.phase.PhpQSAR method) importCombLibSelectFile() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) importConstraints() (schrodinger.infra.phase.PhpSiteConstrainer method) ImportController (class in schrodinger.application.livedesign.import_controller) ImportExportBasePanel (class in schrodinger.application.livedesign.ld_base_classes) ImportExportThreadRunner (class in schrodinger.application.livedesign.ld_base_classes) importFilterFile() (schrodinger.ui.ligfilter.LigfilterFrame method) importFragmentCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) importFromAnyFile() (schrodinger.infra.phase.PhpExclVol method) importFromFile() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) (schrodinger.infra.phase.PhpDeltaHypo method) (schrodinger.infra.phase.PhpExclVol method) (schrodinger.infra.phase.PhpFeatureData method) (schrodinger.infra.phase.PhpFeatureRules method) (schrodinger.infra.phase.PhpSiteMask method) importFromFilePaths() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromMaestro() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromMMTableFile() (schrodinger.infra.phase.PhpExclVol method) importFromPDB() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromProjectTable() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importFromStream() (schrodinger.infra.phase.PhpDeltaHypo method) (schrodinger.infra.phase.PhpExclVol method) (schrodinger.infra.phase.PhpFeatureData method) (schrodinger.infra.phase.PhpFeatureRules method) (schrodinger.infra.phase.PhpSiteMask method) importFromWorkspace() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) importLA() (in module schrodinger.trajectory.prody.ensemble) importModel() (schrodinger.infra.phase.PhpQSAR method) importMolecules() (schrodinger.infra.phase.PhpQSAR method) importMoleculesAndActivities() (schrodinger.infra.phase.PhpQSAR method) importName() (in module schrodinger.pipeline.pipeline) importPalette() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) importPharm() (schrodinger.infra.phase.PhpQSAR method) importRegion() (schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate method) importStructure() (schrodinger.project.Project method) importStructureFile() (schrodinger.project.Project method) importTabularData() (schrodinger.application.livedesign.import_controller.ImportController method) ImportThreadRunner (class in schrodinger.application.livedesign.ld_import) ImportToolBar (class in schrodinger.application.bioluminate.ssv.toolbars) ImportWidget (class in schrodinger.application.bioluminate.bwidgets) importWorkspace() (schrodinger.application.matsci.builderwidgets.SketcherBox method) impose_molecules_on_structure() (in module schrodinger.application.jaguar.autots_rmsd) improper_dihedral_iterator() (in module schrodinger.structutils.analyze) in_dev_env() (in module schrodinger) IN_FP_EXT (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) in_workspace (schrodinger.project.ProjectRow attribute) InBounds() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) InChI (class in schrodinger.application.desmond.packages.msys) include() (schrodinger.ui.ligfilter.AddDefinitionDialog method) INCLUDE_USE_CONSISTENT_ORBITALS_CB (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals attribute) included (schrodinger.application.jaguar.gui.input_tab_widgets.UseFrom attribute) (schrodinger.project.EntrySurface attribute) included_rows (schrodinger.project.EntryGroup attribute) (schrodinger.project.Project attribute) includeOnly() (schrodinger.project.ProjectRow method) includeRows() (schrodinger.project.Project method) includes() (schrodinger.utils.ligfilter.Definition method) Inclusion (class in schrodinger.protein.sequence) INCLUSION (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) IncompatibleLicenseError IncompleteExtraOptionsError IncompleteOutput inContext() (schrodinger.application.desmond.antlr3.tree.TreeParser method) incorporation (schrodinger.tasks.jobtasks.JobOptions attribute) incorporationChanged (schrodinger.tasks.jobtasks.JobOptions attribute) incr() (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) INCREMENT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) increment_state_of_changeable() (schrodinger.protein.assignment.ProtAssign method) incrementTorsionValue() (schrodinger.application.matsci.amorphous.TorsionAngler method) INDENT (schrodinger.application.matsci.desmondutils.MSJStringer attribute) index (schrodinger.application.desmond.fep_scholar_util.MetaAtom attribute) (schrodinger.project.ProjectRow attribute) (schrodinger.structure._StructureAtom attribute) index() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.infra.util.OneIndexedList method) (schrodinger.protein.sequence.Sequence method) index_in_current_file (schrodinger.structure.MultiFileStructureReader attribute) index_of_flag_in_args() (in module schrodinger.application.mopac.mopac_parser) INDEX_PATTERN (schrodinger.utils.sea.Map attribute) INDEX_PATTERN2 (schrodinger.utils.sea.Map attribute) indexChanged() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) IndexedFileLoader (class in schrodinger.application.desmond.packages.msys) indexes (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) INDICES (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) indices (schrodinger.protein.alignment.ResidueSelection attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) indicies_from_bonds_deep() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) IndividualStructureBase (class in schrodinger.application.livedesign.maestro_data_types) InfAutofill (class in schrodinger.application.desmond.util) info() (in module schrodinger.application.desmond.packages.cui) (in module schrodinger.maestro.maestro) (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) (schrodinger.pipeline.stage.Stage method) (schrodinger.tasks.runners.AbstractTaskReporter method) (schrodinger.tasks.runners.CmdlineTaskReporter method) (schrodinger.tasks.runners.PanelTaskReporter method) (schrodinger.tasks.runners.TaskRunner method) infoUpdated (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel attribute) InfraReader (class in schrodinger.structure) Init (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom.NextGeomFrom attribute) init() (in module schrodinger.protein.remediate) (schrodinger.application.bioluminate.interaction_calculator.Interactions class method) (schrodinger.application.bioluminate.interaction_calculator.ResTuple class method) init_bennett() (in module schrodinger.application.desmond.fepana) init_count (schrodinger.job.queue.BaseJob attribute) (schrodinger.job.queue.SubprocessJob attribute) init_ff() (schrodinger.application.desmond.torsion_related.TorsionPotential method) init_random_seed() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) init_report() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) initActionStates() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) initColor() (schrodinger.utils.colorscheme.MM_ColormapGL method) initFinalize() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) initial (schrodinger.application.jaguar.scan.Scan attribute) INITIAL_GUESS_OPTS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) INITIAL_HESSIAN (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) initial_tokens() (in module schrodinger.application.licensing.lmgrd_log_parser) initialize() (in module schrodinger.structutils.minimize) (schrodinger.application.jaguar.mmjag.MmJag static method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.infra.mmbitset.Bitset static method) (schrodinger.infra.mminit.Initializer method) (schrodinger.infra.mmlist.mmlist static method) (schrodinger.infra.table.Table static method) (schrodinger.project.Project static method) (schrodinger.structutils.minimize.Minimizer static method) initialize_atom_types() (schrodinger.application.jaguar.structure_isomorphism.AutoTSAtomMapper method) (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) initialize_score_storage() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) initializeGA() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization method) initializeGenome() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization method) initializeGrowers() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) initializeMmlibs() (schrodinger.application.ligprep.ionizer.Ionizer method) initializeProgram() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) Initializer (class in schrodinger.infra.mminit) initialSolution() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) Initiator (class in schrodinger.application.matsci.amorphous) initLayOut() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) (schrodinger.models.mappers.MapperMixin method) initMaestroWriter() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) initMMlibs() (in module schrodinger.infra.phase) initSetDefaults() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) (schrodinger.models.mappers.MapperMixin method) initSetOptions() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) initSetUp() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) INPLACE_PROPERTY (schrodinger.structutils.sitealign.SiteMatchLookup attribute) input (schrodinger.tasks.tasks_.AbstractTask attribute) input_namelists (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter attribute) INPUT_SUB_TABS (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) inputChanged (schrodinger.tasks.tasks_.AbstractTask attribute) InputConfig (class in schrodinger.application.inputconfig) inputconfig_subset() (in module schrodinger.application.phase.input) InputEntriesColumns (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesColumnsHB (class in schrodinger.application.jaguar.gui.input_tab_widgets_hb) InputEntriesColumnsPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesModel (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesModelHB (class in schrodinger.application.jaguar.gui.input_tab_widgets_hb) InputEntriesModelPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputEntriesProxyModel (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesView (class in schrodinger.application.jaguar.gui.input_tab_widgets) InputEntriesViewPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) InputError InputFiles (schrodinger.job.jobcontrol.Job attribute) InputGroup (class in schrodinger.application.desmond.gui) InputMultiplicityMixin (class in schrodinger.application.jaguar.gui.base_panel) InputOrder (schrodinger.structutils.interactions.salt_bridge.OrderBy attribute) inputsForStagesDefined() (schrodinger.pipeline.pipeline.Pipeline method) InputSpecs (class in schrodinger.application.phase.input) InputStream (in module schrodinger.application.desmond.antlr3.streams) InputTab (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabBase (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabHB (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabJobMixin (class in schrodinger.application.jaguar.gui.base_panel) InputTabMixin (class in schrodinger.application.jaguar.gui.base_panel) InputTabPka (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputTabWithSubTabs (class in schrodinger.application.jaguar.gui.tabs.input_tab) InputType (class in schrodinger.application.matsci.espresso.qeinput) inRing() (schrodinger.structure.Structure method) inscode (schrodinger.application.qsite.input.Cut attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) (schrodinger.structure._Residue attribute) (schrodinger.structure._StructureAtom attribute) insert() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.infra.phase.PhpSortCapperDoubleDecreasing method) (schrodinger.infra.phase.PhpSortCapperDoubleIncreasing method) (schrodinger.infra.util.OneIndexedList method) (schrodinger.protein.sequence.Sequence method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.sea.List method) insertAfter() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) insertBefore() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) InsertBeforeOp (class in schrodinger.application.desmond.antlr3.streams) insertColumn() (schrodinger.infra.table.Table method) insertion (schrodinger.application.desmond.packages.msys.Residue attribute) InsertionError insertRow() (schrodinger.infra.table.Table method) insertStructuresIntoDB() (schrodinger.structutils.shuffle.Shuffler method) insertSubalignment() (schrodinger.protein.alignment.BaseAlignment method) inside_cell() (in module schrodinger.application.matsci.nano.xtal) insideFace() (schrodinger.application.matsci.shapes.Face method) insideRectangle() (schrodinger.application.matsci.nano.tube.Rectangle method) INSIDETHRESH (schrodinger.application.matsci.nano.tube.Rectangle attribute) install_license() (in module schrodinger.application.licensing.licadmin) install_license_text() (in module schrodinger.application.licensing.licadmin) install_netsuite_license() (in module schrodinger.application.licensing.licadmin) install_remote_pubkey() (in module schrodinger.utils.sshconfig) install_schrod_plist() (in module schrodinger.application.licensing.licadmin) installed_pathname() (in module schrodinger.application.licensing.licadmin) instance() (schrodinger.utils.colorscheme.ColorSchemeManager static method) (schrodinger.utils.colorscheme.MM_ColorRampHolder static method) INT_SIZE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) IntegrationTab (class in schrodinger.application.desmond.gui) INTENSITY_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) INTENSITY_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) InteractingResidue (class in schrodinger.application.bioluminate.interaction_calculator) INTERACTION_NAMES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) InteractionCalculator (class in schrodinger.application.bioluminate.interaction_calculator) InteractionCalculatorError InteractionEnergy (class in schrodinger.application.desmond.packages.energygroup) InteractionEnumerationPanel (class in schrodinger.application.combiglide.combenumdock) InteractionParams (class in schrodinger.application.bioluminate.interaction_calculator) InteractionReader (class in schrodinger.application.prime.residue_interaction) Interactions (class in schrodinger.application.bioluminate.interaction_calculator) interactionSummary() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) InteractionTab (class in schrodinger.application.desmond.gui) Interface (class in schrodinger.application.matsci.nano.interface_mod) Interfaces (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) INTERNAL (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) internal_energy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) InternalCoords (class in schrodinger.application.matsci.rxn_path) Internals (class in schrodinger.application.matsci.coarsegrain) interpolateReactionCoords() (schrodinger.application.matsci.rxn_path.ReactionPath method) INTERPOLATIONCHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) intersectSegmentAndPlane() (schrodinger.application.matsci.shapes.Face method) interval (schrodinger.application.desmond.packages.energygroup.SliceParams attribute)

INTERVAL (schrodinger.application.matsci.desmondutils.MSJStringer attribute) IntParam (class in schrodinger.models.parameters) IntStream (class in schrodinger.application.desmond.antlr3.streams) intvector (class in schrodinger.infra.fast3d) inv_box (schrodinger.application.desmond.packages.analysis.Pbc attribute) invalid_code() (in module schrodinger.protein.getpdb_utility) INVALID_MAP_NAME_MSG (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) invalidateWindowHydrophobicity() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) invalidateWindowIsoelectricPoint() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) InvalidCDFTError InvalidInput InvalidProjectException InvalidProjectVersion InvalidStageFileError invariant_map (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter attribute) inverse() (schrodinger.analysis.reaction.Reaction method) (schrodinger.application.matsci.qexsd.qespresso.utils.mapping.BiunivocalMap method) invert_reaction_smarts() (in module schrodinger.analysis.reaction) invertNitrogens() (schrodinger.infra.fast3d.Engine method) invoke_picking_loss_callback() (in module schrodinger.maestro.maestro) inWorkspace() (schrodinger.project.ProjectRow method) ion_action (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) ION_DYNAMICS_KEY (schrodinger.application.matsci.espresso.qeinput.IonControlType attribute) IonControlType (class in schrodinger.application.matsci.espresso.qeinput) ionizeCommandParser() (schrodinger.application.ligprep.ionizer.Ionizer method) Ionizer (class in schrodinger.application.ligprep.ionizer) ionizeStructure() (schrodinger.application.ligprep.ionizer.Ionizer method) ip_default (schrodinger.application.jaguar.results.JaguarOptions attribute) ir_intensity_precision (schrodinger.application.jaguar.results.NormalMode attribute) iradius (schrodinger.application.matsci.elementalprops.ElementalProperties attribute) irc_point() (in module schrodinger.application.jaguar.textparser) irc_step (schrodinger.application.jaguar.output.JaguarOutput attribute) irc_summary() (in module schrodinger.application.jaguar.textparser) IRCEndpointError IRCFailure IrcTab (class in schrodinger.application.jaguar.gui.tabs.irc_tab) IRCVettingFailure is3d() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) is_aacg_cms_file() (in module schrodinger.application.aacg.utils) is_aacg_ffio_struct() (in module schrodinger.application.aacg.utils) is_abstract (schrodinger.models.parameters.Param attribute) is_abstract_param() (in module schrodinger.models.parameters) is_alchemical() (in module schrodinger.application.desmond.restraint) is_another_best_config() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) is_atom_list() (in module schrodinger.utils.sea) is_bond_rotatable() (in module schrodinger.structutils.analyze) is_bs_spectrum_file_key() (in module schrodinger.application.matsci.bandshape_utils) is_builtin_fragment() (in module schrodinger.utils.cgxutils) is_chiral_atom() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) is_cms_file() (in module schrodinger.utils.fileutils) is_coarse_grain() (in module schrodinger.application.matsci.coarsegrain) is_concat() (in module schrodinger.application.desmond.config) is_connected_subgraph() (in module schrodinger.infra.phase) is_counted() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.License method) is_covalent() (in module schrodinger.application.desmond.starter.generator.fep_plus) is_covalently_bound (schrodinger.structutils.analyze.Ligand attribute) is_csv_file() (in module schrodinger.utils.fileutils) is_datetime() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) is_docking_keyword() (in module schrodinger.application.glide.glide) is_equal() (in module schrodinger.utils.sea) is_equivalent_to_mininplace() (in module schrodinger.application.glide.glide) is_expired() (schrodinger.application.licensing.flexlm.LicenseLine method) is_false() (in module schrodinger.application.glide.glide) is_fep() (in module schrodinger.application.desmond.config) is_from_atom() (schrodinger.application.canvas.r_group.TempAtom method) is_function_registered() (in module schrodinger.maestro.maestro) is_gap (schrodinger.protein.residue.AbstractSequenceElement attribute) (schrodinger.protein.residue.Gap attribute) is_gap() (in module schrodinger.protein.residue) is_gcmc() (in module schrodinger.application.desmond.config) is_gridgen_job() (in module schrodinger.application.glide.glide) is_gridgen_keyword() (in module schrodinger.application.glide.glide) is_gzipped_structure_file() (in module schrodinger.utils.fileutils) is_halogen (schrodinger.structure._StructureAtom attribute) is_harmonic_angle() (in module schrodinger.application.matsci.coarsegrain) is_hypothesis_entry() (in module schrodinger.application.phase.pt_hypothesis) is_hypothesis_file() (in module schrodinger.utils.fileutils) is_infinite() (in module schrodinger.application.matsci.nano.xtal) is_inter_sequence (schrodinger.protein.residue.DisulfideBond attribute) is_intra_sequence (schrodinger.protein.residue.DisulfideBond attribute) is_ipv4_addr() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.utils.licutils) is_leaf() (schrodinger.application.desmond.reorder_atom.Node method) is_lennard_jones() (in module schrodinger.application.matsci.coarsegrain) is_library() (schrodinger.application.licensing.flexlm.License method) is_license_available() (in module schrodinger.utils.license) is_like_lennard_jones() (in module schrodinger.application.matsci.cgforcefield) is_list() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method) is_local_server() (schrodinger.application.licensing.licadmin.LicenseResource method) is_maestro_elements() (in module schrodinger.maestro.maestro) is_maestro_file() (in module schrodinger.utils.fileutils) is_martini_antifreeze_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_charge_type() (in module schrodinger.application.matsci.coarsegrain) is_martini_ring_type() (in module schrodinger.application.matsci.coarsegrain) is_meta() (in module schrodinger.application.desmond.config) is_metal() (in module schrodinger.application.prime.primefix) is_minimize() (in module schrodinger.application.desmond.config) is_mopac_file() (in module schrodinger.application.mopac.utils) is_nodelocked() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Server method) is_not_gap() (in module schrodinger.protein.residue) is_ompi_allowed() (in module schrodinger.application.matsci.jaguarworkflows) is_open() (schrodinger.application.licensing.flexlm.License method) (schrodinger.infra.mmgpgpu.ifstream method) (schrodinger.infra.mmgpgpu.ofstream method) (schrodinger.infra.mmjob.ifstream method) (schrodinger.infra.mmjob.ofstream method) (schrodinger.infra.mmsurf.ifstream method) (schrodinger.infra.mmsurf.ofstream method) (schrodinger.utils.colorscheme.ifstream method) (schrodinger.utils.colorscheme.ofstream method) is_opls2005_model() (in module schrodinger.application.matsci.desmondutils) is_opls2_available() (in module schrodinger.utils.license) is_opls3_model() (in module schrodinger.application.matsci.desmondutils) is_optional() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement method) is_P1() (in module schrodinger.application.matsci.nano.xtal) is_parent() (in module schrodinger.application.desmond.util) is_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) is_permanent() (schrodinger.application.licensing.flexlm.Feature method) is_permanent_counted() (schrodinger.application.licensing.flexlm.License method) is_permanent_library() (schrodinger.application.licensing.flexlm.License method) is_permanent_nodelocked() (schrodinger.application.licensing.flexlm.License method) is_phase_database() (in module schrodinger.infra.phase) is_phdb_path() (in module schrodinger.application.hitexpander) is_poseviewer_file() (in module schrodinger.utils.fileutils) is_position_restraint() (in module schrodinger.application.desmond.restraint) is_powerof2() (in module schrodinger.application.desmond.util) (in module schrodinger.utils.sea) is_prepped() (in module schrodinger.application.desmond.feputils) is_projected (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) is_pv_file() (in module schrodinger.application.glide.poseviewconvert) is_reagent_file() (in module schrodinger.analysis.reaction) is_remd() (in module schrodinger.application.desmond.config) is_repulsive_harmonic() (in module schrodinger.application.matsci.coarsegrain) is_ring_atom() (in module schrodinger.application.desmond.r_group_asl) is_ring_open_or_closed() (in module schrodinger.application.desmond.fep_mapping) is_root() (schrodinger.application.desmond.reorder_atom.Node method) is_rotabond() (in module schrodinger.application.desmond.r_group_asl) is_same() (schrodinger.application.desmond.cms.Restrain method) is_sd_file() (in module schrodinger.utils.fileutils) is_selected (schrodinger.project.ProjectRow attribute) is_server() (in module schrodinger.application.licensing.flexlm) (schrodinger.application.licensing.licadmin.LicenseResource method) is_shifted_lennard_jones() (in module schrodinger.application.matsci.coarsegrain) is_shown() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) is_shown_only() (schrodinger.application.desmond.maestro.NewEntryGroup method) is_signed() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) is_small_struc() (in module schrodinger.application.desmond.packages.analysis) is_smarts_bonding_pair() (in module schrodinger.application.matsci.smartsutils) is_smiles_file() (in module schrodinger.utils.fileutils) is_stub() (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.licensing.licadmin.LicenseResource method) is_subdir() (in module schrodinger.application.desmond.util) is_triclinic_box() (in module schrodinger.application.desmond.config) is_trigonometric_angle() (in module schrodinger.application.matsci.coarsegrain) is_valid_epv_file() (in module schrodinger.application.glide.utils) is_valid_hostip() (in module schrodinger.job.jobcontrol) is_valid_hostname() (in module schrodinger.job.jobcontrol) is_valid_jobname() (in module schrodinger.utils.fileutils) is_valid_pv_file() (in module schrodinger.application.glide.utils) is_vrun() (in module schrodinger.application.desmond.config) is_water() (in module schrodinger.application.desmond.remd) isAcceptableEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) isAccepted() (schrodinger.application.matsci.montecarlo.Metropolizer method) isAntibodyChain() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) isAromatic() (schrodinger.structure._Ring method) isAtomAromatic() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomBetweenTwoRings() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomBoundToAromaticRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomInRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isAtomInSmallRing() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isBandshapeTable() (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile static method) isBondRingEdge() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isBrancher() (schrodinger.application.matsci.amorphous.Monomer method) isClassProperty() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property method) isColorSchemeChanged() (schrodinger.utils.colorscheme.ColorSchemeManager method) isColumnFixed() (schrodinger.project.Project method) IsCompatible() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) isComplete() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobDJ method) isConformationalSearchesChecked() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) isConnectedToResidue() (schrodinger.structure._Residue method) isCPUHost() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) isCustomColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) isCustomMaestroAssay() (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) isDefault() (schrodinger.models.parameters.CompoundParam method) isDefined() (schrodinger.protein.membrane.Membrane_Model method) isDistance() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) isDynamic() (schrodinger.application.desmond.packages.staf.GeomAnalyzerBase method) isDynamicRGBColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) iselement() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) isEnergy() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) isEOF() (schrodinger.infra.structure.PyStructureReaderException method) isEquivalent() (schrodinger.application.jaguar.input.GenOptions method) (schrodinger.structure.Structure method) isFastMode() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) isFilled() (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.PipeIO method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) isFragmentLibraryFile() (schrodinger.infra.fast3d.Engine static method) isGoodDim() (schrodinger.application.matsci.espresso.utils.MemoryEstimator method) isGPUHost() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) isGroupShown() (schrodinger.graphics3d.common.Primitive method) isHeteroaromatic() (schrodinger.structure._Ring method) isInfiniteModel() (schrodinger.application.desmond.gui.InputGroup method) isInGuessMode() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) isInside() (schrodinger.application.matsci.nano.particle.Nanoparticle method) isInVector() (in module schrodinger.infra.phase) isItemChecked() (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) isItemEnabled() (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) isKetoneCarbon() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isKeyConsistentWithPanel() (schrodinger.application.desmond.gui.GuiApp method) isLst() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) isMember() (schrodinger.application.matsci.clusterstruct.SpeciesData method) isMetal() (schrodinger.application.matsci.espresso.qeoutput.BandStructure method) isNanValue() (in module schrodinger.infra.phase) isNil() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) isNonDefault() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword method) isoelectric_point (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) isoelectric_point_window_padding (schrodinger.protein.sequence.ProteinSequence attribute) isoelectronic_mutator() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) ISOLATE_PRODUCTS (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) isolateProducts() (schrodinger.application.matsci.rxn_channel.rxn_channel.Products method) IsomerError isomeric_atom_lists() (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) isomorph() (in module schrodinger.application.desmond.packages.viparr1.viparr.isomorph) isOnlySingleBonded() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isotope (schrodinger.structure._StructureAtom attribute) isovalue (schrodinger.surface.Surface attribute) isPlaceholderItemSelected() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) isPointInBox() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isPointInHull() (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isPolymer() (schrodinger.application.matsci.amorphous.PolymerToFragments method) isPopulated() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) isQueue() (schrodinger.job.jobcontrol.Host method) isQueued() (schrodinger.job.jobcontrol.Job method) isReady() (schrodinger.application.glide.http_client.GlideServerManager method) isReferenceSeq() (schrodinger.protein.alignment.BaseAlignment method) isRingAromatic() (schrodinger.structutils.assignbondorders.AssignBondOrders method) isRowSelected() (schrodinger.infra.table.Table method) isRunning() (schrodinger.application.desmond.feputils.ProteinProcessManager method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) (schrodinger.tasks.jobtasks.AbstractJobTask method) (schrodinger.tasks.runners.TaskRunner method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.tasks.tasks.BlockingFunctionTask method) (schrodinger.tasks.tasks.ThreadFunctionTask method) isSchemeNameInUse() (schrodinger.utils.colorscheme.ColorSchemeManager method) isScriptProperty() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property method) isShown() (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.gridbox.GridBox method) isSolventModelUsed() (schrodinger.application.matsci.mswidgets.CompactSolventSelector method) isStandardColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) isStandardResidue() (schrodinger.structure._Residue method) isStartingMaterial() (schrodinger.analysis.reaction.RouteNode method) isStored() (schrodinger.infra.phase.PhpDatabaseFp method) isStructureProperty() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property method) isSubColorSchemeName() (schrodinger.utils.colorscheme.ColorSchemeManager method) issued_str() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) istream (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) isUseConsistentOrbitalsChecked() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals method) isValid() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.protein.residue.DisulfideBond method) (schrodinger.protein.sequence.ProteinSequence class method) (schrodinger.protein.sequence.Sequence class method) (schrodinger.utils.license.License method) isValidArchiveName() (schrodinger.infra.phase.PhpProject method) isValidAtomIndex() (schrodinger.application.matsci.reordergui.StructureFrame method) isValidIndex() (schrodinger.utils.colorscheme.MM_Colormap method) isValidPoint() (schrodinger.application.matsci.amorphous.Box method) (schrodinger.application.matsci.amorphous.BoxWithInnerHull method) isValidProjectName() (schrodinger.infra.phase.PhpProject method) isVisible() (schrodinger.application.matsci.chargegui.ChargePropertySelector method) isWithinCutoff() (schrodinger.application.desmond.packages.analysis.Pbc method) isZwitterionChecked() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) ItemRow (class in schrodinger.application.matsci.builderwidgets) ItemRowWithTemplates (class in schrodinger.application.matsci.builderwidgets) items() (schrodinger.utils.mmutil.StringStringMap method) (schrodinger.utils.scollections.IdentityDict method) itemSelected (schrodinger.application.livedesign.panel_components.LDSelectionTreeView attribute) itemSelected() (schrodinger.application.matsci.reordergui.StructureListWidget method) Iter (class in schrodinger.application.desmond.enhsamp) iter() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) iter_fingerprints() (schrodinger.utils.multifpfile.MultiFPFile method) iterate_to_convergence() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) iterateNeighboringAtoms() (schrodinger.structutils.measure.DistanceCellIterator method) iterateResidues() (schrodinger.application.bioluminate.reactive_residues.ReactiveResidues method) iterateRows() (schrodinger.application.desmond.fep_gui.ResiduesModel method) IterationError iterator() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) iterInputs() (schrodinger.pipeline.stage.Stage method) iteritems() (schrodinger.utils.cgxutils.FragmentLibrary method) (schrodinger.utils.mmutil.StringStringMap method) iterkeys() (schrodinger.utils.mmutil.StringStringMap method) iterNeighbors() (schrodinger.protein.sequence.Sequence method) iterpose() (schrodinger.trajectory.prody.ensemble.Ensemble method) iterResidues() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) itervalues() (schrodinger.utils.mmutil.StringStringMap method)

J

jagInputEdited() (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) jaguar_atoms() (in module schrodinger.application.qsite.output) jaguar_input_keywords() (in module schrodinger.application.jaguar.jaguar_keyword_utils) jaguar_keywords_xml_filename() (in module schrodinger.application.jaguar.jaguar_keyword_utils) JaguarAtomicResults (class in schrodinger.application.jaguar.results) JaguarConfigError JaguarError JaguarFailedException JaguarInput (class in schrodinger.application.jaguar.input) JaguarIOError JaguarJob (class in schrodinger.application.matsci.mecp_mod) JaguarJobs (class in schrodinger.application.matsci.mecp_mod) JaguarKeywordConflict JaguarKeywordError JaguarKeywordException JaguarKeywordFormatError JaguarKeywordValueError JaguarKeywordValueTypeError JaguarOptions (class in schrodinger.application.jaguar.results) JaguarOutput (class in schrodinger.application.jaguar.output) JaguarParseError JaguarResults (class in schrodinger.application.jaguar.results) JaguarRuntimeError JaguarSettingError JaguarSettingWarning JaguarUnsupportedBasisSet JaguarUserFacingException jar (schrodinger.application.desmond.picklejar.PickleJar attribute) jbw() (schrodinger.application.macromodel.utils.ComUtil method) jbw_sd() (schrodinger.application.macromodel.utils.ComUtil method) jc_backend_reg_output() (in module schrodinger.application.desmond.packages.cui) jc_reg_input() (in module schrodinger.application.desmond.packages.cui) jc_reg_output() (in module schrodinger.application.desmond.packages.cui) JMSStep (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) JMSWorkFlow (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) Job (class in schrodinger.job.jobcontrol) job_belongs_to_panel() (in module schrodinger.tasks.jobtasks) job_capacity() (in module schrodinger.application.licensing.licadmin) job_capacity_by_product() (in module schrodinger.application.licensing.licadmin) job_config (schrodinger.tasks.jobtasks.AbstractJobTask attribute) job_configChanged (schrodinger.tasks.jobtasks.AbstractJobTask attribute) Job_Details (class in schrodinger.application.desmond.simulation_block_test) job_dir (schrodinger.tasks.jobtasks.AbstractJobTask attribute) job_dirChanged (schrodinger.tasks.jobtasks.AbstractJobTask attribute) job_incorporation_function_add() (in module schrodinger.maestro.maestro)

job_incorporation_function_remove() (in module schrodinger.maestro.maestro) JOB_NAME (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) job_options (schrodinger.tasks.jobtasks.AbstractJobTask attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) job_optionsChanged (schrodinger.tasks.jobtasks.AbstractJobTask attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) job_started() (in module schrodinger.maestro.maestro) job_submitted (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration attribute) JobConfig (class in schrodinger.tasks.jobtasks) JobcontrolException JobControlJob (class in schrodinger.job.queue) JobDJ (class in schrodinger.job.queue) JobDJOptions() (schrodinger.pipeline.stage.Stage method) JobFailure jobid() (in module schrodinger.application.jaguar.textparser) JobLaunchFailure JobLaunchOptions (class in schrodinger.infra.mmjob) jobname (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) JOBNAME (schrodinger.application.matsci.desmondutils.MSJStringer attribute) jobname (schrodinger.application.qsite.input.QSiteInput attribute) (schrodinger.tasks.jobtasks.JobConfig attribute) jobnameArg() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) jobnameChanged (schrodinger.tasks.jobtasks.JobConfig attribute) jobnameData() (schrodinger.application.jaguar.gui.base_panel.AutomaticJobnameMixin method) JobOptions (class in schrodinger.tasks.jobtasks) jobOptions() (schrodinger.tasks.runners.JobTaskRunner method) jobs() (schrodinger.application.licensing.licadmin.LicenseResource method) jobsCount() (schrodinger.job.queue.RunningJobs method) JobSpecification (class in schrodinger.job.launchapi) JobSpecificationArgsBuilder (class in schrodinger.job.launchapi) JobSpecificationBuilder (class in schrodinger.job.launchapi) JobSpecificationKeyError JobStatusLoop (class in schrodinger.tasks.jobtasks) JobTaskRunner (class in schrodinger.tasks.runners) jobUsesTPP() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) join_cont_lines() (in module schrodinger.application.licensing.licadmin) join_structure_files() (in module schrodinger.application.jaguar.output) joinerChanged() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) JsonableClassMixin (class in schrodinger.models.json) jsonData() (schrodinger.application.matsci.freevolume.JsonObject method) JSONDecodeError JSONEncodeError JSONEncoder (class in schrodinger.models.json) JsonObject (class in schrodinger.application.matsci.freevolume)

K

Kabat (schrodinger.protein.annotation.AntibodyCDRScheme attribute) Key (class in schrodinger.utils.sea) key (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) (schrodinger.application.desmond.packages.msys.InChI attribute) (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) key_iterator() (schrodinger.utils.mmutil.StringStringMap method) key_value() (schrodinger.utils.sea.Map method) KEYS (schrodinger.application.matsci.mecp_mod.JaguarJob attribute) keys() (schrodinger.application.desmond.packages.msys.Ct method) (schrodinger.application.desmond.packages.msys.Param method) (schrodinger.application.desmond.packages.msys.PropertyMap method) (schrodinger.application.desmond.packages.msys.Term method) (schrodinger.infra.mmim.MMIMDict method) (schrodinger.infra.table.Table method) (schrodinger.job.jobcontrol.Job method) (schrodinger.structure._StructureAtomProperty method) (schrodinger.structure._StructureBondProperty method) (schrodinger.structure._StructureProperty method) (schrodinger.utils.mmutil.StringStringMap method) (schrodinger.utils.scollections.IdentityDict method) (schrodinger.utils.sea.Map method) keyvalue (schrodinger.application.jaguar.gui.utils.Solvent attribute) Keyword (class in schrodinger.application.jaguar.keywordDB) keyword() (in module schrodinger.application.jaguar.reactiq_keywords)

keyword_coverage() (in module schrodinger.application.jaguar.jaguar_keyword_utils) keyword_dict_to_string() (in module schrodinger.application.matsci.jaguarworkflows) keyword_spec() (in module schrodinger.application.glide.glide) keyword_string_to_dict() (in module schrodinger.application.matsci.jaguarworkflows) keyword_value_pair_is_valid() (in module schrodinger.application.jaguar.validation) keyword_value_pairs_are_valid() (in module schrodinger.application.jaguar.validation) KeywordEdit (class in schrodinger.application.matsci.qualityslider) keywords (schrodinger.application.jaguar.reactiq_input.ReactiqInput attribute) keywordsChanged (schrodinger.application.matsci.mswidgets.SolventDialog attribute) kill() (schrodinger.job.jobcontrol.Job method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.tasks.tasks_.SubprocessCmdTask method) killJobs() (schrodinger.job.queue.JobDJ method) known_hostname() (in module schrodinger.utils.sshconfig) KNOWN_LINES (schrodinger.application.matsci.desmondutils.MSJStringer attribute) KPLS_EXT (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) KPoint (class in schrodinger.application.matsci.espresso.qeoutput) KpointsType (class in schrodinger.application.matsci.espresso.qeinput) KptLegend (class in schrodinger.application.matsci.espresso.qeoutput) KPTS_MESH_KEY (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) KPTS_TYPES (schrodinger.application.matsci.espresso.qeinput.KpointsType attribute) kT (in module schrodinger.protein.analysis) KYTE_DOOLITTLE_SCALE (schrodinger.application.bioluminate.patch_utils.patch_finder.ProteinProperties attribute)

L

L1 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) L2 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) L3 (schrodinger.protein.annotation.AntibodyCDRLabel attribute) l_qn (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) LA() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) label (schrodinger.application.canvas.topo_descriptors.Descriptor attribute) (schrodinger.application.matsci.espresso.qeoutput.KptLegend attribute) (schrodinger.protein.analysis.Report.data_set attribute) (schrodinger.protein.annotation.AntibodyCDR attribute) label_color (schrodinger.structure._StructureAtom attribute) label_format (schrodinger.structure._StructureAtom attribute) label_indexes() (in module schrodinger.application.jaguar.structure_isomorphism) label_pbc_bond() (in module schrodinger.application.matsci.nano.xtal) label_pbc_bonds() (in module schrodinger.application.matsci.nano.xtal) LABEL_TEXT (schrodinger.application.matsci.sliceplot.SlicePlot attribute) label_user_text (schrodinger.structure._StructureAtom attribute) labelAsuAtoms() (schrodinger.application.matsci.nano.xtal.Crystal method) labelAtoms() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) labelChains() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) labelResidues() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) LABELS (schrodinger.application.matsci.qualityslider.QualitySlider attribute) LabelSpinner (class in schrodinger.application.desmond.feputils) labelSymEquivPos() (schrodinger.application.matsci.nano.xtal.Crystal method) lambda_type() (in module schrodinger.application.desmond.config) LARGE_RHO_K (schrodinger.application.matsci.mecp_mod.BFGS attribute) last (schrodinger.application.desmond.packages.energygroup.SliceParams attribute) last_added_entry (schrodinger.project.Project attribute) last_entry_unique_id (schrodinger.application.desmond.maestro.NewEntry attribute) last_issued() (schrodinger.application.licensing.flexlm.License method) last_sequences_imported (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) LatticeFeatures (class in schrodinger.application.matsci.mlearn.features) launch() (in module schrodinger.job.launcher) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.job.launcher.Launcher method) launch_directory (schrodinger.infra.mmjob.JobLaunchOptions attribute) launch_file() (in module schrodinger.application.jaguar.input) launch_from_job_spec() (in module schrodinger.job.jobcontrol) launch_job() (in module schrodinger.job.jobcontrol) launch_local_job() (in module schrodinger.job.launcher) launch_path() (in module schrodinger.application.jaguar.file_logger) launch_pre_analysis() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) launch_protein_reliability() (in module schrodinger.application.desmond.feputils) launch_SID() (schrodinger.application.desmond.replica_sid_generator.FEPReport method) launch_subjobs() (in module schrodinger.application.macromodel.paraUtils) launchBackend() (schrodinger.job.app.App method) Launcher (class in schrodinger.job.launcher) launchFromJobSpec() (schrodinger.application.matsci.guibase.MultiJobApp method) launchJaguarJob() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) LaunchParameters (class in schrodinger.job.launchparams) layOut() (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.matsci.jobdirdlg.NewJobDirDialog method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) (schrodinger.application.matsci.reordergui.ReorderAtomsDialog method) lazy_canvas_import() (in module schrodinger.structutils.analyze) LazyParser (class in schrodinger.application.desmond.packages.cui) LB() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) lcm() (in module schrodinger.application.matsci.nano.xtal) lcm_approx() (in module schrodinger.application.matsci.nano.interface_mod) ld_data (schrodinger.application.livedesign.panel_components.LDDataCheckboxItem attribute) LDData (class in schrodinger.application.livedesign.data_classes) LDDataCheckboxItem (class in schrodinger.application.livedesign.panel_components) LDDataSelectionModel (class in schrodinger.application.livedesign.panel_components) LDDataSelectionTreeView (class in schrodinger.application.livedesign.panel_components) LDDataSelectionTreeWidget (class in schrodinger.application.livedesign.panel_components) LDFolderTree (class in schrodinger.application.livedesign.ld_folder_tree) LDInputType (class in schrodinger.application.livedesign.ld_base_classes) LDOS_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) LDSelectionModel (class in schrodinger.application.livedesign.panel_components) LDSelectionTreeView (class in schrodinger.application.livedesign.panel_components) LDTreeItem (class in schrodinger.application.livedesign.panel_components) LE_WIDTH (schrodinger.application.desmond.gui.SimOptionsFrame attribute) LEAK_VERSIONS (schrodinger.application.licensing.licadmin.LicenseResource attribute) leave_scope() (schrodinger.application.desmond.enhsamp.binding method) leaveEvent() (schrodinger.application.matsci.builderwidgets.StructureLabel method) leaving_atoms (schrodinger.structutils.rgroup_enumerate.RGroup attribute) leftClicked (schrodinger.application.combiglide.combenumdock.editableViewerTable attribute) leg1_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) leg2_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) length (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue attribute) LENGTH (schrodinger.application.matsci.nano.tube.NanoTube attribute) length (schrodinger.structure._StructureBond attribute) lengthAboutToChange (schrodinger.protein.sequence.Sequence attribute) lengthChanged (schrodinger.protein.sequence.Sequence attribute) lenOrig (schrodinger.infra.phase.PhpPackedFp attribute) LESS_THAN (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property attribute) lessThan() (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) Let (class in schrodinger.application.desmond.enhsamp) letUserSelectValues() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) Level (class in schrodinger.infra.mmerr) level (schrodinger.application.licensing.licerror.LicenseError attribute) level() (schrodinger.infra.mmerr.ErrorHandler method) level_of_detail_callback_add() (in module schrodinger.maestro.maestro) level_of_detail_callback_remove() (in module schrodinger.maestro.maestro) Lexer (class in schrodinger.application.desmond.antlr3.recognizers) LIB (schrodinger.job.util.DirectoryType attribute) License (class in schrodinger.application.licensing.flexlm) (class in schrodinger.infra.licensing) (class in schrodinger.utils.license) license_class() (schrodinger.application.licensing.flexlm.License method) license_description() (schrodinger.application.licensing.flexlm.License method) license_directory() (in module schrodinger.application.licensing.licadmin) license_is_dummy() (in module schrodinger.utils.licutils) license_is_remote() (in module schrodinger.utils.licutils) license_list() (in module schrodinger.utils.licutils) license_requires_server() (in module schrodinger.utils.licutils) LicenseError (class in schrodinger.application.licensing.licerror) LicenseException licenseExists() (schrodinger.infra.licensing.License static method) LicenseFeature (class in schrodinger.application.licensing.licadmin) LicenseLine (class in schrodinger.application.licensing.flexlm) LicenseResource (class in schrodinger.application.licensing.licadmin) LicfileError lig_to_fullsys_aid() (in module schrodinger.application.desmond.automatic_analysis_generator) Ligand (class in schrodinger.application.matsci.buildcomplex) (class in schrodinger.application.matsci.siteselector.siteselector) (class in schrodinger.structutils.analyze) LIGAND (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) ligand1_alchemical_atom_total (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_alchemical_mols (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_atomic_mass (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_cpx_asl (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_cpx_sid_lighb() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_molsa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_psa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_sasa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_sid_waters() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_cpx_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) ligand1_fragments() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_hash (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_mol_formula (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_pdb_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_rot_bonds (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_smiles (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_sol_asl (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_sol_sid_lighb() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_molsa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_psa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_sol_sid_sasa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand1_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) ligand1_total_atoms (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_total_fragments (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_total_heavy (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_total_hot (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand1_total_rot_bonds (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_alchemical_atom_total (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_alchemical_mols (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_atomic_mass (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_cpx_asl (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_cpx_sid_lighb() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_molsa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_psa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_sasa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_sid_waters() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_cpx_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) ligand2_fragments() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_hash (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_mol_formula (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_pdb_name (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_rot_bonds (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_smiles (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_sol_asl (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_sol_sid_lighb() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_molsa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_psa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_rb_strain() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_rgyr() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_rmsd() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_sol_sid_sasa() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData method) ligand2_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) ligand2_total_atoms (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_total_fragments (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_total_heavy (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_total_hot (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand2_total_rot_bonds (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ligand_action (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) ligand_asl (schrodinger.structutils.analyze.Ligand attribute) LIGAND_CONTACTS (in module schrodinger.protein.annotation) ligand_contacts (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) ligand_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute) ligand_name() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method) LIGAND_SELECTIVITY (schrodinger.application.desmond.constants.FEP_TYPES attribute) ligand_st_mol_formula (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) ligand_torsions (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) LigandRMSD (class in schrodinger.application.desmond.packages.analysis) Ligands (class in schrodinger.application.livedesign.maestro_data_types) ligands (schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) LigandSelector (class in schrodinger.application.matsci.siteselector.siteselector) LigfilterFrame (class in schrodinger.ui.ligfilter) LigFilterStage (class in schrodinger.pipeline.stages.filtering) LIGHT (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) LIGHT_COLS (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) LIGHT_FR_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) LIGHT_FR_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) LIGHT_IDEN (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) LIGHT_SIM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) lignum_reader() (in module schrodinger.application.glide.ensemble_selection) LigPrep3Volumizer (class in schrodinger.infra.fast3d) LigPrepStage (class in schrodinger.pipeline.stages.ligprep) LIKELY (schrodinger.protein.residue.HELIX_PROPENSITY attribute) limits (schrodinger.protein.sequence.SecondaryStructure attribute) line (schrodinger.application.desmond.antlr3.tree.CommonTree attribute) line_match_final_log() (in module schrodinger.application.desmond.replica_exchange_review) LINE_ORDER (schrodinger.application.matsci.desmondutils.MSJStringer attribute) line_search_wolfe1() (schrodinger.application.matsci.mecp_mod.BFGS method) line_width (schrodinger.graphics3d.box.Box attribute) LINEAR (in module schrodinger.application.matsci.buildcomplex) linear_equation() (schrodinger.application.matsci.nano.tube.Rectangle method) LINEAR_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) LinearError LinearSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) LinearWriter (class in schrodinger.pipeline.input) lineEditUpdated() (schrodinger.ui.residueselector.MutationSelectorPopUp method) LineIntersectsTriangle() (in module schrodinger.application.desmond.packages.msys) LineMarker (class in schrodinger.maestro.markers) Lines (class in schrodinger.graphics3d.lines) lineterminator (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) LINKAGE_TYPES (schrodinger.application.canvas.cluster.CanvasFingerprintCluster attribute) LinkedList (class in schrodinger.job.queue)

LinkedListNode (class in schrodinger.job.queue) linkFollowed() (schrodinger.infra.exception_handler_dir.exception_dialog.ExceptionDialog method) LipidDirector (class in schrodinger.application.desmond.packages.analysis) lipophilic_ChemScore_value() (in module schrodinger.application.bioluminate.interaction_calculator) List (class in schrodinger.utils.sea) list2jmonitorcmdline() (in module schrodinger.job.jobcontrol) list2str() (in module schrodinger.application.desmond.meta) list_to_csv() (in module schrodinger.structutils.rgroup_enumerate) list_to_string() (in module schrodinger.application.matsci.nano.interface_mod) listElements() (in module schrodinger.infra.propedit) ListParam (class in schrodinger.models.parameters) listProps() (in module schrodinger.infra.propedit) Lit (class in schrodinger.application.desmond.enhsamp) LiveDesignLoginDialog (class in schrodinger.application.livedesign.login) LiveDesignProjectsCombo (class in schrodinger.application.livedesign.panel_components) liveReportSelected (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelector attribute) LiveReportSelectionComboBox (class in schrodinger.application.livedesign.panel_components) LiveReportSelectionPopup (class in schrodinger.application.livedesign.panel_components) LiveReportSelector (class in schrodinger.application.livedesign.panel_components) lj14_energy() (in module schrodinger.application.qsite.output) lj_energy() (in module schrodinger.application.qsite.output) llmd() (schrodinger.application.macromodel.utils.ComUtil method) lmdiag() (schrodinger.application.licensing.licadmin.LicenseResource method) lmgrd_lines() (in module schrodinger.application.licensing.licadmin) lmod() (schrodinger.application.macromodel.utils.ComUtil method) lmp2() (in module schrodinger.application.jaguar.textparser) LMP2_KEYWORDS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) LMP2_ROWS (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) lmstat() (schrodinger.application.licensing.licadmin.LicenseResource method) lo_precision (schrodinger.application.jaguar.results.JaguarResults attribute) Load() (in module schrodinger.application.desmond.packages.msys) load() (schrodinger.analysis.transformations.TransformsRepository method) load_arrows() (in module schrodinger.trajectory.prody.test_arrow) load_data() (schrodinger.application.desmond.bennett.CalcBAR method) load_force_field_parameters() (in module schrodinger.application.matsci.cgforcefield) load_fortran_input() (schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method) load_graph() (schrodinger.application.desmond.title_to_hex.Analysis method) load_gui() (in module schrodinger.application.desmond.report_helper) load_job_products() (in module schrodinger.application.licensing.licadmin) load_job_reqs() (in module schrodinger.application.licensing.licadmin) load_keywords() (in module schrodinger.application.jaguar.keywordDB) load_shared_library() (in module schrodinger.application.desmond.packages.msys.molfile) loadAccuracyAndInitialGuessSettings() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) loadAssayData() (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) LoadCNSFile() (in module schrodinger.analysis.visanalysis.volumedataio) loadCommon() (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) loadConstraintCoordinates() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) loadConvergenceCriteriaSettings() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) loadConvergenceKeywords() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) loadConvergenceMethodsSettings() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) loadData() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) (schrodinger.application.livedesign.panel_components.LDSelectionModel method) loadDatabases() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) LoadDMS() (in module schrodinger.application.desmond.packages.msys) loadEndpointData() (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) loadEnumeration() (schrodinger.application.matsci.nano.slab.ParserWrapper method) loadFFCombo() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) loadFile() (schrodinger.analysis.transformations.TransformsRepository method) loadHKLOptions() (schrodinger.application.matsci.nano.slab.ParserWrapper method) LoadingIcon (class in schrodinger.application.bioluminate.bwidgets) loadIt() (schrodinger.application.matsci.mecp_mod.ParserWrapper method) (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.particle.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.ParserWrapper method) (schrodinger.application.matsci.nano.xtal.ParserWrapper method) (schrodinger.application.matsci.rxn_path.ParserWrapper method) loadJobs() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) loadLDClient() (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) loadLiveReports() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) LoadMAE() (in module schrodinger.application.desmond.packages.msys) LoadMany() (in module schrodinger.application.desmond.packages.msys) loadMappings() (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) loadMmJag() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) LoadMol2() (in module schrodinger.application.desmond.packages.msys) loadNextTask() (schrodinger.tasks.runners.JobTaskRunner method) (schrodinger.tasks.runners.TaskRunner method) loadOptions() (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) loadOrbitalsSettings() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) LoadPDB() (in module schrodinger.application.desmond.packages.msys) loadPerAtomSettings() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) LoadPrmTop() (in module schrodinger.application.desmond.packages.msys) loadRequired() (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) loadRow() (schrodinger.application.livedesign.panel_components.LDSelectionModel method) loadRows() (schrodinger.application.livedesign.panel_components.LDSelectionModel method) loads() (schrodinger.analysis.transformations.TransformsRepository method) loadSettings() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MullikenSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MultipoleSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.RamanSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabIGO method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinExcitedStateController method) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) loadSettingsFromKeywords() (schrodinger.application.matsci.mswidgets.EmbeddedSolventWidget method) loadSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) loadStructIntoStructView() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) loadStructures() (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) loadTemplate() (schrodinger.application.matsci.builderwidgets.SketcherBox method) loadToggled() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) LoadVisFile() (in module schrodinger.analysis.visanalysis.volumedataio) LoadXYZ() (in module schrodinger.application.desmond.packages.msys) loadZoomStruct() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) local_pol_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) local_pol_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) local_pol_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) local_server_files() (in module schrodinger.application.licensing.licadmin) local_server_resource() (in module schrodinger.application.licensing.licadmin) local_server_resources() (in module schrodinger.application.licensing.licadmin) LOCALIZATION_METHODS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) LocalServerProcess (class in schrodinger.application.licensing.licadmin) locate_pymol() (in module schrodinger.utils.fileutils) locateAndRotate() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) locateVoids() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) LOCATION (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) location() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.licensing.licadmin.LicenseResource method) LOCK (schrodinger.maestro.markers.Icons attribute) lock_protonation() (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) lock_protonation_states() (schrodinger.protein.assignment.ProtAssign method) lockedColumns() (schrodinger.protein.alignment.BaseAlignment method) LockedProjectException log() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) (in module schrodinger.application.matsci.textlogger) (in module schrodinger.pipeline.pipeline) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.montecarlo.Metropolizer method) (schrodinger.job.app.App method) log_banner() (in module schrodinger.utils.installation_check) log_deleted_lines() (schrodinger.application.licensing.flexlm.License method) log_displacements() (in module schrodinger.application.matsci.mecp_mod) log_energy_and_forces() (in module schrodinger.application.matsci.mecp_mod) log_error() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) (in module schrodinger.application.matsci.textlogger) log_geometry() (in module schrodinger.application.matsci.mecp_mod) log_initial_data() (in module schrodinger.application.matsci.textlogger) log_jobinfo() (in module schrodinger.application.matsci.textlogger) log_msg() (in module schrodinger.application.matsci.textlogger) log_namespace() (in module schrodinger.application.matsci.textlogger) log_vector() (in module schrodinger.application.matsci.mecp_mod) logActivity() (schrodinger.infra.phase.PhpProject method) logEnergyAndForces() (schrodinger.application.matsci.mecp_mod.MECPStep method) logError() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) logfile() (schrodinger.application.licensing.licadmin.LicenseResource method) LogFormatter (class in schrodinger.application.hitexpander) logger (schrodinger.application.desmond.packages.timer.Timer.Args attribute) logging_config() (in module schrodinger.utils.log) logging_summary_callback() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) logHeader() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) logHessianEigVals() (schrodinger.application.matsci.mecp_mod.MECPStep method) logInitialGeometry() (schrodinger.application.matsci.mecp_mod.MECPStep method) logistic() (in module schrodinger.application.desmond.bennett) logistic_full() (in module schrodinger.application.desmond.bennett) logistic_function() (in module schrodinger.application.desmond.bennett) logistic_function_full() (in module schrodinger.application.desmond.bennett) logJobData() (schrodinger.application.matsci.mecp_mod.MECPStep method) logn() (in module schrodinger.pipeline.pipeline) lognoret() (schrodinger.pipeline.stage.Stage method) lognotret() (schrodinger.job.app.App method) logP() (schrodinger.application.macromodel.utils.ComUtil method) logParams() (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) logResult() (schrodinger.structutils.smilesfilter.FilterReporter method) logStepInfo() (schrodinger.application.matsci.mecp_mod.MECPStep method) logSummary() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) (schrodinger.application.matsci.mecp_mod.MECPStep method) logSummaryHeader() (schrodinger.application.matsci.mecp_mod.MECPStep method) loneelectrons() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method) LONEPAIR (schrodinger.maestro.markers.Icons attribute) long_code (schrodinger.protein.residue.Residue attribute) long_range_dispersion_energy() (in module schrodinger.application.desmond.fepana) LOOP (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute) loop() (schrodinger.application.macromodel.utils.ComUtil method) lower_bound() (schrodinger.utils.mmutil.StringStringMap method) LowMemoryVolGraph (class in schrodinger.application.matsci.amorphous) LRSort (class in schrodinger.application.livedesign.panel_components) LRSortCombo (class in schrodinger.application.livedesign.panel_components) LRSortMethodChanged (schrodinger.application.livedesign.panel_components.BaseLiveReportSelectionPopup attribute) (schrodinger.application.livedesign.panel_components.LRSortCombo attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelector attribute) ls (in module schrodinger.application.desmond.packages.msys.molfile) LST_SEARCH_ALONG (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) LT() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.TokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) LT_token() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) LT_tree() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) lumo() (in module schrodinger.application.jaguar.textparser) lumo_prop (schrodinger.application.mopac.results71.MopacResults71 attribute)

M

m2ioPropertyName() (schrodinger.application.canvas.topo_descriptors.TopologicalDescriptors method) m_glide_XPviz_exposure() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_hbonds() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_hexpairs() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_hexsp() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_blkpchg() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_charge() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_ddpen() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_polar() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penal_twistam() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_penalties() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_phobcon_hb() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_phobpack() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_picat() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_rotbonds() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_stacking() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_water_ligand() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_water_protein() (in module schrodinger.application.glide.xpdes) m_glide_XPviz_watmol() (in module schrodinger.application.glide.xpdes) m_qn (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) mADDOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mae() (in module schrodinger.application.jaguar.textparser) mae_in() (in module schrodinger.application.jaguar.textparser) MAESTRO (schrodinger.protein.sequence.Sequence.ORIGIN attribute) maestro_create_group() (in module schrodinger.application.livedesign.ld_import) MAESTRO_EXPORT_MAP_DIR_PATH (schrodinger.application.livedesign.ld_export.ExportMapManager attribute) maestro_rotate_cell() (in module schrodinger.application.matsci.nano.slab) maestro_select_only() (in module schrodinger.application.livedesign.maestro_data_types) MAESTRO_STATUS_MESSAGE (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) MaestroAnalysis (class in schrodinger.application.desmond.packages.staf) MaestroArrow (class in schrodinger.graphics3d.arrow) MaestroCommand MaestroCube (class in schrodinger.graphics3d.polyhedron) MaestroDodecahedron (class in schrodinger.graphics3d.polyhedron) MaestroIcosahedron (class in schrodinger.graphics3d.polyhedron) MaestrolessLigandListModel (class in schrodinger.ui.picking) MaestrolessPickLigandDialog (class in schrodinger.ui.picking) MaestrolessPickResidueDialog (class in schrodinger.ui.picking) MaestroNotAvailableError MaestroOctahedron (class in schrodinger.graphics3d.polyhedron) MaestroPolygon (class in schrodinger.graphics3d.polygon) MaestroPolyhedronCore (class in schrodinger.graphics3d.polyhedron) MaestroReader (class in schrodinger.structure) MaestroReaderWithPositions (class in schrodinger.structure) MaestroSphere (class in schrodinger.graphics3d.sphere) MaestroTetrahedron (class in schrodinger.graphics3d.polyhedron) MaestroTextReader (class in schrodinger.structure) MaestroTorus (class in schrodinger.graphics3d.torus) MaestroWriter (class in schrodinger.structure) MAGGLASS (schrodinger.maestro.markers.Icons attribute) MagSpecies (class in schrodinger.application.matsci.espresso.qeinput) maid() (in module schrodinger.application.desmond.reorder_atom) main() (in module schrodinger.application.canvas.r_group_dee) (in module schrodinger.application.desmond.bennett) (in module schrodinger.application.desmond.enhanced_sampling.mexpLexer) (in module schrodinger.application.desmond.enhanced_sampling.mexpParser) (in module schrodinger.application.desmond.packages.parch) (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) (in module schrodinger.application.desmond.title_to_hex) (in module schrodinger.application.jaguar.check_headers) (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.lmgrd_log_parser) (in module schrodinger.application.matsci.enumeration) (in module schrodinger.application.matsci.reordergui) (in module schrodinger.application.mopac.mopac_backend) (in module schrodinger.application.mopac.mopac_startup) (in module schrodinger.application.watermap.watermap_inp) (in module schrodinger.infra.epydoc_to_sphinx) (in module schrodinger.protein.getpdb_utility) (in module schrodinger.protein.reliability) (in module schrodinger.utils.installation_check) main_wrapper() (in module schrodinger.utils.cmdline) mainFunction() (schrodinger.tasks.tasks_.AbstractFunctionTask method) mainProduct() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.prime.MMGBSAStage method) maintain_planarity (schrodinger.structutils.minimize.Minimizer attribute) make_canonical_solvent() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) make_chorus_orthorhombic() (in module schrodinger.application.matsci.desmondutils) make_family_map() (in module schrodinger.application.livedesign.panel_components) make_fep_cmd() (in module schrodinger.application.desmond.fep_scholar_util) (in module schrodinger.application.desmond.feputils) make_fp_generator() (in module schrodinger.utils.multifpfile) make_fp_generator_from_canvas_fpfile() (in module schrodinger.application.hitexpander) make_glued_topology() (in module schrodinger.application.desmond.packages.topo) make_ld_item_tree() (in module schrodinger.application.livedesign.panel_components) make_local_protein() (schrodinger.protein.analysis.Report method) make_mapper() (in module schrodinger.models.mappers) make_one_letter_map() (in module schrodinger.protein.residue) make_outmaefile() (in module schrodinger.application.jaguar.file_logger) make_p1() (in module schrodinger.application.matsci.nano.xtal) make_prop_dict() (in module schrodinger.application.livedesign.data_classes) make_property() (in module schrodinger.application.desmond.ffiostructure) make_property_fepio() (in module schrodinger.application.desmond.ffiostructure) make_scheme_cb() (in module schrodinger.application.bioluminate.antibody.utils) make_schrodinger_cmd() (in module schrodinger.tasks.jobtasks) make_scratch_dir() (in module schrodinger.application.mopac.utils) make_smapfile() (in module schrodinger.application.jaguar.file_logger) make_three_letter_map() (in module schrodinger.protein.residue) make_variants() (in module schrodinger.protein.residue) make_whole() (in module schrodinger.application.desmond.packages.topo) make_whole_cms() (in module schrodinger.application.desmond.packages.topo) makeAllTitlesUnique() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) makeCartesianCoords() (schrodinger.application.jaguar.input.JaguarInput method) makeCmd() (schrodinger.tasks.tasks_.SubprocessCmdTask method) makeCmdList() (schrodinger.tasks.jobtasks.AbstractJobTask method) (schrodinger.tasks.jobtasks.CmdJobTask method) MakeConsistent() (in module schrodinger.analysis.visanalysis.volumedatautils) makeFingerPrintInfile() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS method) makeFpOptionsDict() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS method) makeFragment() (schrodinger.application.matsci.nano.sheet.HoneycombCell method) makeInternalCoords() (schrodinger.application.jaguar.input.JaguarInput method) makeMaestroInfile() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS method) makeMultiWalledTubes() (schrodinger.application.matsci.nano.tube.NanoTubes method) makeNanoSheets() (schrodinger.application.matsci.nano.sheet.NanoSheets method) makeNestedRowVisible() (schrodinger.infra.table.Table method) makeOptions() (schrodinger.infra.phase.PhpAlignCore static method) makePolymer() (schrodinger.application.matsci.amorphous.PolymerToFragments method) makeResidueSelection() (schrodinger.protein.alignment.BaseAlignment method) makeRxnComplex() (schrodinger.application.matsci.rxn_path.ReactionCoords method) makeSchrodingerCmd() (schrodinger.tasks.jobtasks.AbstractJobTask method) makeSeqElement() (schrodinger.protein.sequence.Sequence class method) makeSingleWalledTubes() (schrodinger.application.matsci.nano.tube.NanoTubes method) makeTemplate() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) makeVariant() (schrodinger.protein.residue.ElementType method) mALPHA() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) manage_failures_callback() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) manage_skips_callback() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) manageTemplates() (schrodinger.application.matsci.builderwidgets.SketcherBox method) manageXvolIsOpen() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) MANUAL_SEQUENCE (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) manual_update (schrodinger.structure.Structure attribute) Map (class in schrodinger.utils.sea) map_by_lone_element() (in module schrodinger.application.matsci.reorder) map_by_smarts() (in module schrodinger.application.matsci.reorder) map_by_smiles() (in module schrodinger.application.matsci.reorder) map_by_superposition() (in module schrodinger.application.matsci.reorder) map_core_hydrogen() (in module schrodinger.application.desmond.fep_mapping) MAP_ERROR_MSG (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) MAP_EXISTS_MSG (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) map_hydrogens() (in module schrodinger.application.matsci.reorder) map_neighboring_hydrogens() (in module schrodinger.application.matsci.reorder) MAP_SELECT_TEXT (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) mapAtom() (schrodinger.application.matsci.reordergui.ComparisonFrame method) (schrodinger.application.matsci.reordergui.ReferenceFrame method) mapCompAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) mapPair() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) MAPPER_INDEX (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper attribute) MapperMixin (class in schrodinger.models.mappers) MapperMsjGenerator (class in schrodinger.application.desmond.mapper_msj_generator) Mapping (class in schrodinger.utils.pymol) MappingAnnotator (class in schrodinger.application.desmond.fep_scholar_util) MappingError mapSites() (schrodinger.infra.phase.PhpProject method) MARGIN (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) mark() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) mark_atom() (in module schrodinger.application.desmond.maestro) (schrodinger.application.desmond.maestro.Workspace method) mark_eta_positions() (in module schrodinger.application.matsci.builderwidgets) mark_fullsystem_ct() (in module schrodinger.application.desmond.cms) markAtomMapped() (schrodinger.application.matsci.reordergui.ComparisonListWidget method) (schrodinger.application.matsci.reordergui.ReferenceListWidget method) (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.application.matsci.reordergui.StructurePic method) markAtomsBeforeSpearCheck() (schrodinger.structutils.ringspear.SpearRing static method) markAtomUnmapped() (schrodinger.application.matsci.reordergui.ReferenceListWidget method) (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.application.matsci.reordergui.StructurePic method) markBackboneAtom() (schrodinger.application.matsci.amorphous.BaseMoiety method) markBranchingFrag() (schrodinger.application.matsci.amorphous.PolymerFragment method) Marker (class in schrodinger.maestro.markers) MARKER_SETTINGS (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute) MARKER_TAB_CLASSES (schrodinger.application.jaguar.gui.base_panel.MarkerMixin attribute) (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin attribute) (schrodinger.application.jaguar.gui.base_panel.OptimizationTabMarkerMixin attribute) (schrodinger.application.jaguar.gui.base_panel.ScanTabMarkerMixin attribute) MarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) markForRestart() (schrodinger.job.queue.JobDJ method) MARKING_INFO (schrodinger.application.matsci.builderwidgets.SketcherBox attribute) markResidues() (schrodinger.application.matsci.amorphous.PolymerToFragments method) markShiftedDesignators() (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector method) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector method) markSidegroupFrag() (schrodinger.application.matsci.amorphous.PolymerFragment method) maskValue (schrodinger.infra.phase.PhpSiteMaskData attribute) mass (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) MassAvgVel (class in schrodinger.application.desmond.packages.analysis) match() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.packages.msys.Graph method) (schrodinger.application.desmond.packages.msys.SmartsPattern method) match_by_cartesian_coordinates() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) match_by_distance() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) match_compstr() (schrodinger.utils.ligfilter.Criterion method) match_core_hydrogens() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) match_hbond() (in module schrodinger.structutils.analyze) matchAll() (schrodinger.application.desmond.packages.msys.Graph method) matchAny() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) matched_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer attribute) matched_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer attribute) matches() (schrodinger.application.bioluminate.propfilter.StringDatabaseCriterion method) (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.utils.ligfilter.AslCriterion method) (schrodinger.utils.ligfilter.Criterion method) (schrodinger.utils.ligfilter.PredefinedCriterion method) (schrodinger.utils.ligfilter.PropertyCriterion method) (schrodinger.utils.ligfilter.SmartsCriterion method) matches_canonical_filename() (in module schrodinger.application.licensing.flexlm) matchRange() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) matdynStr() (schrodinger.application.matsci.espresso.qeinput.KpointsType method) material (schrodinger.graphics3d.arrow.MaestroArrow attribute) (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.graphics3d.torus.MaestroTorus attribute) MaterialEnumerationDialog (class in schrodinger.application.combiglide.combenumdock) matrix_matches (schrodinger.structutils.sitealign.BindingSiteAligner attribute) matrix_reciprocal() (in module schrodinger.application.canvas.topo_descriptors) matrix_to_vector() (in module schrodinger.application.matsci.mecp_mod) matter_is_conserved() (in module schrodinger.application.jaguar.reactiq_validation) MATURE_AFEP (schrodinger.application.desmond.systype.DesmondTyper attribute) MATURE_FEP (schrodinger.application.desmond.systype.DesmondTyper attribute) MATURE_REGULAR (schrodinger.application.desmond.systype.DesmondTyper attribute) max (schrodinger.analysis.enrichment.StatisticalSummary attribute) MAX (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property attribute) max_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) max_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) MAX_ANGLE (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) max_atom_count (schrodinger.structutils.analyze.AslLigandSearcher attribute) max_connect_distance() (in module schrodinger.application.matsci.nano.xtal) max_cycles (schrodinger.infra.phase.PhpHypoOptimizerSettings attribute) max_ef_value (schrodinger.analysis.enrichment.Calculator attribute) max_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) MAX_GROUPS (schrodinger.application.desmond.packages.energygroup.Bulk attribute) max_hbond_distance (schrodinger.protein.assignment.ProtAssign.changeable attribute) max_hypo_drift (schrodinger.infra.phase.PhpHypoOptimizerSettings attribute) max_index (schrodinger.analysis.enrichment.StatisticalSummary attribute) max_length (schrodinger.protein.alignment.BaseAlignment attribute) MAX_NUM_ATOMS (schrodinger.application.livedesign.maestro_data_types.Ligands attribute) (schrodinger.application.livedesign.maestro_data_types.OrganometallicCompounds attribute) (schrodinger.application.livedesign.maestro_data_types.TargetlessBase attribute) MAX_NUM_UNPRODUCTIVE_CYCLES (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions attribute) max_pair_vdw_distance() (in module schrodinger.application.matsci.rxn_path) max_potential_energy (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute) MAX_ROW_COUNT (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) MAX_STEPS (schrodinger.application.matsci.desmondutils.MSJStringer attribute) max_steps (schrodinger.structutils.minimize.Minimizer attribute) maxat_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) maxat_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) maxat_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) maxFailuresReached() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) MAXIMUM_ITER_TEXT (schrodinger.application.jaguar.gui.theory_tab_widgets.HFExcitedStateWidget attribute) maximum_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) mbaeCsLmod() (schrodinger.application.macromodel.utils.ComUtil method) mbaeCsMcmm() (schrodinger.application.macromodel.utils.ComUtil method) mbaeCsMcmmLmod() (schrodinger.application.macromodel.utils.ComUtil method) mbaeMiniEdiff() (schrodinger.application.macromodel.utils.ComUtil method) mbaeMiniInter() (schrodinger.application.macromodel.utils.ComUtil method) mBCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mBOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MBYTE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) mCCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mcl() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) mclc1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) mcmm() (schrodinger.application.macromodel.utils.ComUtil method) mcmmllmd() (schrodinger.application.macromodel.utils.ComUtil method) mcmmlmod() (schrodinger.application.macromodel.utils.ComUtil method) mCOLON() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mCOMMA() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mCOMMENT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mCOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) McproTyper (class in schrodinger.application.desmond.systype) mcsd() (schrodinger.application.macromodel.utils.ComUtil method) MCSFailure MD (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) md (schrodinger.application.desmond.config.TAG_SPECS attribute) MdAtomSelector (class in schrodinger.application.matsci.mswidgets) MDC_DEFAULT_HEIGHT (schrodinger.application.desmond.gui.AdvOptionsFrame attribute) MDC_DEFAULT_WIDTH (schrodinger.application.desmond.gui.AdvOptionsFrame attribute) MdcAdvancedDialog (class in schrodinger.application.desmond.gui) MdcMiscTab (class in schrodinger.application.desmond.gui) MdGroup (class in schrodinger.application.desmond.gui) mDIGIT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mDIVOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MDMSJStringer (class in schrodinger.application.matsci.desmondutils) MdType (class in schrodinger.application.matsci.espresso.qeinput) mdyn() (schrodinger.application.macromodel.utils.ComUtil method) mean (schrodinger.analysis.enrichment.StatisticalSummary attribute) mean_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mean_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mean_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mean_hydrophobicity (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) mean_isoelectric_point (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) mean_neg_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mean_neg_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mean_neg_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mean_pos_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mean_pos_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mean_pos_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) measure() (in module schrodinger.protein.assignment) (schrodinger.structure.Structure method) measure_bond_angle() (in module schrodinger.structutils.measure) measure_dihedral_angle() (in module schrodinger.structutils.measure) measure_distance() (in module schrodinger.structutils.measure) measure_plane_angle() (in module schrodinger.structutils.measure) Measurement (class in schrodinger.application.desmond.measurement) MECP (class in schrodinger.application.matsci.mecp_mod) MECPStep (class in schrodinger.application.matsci.mecp_mod) median (schrodinger.analysis.enrichment.StatisticalSummary attribute) MEDIUM (schrodinger.application.matsci.qualityslider.QualitySlider attribute) MEMBRANE_ENVIRON (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions attribute) Membrane_Model (class in schrodinger.protein.membrane) MEMO_RULE_FAILED (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) MEMO_RULE_UNKNOWN (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) memoize() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) memory_leak_server() (schrodinger.application.licensing.licadmin.LicenseResource method) memory_usage_psutil() (in module schrodinger.application.matsci.jobutils) MemoryEstimator (class in schrodinger.application.matsci.espresso.utils) mEQ() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) merge() (in module schrodinger.application.desmond.packages.traj) (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge) (in module schrodinger.infra.propedit) (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.matsci.zmutils.ZMatrix method) (schrodinger.infra.phase.PhpHypoAdaptor method) (schrodinger.structure.Structure method) merge_atom_group() (schrodinger.application.desmond.cms.Cms method) merge_atom_group_from_asl() (schrodinger.application.desmond.cms.Cms method) merge_blocks() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) merge_blocks2() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) merge_ct() (in module schrodinger.application.desmond.ffiostructure) merge_dicts() (in module schrodinger.protein.residue) merge_files() (in module schrodinger.structutils.sort) merge_ghost_solvent() (in module schrodinger.application.desmond.gcmc_utils) merge_ghost_solvent_file() (in module schrodinger.application.desmond.gcmc_utils) merge_lists() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge) merge_op_positions() (in module schrodinger.infra.propedit) merge_pv_files() (in module schrodinger.structutils.sort) merge_relative_restraint() (in module schrodinger.application.desmond.cms) merge_rules() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge) merge_st_iters() (in module schrodinger.structutils.sort) merge_with() (schrodinger.application.desmond.cms.Restrain method) mergeByIndex() (schrodinger.application.canvas.utils.ChmCSVTools method) mergeByName() (schrodinger.application.canvas.utils.ChmCSVTools method) MergeDuplicatesStage (class in schrodinger.pipeline.stages.filtering) mergeGlideOutputs() (schrodinger.pipeline.stages.glide.DockingStage method) mergeNonbonds() (schrodinger.application.matsci.coarsegrain.Internals method) MergeStage (class in schrodinger.pipeline.stages.glide) MERIDIONAL (in module schrodinger.application.matsci.buildcomplex) mesh (schrodinger.surface.Style attribute) (schrodinger.surface.Surface.Style attribute) message (schrodinger.application.desmond.packages.msys.InChI attribute) (schrodinger.application.desmond.packages.timer.Timer.Args attribute) (schrodinger.application.licensing.licerror.LicenseError attribute) Meta (class in schrodinger.application.desmond.enhsamp) (class in schrodinger.application.desmond.meta) META (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) meta (schrodinger.application.desmond.config.TAG_SPECS attribute) META_ASL (schrodinger.application.desmond.cms.Cms attribute) meta_template (schrodinger.application.desmond.meta.Meta attribute) meta_term() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) meta_well_tempered_template (schrodinger.application.desmond.meta.Meta attribute) MetaAtom (class in schrodinger.application.desmond.fep_scholar_util) MetaDynamicsAnalysis (class in schrodinger.application.desmond.meta) MetalConstraint (class in schrodinger.application.glide.glide) MetalInter (class in schrodinger.application.desmond.packages.analysis) MetalL (schrodinger.application.desmond.packages.analysis.MetalInter attribute) METALLOPROTEIN (schrodinger.application.desmond.constants.FEP_TYPES attribute) MetalloproteinEdgeData (class in schrodinger.application.desmond.fep_edge_data) MetalMsjGenerator (class in schrodinger.application.desmond.mapper_msj_generator) MetalP (schrodinger.application.desmond.packages.analysis.MetalInter attribute) MetaSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) (class in schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) MetCoordConstraint (class in schrodinger.application.glide.glide) method (schrodinger.application.mopac.mopac_results.MopacResults attribute) (schrodinger.application.mopac.results2012.MopacResults2012 attribute) (schrodinger.application.mopac.results71.MopacResults71 attribute)

method_changed (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) METHOD_NAMEMAP (schrodinger.application.desmond.gui.EnsembleTab attribute) method_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) method_synonyms (schrodinger.application.mopac.mopac_launchers.MopacLauncher attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher2012 attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher71 attribute) methodChanged() (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) MethodOptionAction (class in schrodinger.application.mopac.mopac_parser) Metropolizer (class in schrodinger.application.matsci.montecarlo) mEXP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mexpLexer (class in schrodinger.application.desmond.enhanced_sampling.mexpLexer) mexpLexer.DFA12 (class in schrodinger.application.desmond.enhanced_sampling.mexpLexer) mexpParser (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.atom_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.bind_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.block_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.comp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.decl_meta_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.decl_output_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.decl_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA1 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA15 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA17 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA18 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA19 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA20 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA21 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA22 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA24 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.DFA25 (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.expComp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.expr_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.exprOrBind_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.factor_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.fcnCall_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.header_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.if__return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.iter_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.meta_term_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.output_term_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.prog_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.series_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.signedExpComp_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.static_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mexpParser.varWithType_return (class in schrodinger.application.desmond.enhanced_sampling.mexpParser) mIDENT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MIDFIX (schrodinger.application.matsci.nano.check.CheckInput attribute) midpoint_violations() (in module schrodinger.application.desmond.packages.msys.groups) MIDWAY (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) min (schrodinger.analysis.enrichment.StatisticalSummary attribute) MIN (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property attribute) min_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) min_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) MIN_ANGLE (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) min_atom_count (schrodinger.structutils.analyze.AslLigandSearcher attribute) min_converged (schrodinger.structutils.minimize.Minimizer attribute) MIN_EMPTY_BANDS (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) min_energy (schrodinger.structutils.minimize.Minimizer attribute) min_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) min_func() (in module schrodinger.application.desmond.bennett) min_hypo_change (schrodinger.infra.phase.PhpHypoOptimizerSettings attribute) min_index (schrodinger.analysis.enrichment.StatisticalSummary attribute) min_method (schrodinger.structutils.minimize.Minimizer attribute) MIN_NODES (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) min_rms_gradient (schrodinger.structutils.minimize.Minimizer attribute) MIN_STRUCTURES (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) MIN_TERM_FRAGS (schrodinger.application.matsci.nano.constants.Constants attribute) MIN_TOKEN_INDEX (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream attribute) MinAdvancedDialog (class in schrodinger.application.desmond.gui) minat_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) minat_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) minat_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) MINDEX (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) mini() (schrodinger.application.macromodel.utils.ComUtil method) Minimization (class in schrodinger.application.macromodel.input) MinimizationTab (class in schrodinger.application.desmond.gui) MINIMIZE (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) minimize (schrodinger.application.desmond.config.TAG_SPECS attribute) MINIMIZE (schrodinger.application.matsci.desmondutils.MSJStringer attribute) minimize() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.matsci.mecp_mod.BFGS method) (schrodinger.structutils.minimize.Minimizer method) minimize_complex() (in module schrodinger.application.matsci.buildcomplex) minimize_geometry() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) minimize_hydrogens() (schrodinger.protein.assignment.ProtAssign method) minimize_structure() (in module schrodinger.structutils.minimize) minimizeAlignment() (schrodinger.protein.alignment.BaseAlignment method) minimizeEtaPosition() (schrodinger.application.matsci.buildcomplex.Ligand method) MinimizeMSJStringer (class in schrodinger.application.matsci.desmondutils) Minimizer (class in schrodinger.structutils.minimize) minimizer (schrodinger.application.bioluminate.protein.PropertyCalculator attribute) MinimizerError MinimizerFrame (class in schrodinger.application.desmond.gui) minimizeVolume() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) minimum_length (schrodinger.structutils.structalign.StructAlign attribute) minimum_similarity (schrodinger.structutils.structalign.StructAlign attribute) minMatch (schrodinger.infra.phase.PhpSiteMaskGroup attribute) MinMiscTab (class in schrodinger.application.desmond.gui) MinOutputFrame (class in schrodinger.application.desmond.gui) Minta (class in schrodinger.application.macromodel.input) minta() (schrodinger.application.macromodel.utils.ComUtil method) minTerminatingFragments() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) minTerminatingFrags() (schrodinger.application.matsci.nano.tube.NanoTube method) mismatch() (schrodinger.application.desmond.antlr3.tree.TreeParser method) MismatchedNotSetException MismatchedRangeException MismatchedSetException MismatchedTokenException MismatchedTreeNodeException mismatchIsMissingToken() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) mismatchIsUnwantedToken() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) MissingExecutableError missingFieldsDetected (schrodinger.application.livedesign.ld_export.ExportThreadRunner attribute) MissingFrontendException MissingHostsFileException MissingLicenseFile MissingLoopFinder (class in schrodinger.structutils.analyze) missingOutput() (schrodinger.pipeline.stages.ligprep.LigPrepStage method) MissingParameterError MissingTokenException MixInBlockStd (class in schrodinger.application.matsci.equilibrium_md) MIXPREVIOUS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) MIXPREVIOUSMAX (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) MIXPREVIOUSMIN (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) mkdir_p() (in module schrodinger.utils.fileutils) mktemp() (in module schrodinger.application.canvas.cluster) mLIT() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mm (schrodinger.application.qsite.input.HydrogenCap attribute) MM_Color (class in schrodinger.utils.colorscheme) MM_Colormap (class in schrodinger.utils.colorscheme) MM_ColormapGL (class in schrodinger.utils.colorscheme) MM_ColorRamp (class in schrodinger.utils.colorscheme) MM_ColorRampHolder (class in schrodinger.utils.colorscheme) MM_CScheme (class in schrodinger.utils.colorscheme) MM_CSchemeRule (class in schrodinger.utils.colorscheme) mmatom (schrodinger.application.qsite.input.Cut attribute) mmc() (schrodinger.application.macromodel.utils.ComUtil method) MmException MMGBSAStage (class in schrodinger.pipeline.stages.prime) MMIMArgList (class in schrodinger.infra.mmim) MMIMDict (class in schrodinger.infra.mmim) MmJag (class in schrodinger.application.jaguar.mmjag) mmjag_function() (in module schrodinger.application.jaguar.basis) mmkey (schrodinger.application.qsite.input.QSiteInput attribute) MMKVArgList (class in schrodinger.infra.mmkv) MMlic3_Init (class in schrodinger.infra.licensing) MMlic3AutoExitOverride (class in schrodinger.infra.licensing) mmlist (class in schrodinger.infra.mmlist) MmObject (class in schrodinger.infra.mmobject) MMOK (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute) MMrange (class in schrodinger.utils.colorscheme) MMSHARE_DATA_DESMOND_DIR (schrodinger.application.desmond.envir.CONST attribute) MMSHARE_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute) MMSHARE_VERSION (schrodinger.application.desmond.envir.CONST attribute) mmsmiles_initialized (schrodinger.structure.SmilesStructure attribute) MMTypingFailure mMULTOP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mNEWLINE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mob_keys (schrodinger.structutils.sitealign.SiteMatchLookup attribute) Mode (class in schrodinger.trajectory.prody.mode) modeChanged() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) model() (schrodinger.models.mappers.AbstractParamMapper method) model_changed_callback() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.RelaxFrame method) MODEL_CLASS (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) model_class (schrodinger.models.mappers.MapperMixin attribute) MODEL_OPTION (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) MODEL_SYSTEM_TYPE (schrodinger.application.desmond.cms.Cms attribute) model_system_type() (schrodinger.application.desmond.cms.Cms method) modelChanged (schrodinger.application.phase.phase_widgets.HypothesesListWidget attribute) modelClass() (schrodinger.models.mappers.AbstractParamMapper method) ModeSet (class in schrodinger.trajectory.prody.modeset) modified_sawtooth() (in module schrodinger.application.matsci.nano.xtal) modify() (schrodinger.application.qsite.input.QMRegion method) modify_fep_launcher_stage() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.VacuumMsjGenerator method) modify_graph_stage() (schrodinger.application.desmond.mapper_msj_generator.CovalentMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MetalMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.ProteinMapperMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.VacuumMsjGenerator method) modify_multisim_stage() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) modifyMinimizer() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) ModuleProxy (class in schrodinger.utils.moduleproxy) Moieties (class in schrodinger.application.matsci.amorphous) MoietyError mol2image() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) Mol2Reader (class in schrodinger.structure) mol2svg() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) Mol2Writer (class in schrodinger.structure) mol_num (schrodinger.structutils.analyze.Ligand attribute) mol_number (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) mol_number_carbon (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) mol_to_qpicture() (in module schrodinger.analysis.reaction) mol_total (schrodinger.structure.Structure attribute) mol_weight() (in module schrodinger.application.jaguar.textparser) mol_weight_precision (schrodinger.application.jaguar.output.JaguarOutput attribute) molchg() (in module schrodinger.application.jaguar.textparser) molecular (schrodinger.surface.MolSurfType attribute) Molecular_formula() (in module schrodinger.utils.ligfilter) MOLECULAR_ORBITALS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) Molecular_weight() (in module schrodinger.utils.ligfilter) MolecularSurfaceArea (class in schrodinger.application.desmond.packages.analysis) Molecule (schrodinger.application.glide.xpdes.TermKeywords attribute) molecule (schrodinger.structure.Structure attribute) (schrodinger.structure.TextualStructure attribute) molecule_history_callback() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) molecule_indices (schrodinger.application.bioluminate.protein.Consensus attribute) molecule_number (schrodinger.structure._Residue attribute) (schrodinger.structure._StructureAtom attribute) molecules (schrodinger.application.bioluminate.protein.Consensus attribute) molecules() (schrodinger.application.desmond.fep_struc.SchrodStruc method) MoleculeTab (class in schrodinger.application.jaguar.gui.tabs.molecule_tab) MoleculeTabBase (class in schrodinger.application.jaguar.gui.tabs.molecule_tab) MoleculeTabNoInputSelector (class in schrodinger.application.jaguar.gui.tabs.molecule_tab) MoleculeTabPka (class in schrodinger.application.jaguar.gui.tabs.molecule_tab) molid (schrodinger.application.qsite.input.Cut attribute) molID (schrodinger.infra.phase.PhpPackedFp attribute) mols (schrodinger.analysis.reaction.ReagentSource attribute) MolSurfType (class in schrodinger.surface) MOMENT_OF_INERTIA (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) MomentOfInertia (class in schrodinger.application.desmond.packages.analysis) MomentOfInertiaDirector (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.application.matsci.order_parameter_mod) monitor_jobtask() (in module schrodinger.tasks.jobtasks) monitorJobTask() (schrodinger.tasks.jobtasks.JobStatusLoop method) MONOCLINIC_NAME (schrodinger.application.matsci.nano.xtal.CrystalSystems attribute) MONODENTATE (in module schrodinger.application.matsci.buildcomplex) Monomer (class in schrodinger.application.matsci.amorphous) MonomerSpeciesSelector (class in schrodinger.application.matsci.clusterstructgui) MonteCarloMolecule (class in schrodinger.application.matsci.montecarlo) mopac (schrodinger.application.qsite.input.QSiteInput attribute) Mopac2012TextParser (class in schrodinger.application.mopac.results2012) MOPAC_EXEC (schrodinger.application.mopac.mopac_launchers.MopacLauncher2012 attribute) MopacBasisError1 MopacBasisError2 MopacBasisError3 MopacBasisError4 MopacBasisError5 MopacIOError MopacLauncher (class in schrodinger.application.mopac.mopac_launchers) MopacLauncher2012 (class in schrodinger.application.mopac.mopac_launchers) MopacLauncher71 (class in schrodinger.application.mopac.mopac_launchers) MopacLicenseError MopacNumericalError MopacPropertyError MopacResults (class in schrodinger.application.mopac.mopac_results) MopacResults2012 (class in schrodinger.application.mopac.results2012) MopacResults71 (class in schrodinger.application.mopac.results71) MopacRuntimeError MopacUserFacingException mousePressEvent() (schrodinger.application.combiglide.combenumdock.editableViewerTable method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView method) (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) mouseReleaseEvent() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) MOVABLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) MOVE (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) move_alchemical_ions() (in module schrodinger.application.desmond.move_alchem_ions) move_atoms_into_cell() (in module schrodinger.application.matsci.nano.xtal) move_atoms_next_to_atom() (in module schrodinger.application.matsci.clusterstruct) move_ions_in_file() (in module schrodinger.application.desmond.move_alchem_ions) move_ions_to_ligands() (in module schrodinger.application.desmond.move_alchem_ions) moveBack() (schrodinger.application.matsci.sliceplot.SlicePlot method) moveby() (schrodinger.application.desmond.packages.traj.Frame method) moveColumn() (schrodinger.infra.table.Table method) moveDown() (schrodinger.application.matsci.mswidgets.StageFrame method) moveForward() (schrodinger.application.matsci.sliceplot.SlicePlot method) moveHeadToOrigin() (schrodinger.application.matsci.amorphous.BaseMoiety method) moveOldTemplates() (schrodinger.application.matsci.builderwidgets.ComplexTemplateSketcher method) moveRows() (schrodinger.infra.table.Table method) moveRowsToGroup() (schrodinger.project.Project method) moveStage() (schrodinger.application.matsci.mswidgets.MultiStageArea method) moveStageDown() (schrodinger.application.matsci.mswidgets.MultiStageArea method) moveStageUp() (schrodinger.application.matsci.mswidgets.MultiStageArea method) moveToGroup() (schrodinger.project.ProjectRow method) moveToPosition() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) moveUp() (schrodinger.application.matsci.mswidgets.StageFrame method) MOVEXBY (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) MOVEYBY (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) mPCLOSE() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mPOPEN() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MSAnalysisMSJStringer (class in schrodinger.application.matsci.desmondutils) mSEMI() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MSGWIDTH (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization attribute) (schrodinger.application.matsci.nano.interface_mod.Interface attribute) (schrodinger.application.matsci.nano.particle.Nanoparticle attribute) (schrodinger.application.matsci.nano.sheet.NanoSheets attribute) (schrodinger.application.matsci.nano.slab.Surface attribute) (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) (schrodinger.application.matsci.nano.tube.NanoTubes attribute) (schrodinger.application.matsci.nano.xtal.Crystal attribute) msj2cfg() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) MSJ_BASE (schrodinger.application.matsci.desmondutils.MSJStringer attribute) MSJ_LAST (schrodinger.application.matsci.desmondutils.MSJStringer attribute) MSJStringer (class in schrodinger.application.matsci.desmondutils) mSTRING() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mSUBTROP() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__45() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__46() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__47() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__48() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__49() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__50() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__51() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__52() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__53() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__54() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__55() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__56() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__57() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mT__58() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mTokens() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) MULLIK (schrodinger.application.mopac.results71.MopacResults71 attribute) mulliken_charge_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) mulliken_charges() (in module schrodinger.application.jaguar.textparser) MullikenSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) mult() (schrodinger.application.macromodel.utils.ComUtil method) MultiDesmondJobApp (class in schrodinger.application.matsci.guibase) MultiFileReader (class in schrodinger.structutils.io) MultiFileStructureReader (class in schrodinger.structure) MultiFileStructureWriter (class in schrodinger.structure) MultiFileWriter (class in schrodinger.structutils.io) MultiFPFile (class in schrodinger.utils.multifpfile) multifpfile_fpreader() (in module schrodinger.application.hitexpander) MultiFPFileWriter (class in schrodinger.utils.multifpfile) multijob_driver() (schrodinger.application.matsci.jobutils.MultijobDriver method) MultiJobApp (class in schrodinger.application.matsci.guibase) MultijobDriver (class in schrodinger.application.matsci.jobutils) multiJobStart() (schrodinger.application.matsci.guibase.MultiJobApp method) multip() (in module schrodinger.application.jaguar.textparser) multiple_align_ct() (in module schrodinger.application.ska) MULTIPLE_STRUC_JOB_TITLE (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin attribute) MULTIPLE_STRUC_PICK_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) MULTIPLE_STRUC_WARNING (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) multipole_esp() (in module schrodinger.application.jaguar.textparser) multipole_moments() (in module schrodinger.application.jaguar.textparser) multipole_mulliken() (in module schrodinger.application.jaguar.textparser) multipole_qm() (in module schrodinger.application.jaguar.textparser) MultipoleSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) MULTISIM_EXEC (schrodinger.application.desmond.envir.CONST attribute) MultiStageArea (class in schrodinger.application.matsci.mswidgets) MultiStructureMixin (class in schrodinger.application.jaguar.gui.base_panel) MultiStructurePanel (class in schrodinger.application.jaguar.gui.base_panel) MultiStructurePanelMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) MultiStructureTab (class in schrodinger.application.jaguar.gui.tabs.multi_structure_tab) MultiWalledNanoTube (class in schrodinger.application.matsci.nano.tube) mut_asl (schrodinger.application.desmond.replica_sid_generator.AlchemAsl attribute) mut_frag_st (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) mut_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) mut_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) mut_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) mut_solv_asl (schrodinger.application.desmond.replica_sid_generator.AlchemAsl attribute) mut_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) MutableSignalMeta (class in schrodinger.models.parameters) mutate() (in module schrodinger.structutils.build) (schrodinger.protein.sequence.Sequence method) MUTATE_METHOD_NAMES (schrodinger.models.parameters.BaseMutableParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.SetParam attribute) mutateResidues() (schrodinger.protein.alignment.BaseAlignment method) Mutation (class in schrodinger.application.bioluminate.protein) mutations (schrodinger.application.bioluminate.protein.Mutator attribute) MUTATIONS_PROPERTY (schrodinger.application.bioluminate.protein.Mutator attribute) MutationSelectorComboBox (class in schrodinger.ui.residueselector) MutationSelectorFrame (class in schrodinger.ui.residueselector) MutationSelectorLineEdit (class in schrodinger.ui.residueselector) MutationSelectorPopUp (class in schrodinger.ui.residueselector) Mutator (class in schrodinger.application.bioluminate.protein) MutClass (class in schrodinger.application.desmond.fep_gui) muts_str_to_list() (in module schrodinger.ui.residueselector) mWS() (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) mysplit() (in module schrodinger.utils.ligfilter)

N

n_qn (schrodinger.application.matsci.espresso.qeoutput.WfcType attribute) NA (schrodinger.application.jaguar.gui.utils.SpinTreatment attribute) nactive (schrodinger.application.desmond.packages.msys.System attribute) (schrodinger.application.desmond.packages.topo.DuckFrame attribute) (schrodinger.application.desmond.packages.traj.Frame attribute) nactive_gids (schrodinger.application.desmond.cms.Cms attribute) name (schrodinger.analysis.reaction.ReactionInstance attribute) (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.application.desmond.packages.msys.Chain attribute) (schrodinger.application.desmond.packages.msys.Ct attribute) (schrodinger.application.desmond.packages.msys.Residue attribute) (schrodinger.application.desmond.packages.msys.System attribute) (schrodinger.application.desmond.packages.msys.TermTable attribute) (schrodinger.application.desmond.packages.msys.molfile.Grid attribute) (schrodinger.application.desmond.packages.msys.molfile.SeqFile attribute) (schrodinger.application.desmond.packages.msys.molfile.StkFile attribute) (schrodinger.application.desmond.packages.traj.Source attribute) NAME (schrodinger.application.desmond.simulation_block_test.BoxSize attribute) (schrodinger.application.desmond.simulation_block_test.E_f attribute) (schrodinger.application.desmond.simulation_block_test.E_k attribute) (schrodinger.application.desmond.simulation_block_test.E_x attribute) (schrodinger.application.desmond.simulation_block_test.Energy attribute) (schrodinger.application.desmond.simulation_block_test.Job_Details attribute) (schrodinger.application.desmond.simulation_block_test.PotentialEnergy attribute) (schrodinger.application.desmond.simulation_block_test.Pressure attribute) (schrodinger.application.desmond.simulation_block_test.T_0 attribute) (schrodinger.application.desmond.simulation_block_test.Temperature attribute) (schrodinger.application.desmond.simulation_block_test.V attribute) (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.desmond.systype.TyperBase attribute) (schrodinger.application.desmond.systype.WatermapTyper attribute) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase attribute) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) name (schrodinger.application.jaguar.gui.utils.Solvent attribute) (schrodinger.application.jaguar.input.JaguarInput attribute) (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword attribute) (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) (schrodinger.application.livedesign.maestro_data_types.Complexes attribute) (schrodinger.application.livedesign.maestro_data_types.CovalentDockingComplexes attribute) (schrodinger.application.livedesign.maestro_data_types.DockedPoses attribute) (schrodinger.application.livedesign.maestro_data_types.Ligands attribute) (schrodinger.application.livedesign.maestro_data_types.OrganometallicCompounds attribute) (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement attribute) NAME (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Slab attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) name (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) (schrodinger.project.EntryGroup attribute) (schrodinger.project_surface.ProjectSurface attribute) (schrodinger.protein.sequence.Sequence attribute) (schrodinger.structure._Chain attribute) (schrodinger.structure._StructureAtom attribute) (schrodinger.surface.Surface attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks_.AbstractTask attribute) name1 (schrodinger.application.matsci.cgforcefield.ShadowData attribute) name2 (schrodinger.application.matsci.cgforcefield.ShadowData attribute) NAME_NOT_UNIQUE_MSG (schrodinger.tasks.tasks_.TaskManager attribute) nameChanged (schrodinger.protein.sequence.Sequence attribute) (schrodinger.tasks.runners.TaskRunner attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks_.AbstractTask attribute) nameContextCallback() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) NAMED_PROPERTIES (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) (schrodinger.application.matsci.cgforcefield.FFIOSite attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwType attribute) (schrodinger.application.matsci.cgforcefield.FFIOVdwTypesCombined attribute) nameNum() (schrodinger.application.desmond.fep_edge_data.ResData method) NAMES (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) namespaces (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) Nanoparticle (class in schrodinger.application.matsci.nano.particle) NanoSheet (class in schrodinger.application.matsci.nano.tube) NanoSheets (class in schrodinger.application.matsci.nano.sheet) NanoTube (class in schrodinger.application.matsci.nano.tube) NanoTubes (class in schrodinger.application.matsci.nano.tube) NanoTubeSheet (class in schrodinger.application.matsci.nano.tube) natoms (schrodinger.application.desmond.packages.msys.Ct attribute) (schrodinger.application.desmond.packages.msys.Residue attribute) (schrodinger.application.desmond.packages.msys.SmartsPattern attribute) (schrodinger.application.desmond.packages.msys.System attribute) (schrodinger.application.desmond.packages.msys.TermTable attribute) (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader attribute) (schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader attribute) (schrodinger.application.desmond.packages.topo.DuckFrame attribute) (schrodinger.application.desmond.packages.traj.Frame attribute) nb_cutoff() (in module schrodinger.application.qsite.output) nb_update() (in module schrodinger.application.qsite.output) nbasis() (in module schrodinger.application.jaguar.textparser) NBILAYERS (schrodinger.application.matsci.nano.constants.Constants attribute) nbonds (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.application.desmond.packages.msys.System attribute) NCELL1 (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) NCELL2 (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) NCELLA (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) NCELLB (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) NCELLC (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) NCELLS (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) nchains (schrodinger.application.desmond.packages.msys.Ct attribute) (schrodinger.application.desmond.packages.msys.System attribute) nconmm() (in module schrodinger.application.qsite.output) ncts (schrodinger.application.desmond.packages.msys.System attribute) ncuts() (in module schrodinger.application.qsite.output) nddo_atoms() (in module schrodinger.application.qsite.output) nddo_hcaps() (in module schrodinger.application.qsite.output) NEAR_METHOD_NAMEMAP (schrodinger.application.desmond.gui.InteractionTab attribute) NEAR_RESIDUES (schrodinger.ui.picking.MaestrolessPickResidueDialog attribute) nearbyRes() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) nearest_asl_atom (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) nearest_atom_distance() (schrodinger.application.bindingsite.intfield.Field method) nearest_atom_indices (schrodinger.surface.Surface attribute) nearest_rotatable_bonds() (in module schrodinger.application.matsci.amorphous) nearMethodChanged() (schrodinger.application.desmond.gui.InteractionTab method) neb_set_system_nat() (in module schrodinger.application.matsci.qexsd.qespresso.options) NEB_TEMPLATE_MAP (schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter attribute) NebDocument (class in schrodinger.application.matsci.qexsd.qespresso.documents) NebInputConverter (class in schrodinger.application.matsci.qexsd.qespresso.converters) NEBInputType (class in schrodinger.application.matsci.espresso.qeinput) NEBPathType (class in schrodinger.application.matsci.espresso.qeinput) need_server() (schrodinger.application.licensing.flexlm.License method) needsExplicitJobname() (schrodinger.job.launchapi.TaskSpecification method) needSyncFeatureDef() (schrodinger.infra.phase.PhpProject method) NEG_HESS_TOL (schrodinger.application.matsci.mecp_mod.BFGS attribute) negative (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute) NEGATIVE (schrodinger.protein.residue.RESIDUE_CHARGE attribute) Neighbor (class in schrodinger.application.matsci.clusterstruct) neighbor() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) neighbor_atom (schrodinger.application.matsci.clusterstruct.Neighbor attribute) NeighborTreatment (class in schrodinger.application.matsci.chargegui) NeighborType (class in schrodinger.application.matsci.nano.sheet) NetsuiteError NEUTRAL (schrodinger.protein.residue.RESIDUE_CHARGE attribute) NEUTRAL_HYDROPHILIC (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) NEUTRAL_HYDROPHOBIC_ALIPHATIC (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) NEUTRAL_HYDROPHOBIC_AROMATIC (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) neutralize() (schrodinger.structure.SmilesStructure method) neutralize_structure() (in module schrodinger.structutils.build) new_best() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) new_instancemethod() (in module schrodinger.infra.fast3d) (in module schrodinger.infra.licensing) (in module schrodinger.infra.mmgpgpu) (in module schrodinger.infra.mmjob) (in module schrodinger.infra.mmreflect) (in module schrodinger.infra.mmsurf) (in module schrodinger.infra.phase) (in module schrodinger.utils.colorscheme) (in module schrodinger.utils.mmutil) new_page() (in module schrodinger.application.desmond.report_helper) NEW_STRUCTURE (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) new_temperature() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) newAssaySelected (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate attribute) (schrodinger.application.livedesign.panel_components.AssaySelectionPopup attribute) newColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) newColorSchemeRule() (schrodinger.utils.colorscheme.ColorSchemeManager method) newEndpointSelected (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit attribute) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopup attribute) NewEntry (class in schrodinger.application.desmond.maestro) NewEntryGroup (class in schrodinger.application.desmond.maestro) newForMaestro() (schrodinger.infra.fast3d.Volumizer static method) newIteration() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) NewJobDirDialog (class in schrodinger.application.matsci.jobdirdlg) NewJobDirFrame (class in schrodinger.application.matsci.jobdirdlg) newLiveReportSelected (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox attribute) (schrodinger.application.livedesign.panel_components.LiveReportSelector attribute) newMolecularSurface() (schrodinger.project.ProjectRow method) (schrodinger.project_surface.ProjectSurface class method) (schrodinger.surface.Surface class method) newParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) newProject() (schrodinger.infra.phase.PhpProject method) next() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.PhpStructureReader method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) next_prime() (in module schrodinger.application.desmond.autopartition) next_sphere_id (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) nextButton() (schrodinger.application.matsci.siteselector.siteselector.LigandSelector method) nextGeom() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom method) nextName() (schrodinger.tasks.runners.TaskRunner method) nextNode() (schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleSubtreeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method) nextOutFile() (schrodinger.pipeline.stages.ligprep.PostLigPrepStage method) nextTask() (schrodinger.tasks.runners.TaskRunner method) (schrodinger.tasks.tasks_.TaskManager method)

nextToken() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.TokenSource method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method) (schrodinger.application.desmond.antlr3.treewizard.TreePatternLexer method) nextTree() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) NFFTX (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) nframes (schrodinger.application.desmond.packages.msys.molfile.SeqFile.Reader attribute) (schrodinger.application.desmond.packages.msys.molfile.StkFile.Reader attribute) nframes() (schrodinger.application.desmond.packages.traj.DtrSource method) (schrodinger.application.desmond.packages.traj.Source method) (schrodinger.application.desmond.packages.traj.XtcSource method) nfrzmm() (in module schrodinger.application.qsite.output) nhcaps() (in module schrodinger.application.qsite.output) nhydrogens (schrodinger.application.desmond.packages.msys.Atom attribute) nil() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) nilNode() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) NINDEX (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) NMA (class in schrodinger.trajectory.prody.nma) nmr_precision (schrodinger.application.jaguar.results.JaguarAtomicResults attribute) NO_DOUBLE_BONDS (schrodinger.application.matsci.nano.constants.Constants attribute) NO_ISOMER (in module schrodinger.application.matsci.buildcomplex) NO_MINIMIZATION (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) NO_PROPENSITY (schrodinger.protein.residue.BETA_STRAND_PROPENSITY attribute) (schrodinger.protein.residue.HELIX_PROPENSITY attribute) (schrodinger.protein.residue.TURN_PROPENSITY attribute) NO_REACTIVE_H (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) NO_SIDE_CHAIN_CHEM (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) NO_SOLVENT_MODEL (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) no_stack() (in module schrodinger.application.jaguar) (in module schrodinger.application.mopac) NO_STERIC (schrodinger.protein.residue.STERIC_GROUP attribute) NO_TENDENCY (schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY attribute) (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) no_zob_restrain (schrodinger.structutils.minimize.Minimizer attribute) NoActivesRankedException noautofit_call() (in module schrodinger.application.desmond.maestro) Node (class in schrodinger.analysis.reaction) (class in schrodinger.application.desmond.enhsamp) (class in schrodinger.application.desmond.reorder_atom) NODE_PLURAL_STRING (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) (schrodinger.application.livedesign.maestro_data_types.Complexes attribute) (schrodinger.application.livedesign.maestro_data_types.DockedPoses attribute) (schrodinger.application.livedesign.maestro_data_types.Ligands attribute) (schrodinger.application.livedesign.maestro_data_types.OrganometallicCompounds attribute) NODE_SINGULAR_STRING (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) (schrodinger.application.livedesign.maestro_data_types.Complexes attribute) (schrodinger.application.livedesign.maestro_data_types.DockedPoses attribute) (schrodinger.application.livedesign.maestro_data_types.Ligands attribute) (schrodinger.application.livedesign.maestro_data_types.OrganometallicCompounds attribute) nodes() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) NOEConstraint (class in schrodinger.application.glide.glide) nofail_geopt() (in module schrodinger.application.jaguar.textparser) nofail_geopt_restart() (in module schrodinger.application.jaguar.textparser) nofitgrow_call() (in module schrodinger.application.desmond.maestro) NoInputTabJobMixin (class in schrodinger.application.jaguar.gui.base_panel) NOMM (schrodinger.application.mopac.structure_launchers.StructureLauncher attribute) NON_AROMATIC_RES (schrodinger.application.bioluminate.interaction_calculator.PiStackFinder attribute) non_default_print_options() (in module schrodinger.application.jaguar.textparser) nonbonded_cutoff (schrodinger.structutils.minimize.Minimizer attribute) nonbonded_info (schrodinger.application.desmond.packages.msys.System attribute) NonbondedSchemas() (in module schrodinger.application.desmond.packages.msys) NONE (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) (schrodinger.maestro.markers.Icons attribute) (schrodinger.tasks.tasks.Status attribute) nops_on() (in module schrodinger.application.jaguar.textparser) norm() (in module schrodinger.application.desmond.cms) normal (schrodinger.structutils.ringspear.SpearRing attribute) normalizeFeatureEquiv() (schrodinger.infra.phase.PhpProject method) NormalMode (class in schrodinger.application.jaguar.results) normals (schrodinger.graphics3d.polyhedron.Polyhedron attribute) NORMTHRESH (schrodinger.application.matsci.rxn_path.ReactionPath attribute) NORXNCOMPLEX (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) not_conserved (schrodinger.protein.annotation.Consensus attribute) NOT_READY (schrodinger.tasks.tasks.Status attribute) NotCDR (schrodinger.protein.annotation.AntibodyCDRLabel attribute) NotInWorkspaceError NOTRUNNING (schrodinger.tasks.tasks_.Status attribute) NotVisible (schrodinger.protein.sequence.Inclusion attribute) noverrides (schrodinger.application.desmond.packages.msys.TermTable attribute) noViableAlt() (schrodinger.application.desmond.antlr3.dfa.DFA method) NoViableAltException nparams (schrodinger.application.desmond.packages.msys.ParamTable attribute) nprops (schrodinger.application.desmond.packages.msys.ParamTable attribute) nresidues (schrodinger.application.desmond.packages.msys.Chain attribute) (schrodinger.application.desmond.packages.msys.System attribute) nterms (schrodinger.application.desmond.packages.msys.TermTable attribute) NucleicAcidAlignment (class in schrodinger.protein.alignment) NucleicAcidSequence (class in schrodinger.protein.sequence) NucleicAcidSequenceAnnotations (class in schrodinger.protein.annotation) Nucleotide (class in schrodinger.protein.residue) NucleotideType (class in schrodinger.protein.residue) nucrep1() (in module schrodinger.application.jaguar.textparser) nucrep2() (in module schrodinger.application.jaguar.textparser) nucrep_precision (schrodinger.application.jaguar.results.JaguarResults attribute) NUM (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) Num_aliphatic_rings() (in module schrodinger.utils.ligfilter) Num_aromatic_rings() (in module schrodinger.utils.ligfilter) Num_atoms() (in module schrodinger.utils.ligfilter) num_basis_functions() (in module schrodinger.application.jaguar.gui.basis_selector) NUM_BITS_PER_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) num_bonds() (in module schrodinger.application.jaguar.structure_isomorphism) NUM_CENTERING_OPERS (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) Num_chiral_centers() (in module schrodinger.utils.ligfilter) num_clusters_selected (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog attribute) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog attribute) NUM_COLS (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) NUM_CONSTRAINT (schrodinger.application.desmond.cms.Constraint attribute) num_constraint() (schrodinger.application.desmond.cms.Constraint method) num_cpu() (in module schrodinger.application.desmond.config) NUM_DECIMAL_COORDS (schrodinger.application.matsci.nano.xtal.Crystal attribute) NUM_EQUIV_SETS (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) num_functions() (in module schrodinger.application.jaguar.basis) num_functions_all_atoms() (in module schrodinger.application.jaguar.basis) num_functions_per_atom() (in module schrodinger.application.jaguar.basis) Num_heavy_atoms() (in module schrodinger.utils.ligfilter) Num_heteroaromatic_rings() (in module schrodinger.utils.ligfilter) NUM_IDX (schrodinger.application.matsci.espresso.qeoutput.PDOS attribute) num_lambda_window() (in module schrodinger.application.desmond.config) Num_molecules() (in module schrodinger.utils.ligfilter) Num_negative_atoms() (in module schrodinger.utils.ligfilter) Num_positive_atoms() (in module schrodinger.utils.ligfilter) NUM_PRIMARY_OPERS (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) NUM_RANDOM_CHANNELS (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) NUM_RANDOM_CHANNELS_METAVAR (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) num_replica() (in module schrodinger.application.desmond.config) Num_residues() (in module schrodinger.utils.ligfilter) Num_rings() (in module schrodinger.utils.ligfilter) num_rl_pairs (schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute) Num_rotatable_bonds() (in module schrodinger.utils.ligfilter) NUM_SCALING (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) NUM_SPACE_GROUPS (schrodinger.application.matsci.nano.xtal.SpaceGroups attribute) NUM_SYM_ATOMS (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) NUM_SYMMETRY_OPERS (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) NUM_UNIQUE_EDGES (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) NUM_UNIQUE_FACES (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) num_wildcard() (schrodinger.utils.sea.Atom static method) numActivities() (schrodinger.infra.phase.PhpQSAR method) NUMATOMS (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) numAtoms() (schrodinger.trajectory.prody.ensemble.Ensemble method) (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) number (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) (schrodinger.structure._Molecule attribute) number_by_entry (schrodinger.structure._StructureAtom attribute) number_by_molecule (schrodinger.structure._StructureAtom attribute) NumberedCanvas (class in schrodinger.application.desmond.report_helper) numBitsByClass (schrodinger.infra.phase.PhpQSARModel attribute) numChoices() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) numClashs() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numConformations() (schrodinger.infra.phase.PhpMMconfAdaptor method) numConfs() (schrodinger.trajectory.prody.ensemble.Ensemble method) numConstraints() (schrodinger.infra.phase.PhpSiteConstrainer method) numDataColumns() (schrodinger.infra.phase.PhpFeatureData method) NUMDECIMAL (schrodinger.application.matsci.nano.tube.NanoTube attribute) NUMDENSEPOINTS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) NUMDIGITS (schrodinger.application.matsci.nano.slab.Surface attribute) numDisulfides() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numDOF() (schrodinger.trajectory.prody.mode.Mode method) (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) numerical_freqs() (in module schrodinger.application.jaguar.textparser) NumericalDatabaseCriterion (class in schrodinger.application.bioluminate.propfilter) NumericLineEdit (class in schrodinger.application.bioluminate.bwidgets) numForceFields() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) numGroupsChanged() (schrodinger.application.desmond.gui.EnsembleTab method) numHbonds() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numModes() (schrodinger.trajectory.prody.mode.VectorBase method) (schrodinger.trajectory.prody.modeset.ModeSet method) (schrodinger.trajectory.prody.nma.NMA method) numMolecules() (schrodinger.infra.phase.PhpQSAR method) numObs() (schrodinger.infra.phase.PhpHiCluster method) numPiStacks() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numPLSFactors() (schrodinger.infra.phase.PhpQSAR method) numPos() (schrodinger.application.canvas.r_group_dee.DEE_EnergyMatrix method) (schrodinger.application.desmond.packages.staf.Positer method) numResources() (schrodinger.application.licensing.licadmin.LocalServerProcess method) numSaltBridges() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numSelected() (schrodinger.trajectory.prody.ensemble.Ensemble method) numShapes() (schrodinger.infra.phase.PhpExclVol method) numSites() (schrodinger.infra.phase.PhpDeltaHypo method) (schrodinger.infra.phase.PhpFeatureRules method) (schrodinger.infra.phase.PhpSiteMask method) numSpecificInteractions() (schrodinger.application.bioluminate.interaction_calculator.Interactions method) numSpheres() (schrodinger.infra.phase.PhpExclVol method) numVolBits() (schrodinger.infra.phase.PhpQSAR method) NWALLS (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube attribute)

O

obj_params_from_value() (in module schrodinger.models.parameters) OCTAHEDRAL (in module schrodinger.application.matsci.buildcomplex) OCTAHEDRAL_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) OctahedralSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) Octahedron (class in schrodinger.application.matsci.shapes) (class in schrodinger.graphics3d.polyhedron) offsetAtomData() (schrodinger.application.matsci.nano.xtal.PBCBond method) ofstream (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) OH_length (schrodinger.protein.assignment.ProtAssign.changeable attribute) ok (schrodinger.application.desmond.packages.msys.InChI attribute) OK (schrodinger.application.jaguar.input.GenOptions attribute) (schrodinger.application.jaguar.output.JaguarOutput attribute) ok_pattern (schrodinger.infra.mmcheck.ReturnCode attribute) okPressed() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) on_lower_edge() (in module schrodinger.application.matsci.nano.xtal) on_move() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) on_same_drive_letter() (in module schrodinger.utils.fileutils) on_upper_edge() (in module schrodinger.application.matsci.nano.xtal) onApplyToRowsClicked() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) onAssaySelected() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) onCategoryChanged() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) onCommitDataToSelected() (schrodinger.application.livedesign.panel_components.ExportTableView method) onCurrentIndexChanged() (schrodinger.application.livedesign.panel_components.LRSortCombo method) onDataChanged() (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) ONE_BY_ARMCHAIR_BASE (schrodinger.application.matsci.nano.sheet.Grow attribute) ONE_BY_ZIGZAG_BASE (schrodinger.application.matsci.nano.sheet.Grow attribute) one_e_terms() (in module schrodinger.application.jaguar.textparser) OneIndexedList (class in schrodinger.infra.util) onEndpointSelected() (schrodinger.application.livedesign.panel_components.EndpointSelectionLineEdit method) onEntryTypeChanged() (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) onHostMenuChanged() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.fep_gui.RESTFEPConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) onItemChanged() (schrodinger.application.livedesign.panel_components.ColumnSelectionModel method) onLiveReportSelected() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) onLRSortMethodChanged() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) onMissingFields() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) onModelParamChanged() (schrodinger.models.mappers.Target method) onModelValueChanged() (schrodinger.models.mappers.SettingsParamMapper method) onMotion() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) onNewAssaySelected() (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) onNoProjectSelected() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) onNumOfFramesChanged() (schrodinger.application.desmond.gui.SimOptionsFrame method) onPress() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) onProjectClosed() (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) onProjectSelected() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) onPropSelectChanged() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) onRelease() (schrodinger.application.bioluminate.sliderchart.SlidableLine method) onShowColumns() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) onShowComboIndexChanged() (schrodinger.ui.picking.MaestrolessPickResidueDialog method) onSimTimeChanged() (schrodinger.application.desmond.gui.SimOptionsFrame method) onStructureChanged() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) (schrodinger.protein.sequence.Sequence method) onTargetSignal() (schrodinger.models.mappers.Target method) onTaskStatusChanged() (schrodinger.tasks.runners.TaskRunner method) onThreadFinished() (schrodinger.tasks.tasks.ThreadFunctionTask method) onTrajIntervalChanged() (schrodinger.application.desmond.gui.SimOptionsFrame method) onURLEntered() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) opacity (schrodinger.graphics3d.arrow.MaestroArrow attribute) (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.graphics3d.torus.MaestroTorus attribute) OPACITY_DEFAULT (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) OPACITY_SELECTED (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) open() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) open_bonding_sites() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) open_csv() (in module schrodinger.application.canvas.driverutils) open_databases() (in module schrodinger.application.bioluminate.antibody.utils) open_file() (in module schrodinger.application.mopac.utils) open_filename() (in module schrodinger.protein.getpdb) open_mmzip() (in module schrodinger.project) open_multiy_csv() (in module schrodinger.application.canvas.driverutils) open_project() (in module schrodinger.project) open_ring_action (schrodinger.infra.phase.PhpAlignCoreOptions attribute) open_ring_policy (schrodinger.infra.phase.PhpAlignCoreOptions attribute) open_url() (in module schrodinger.utils.documentation) openAdvancedDialog() (schrodinger.application.desmond.gui.AdvOptionsFrame method) openCollectionPanel() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) openExportMap() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) openFile() (in module schrodinger.trajectory.prody.writenmd) (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.WholePDB method) openFiles() (schrodinger.protein.getpdb_utility.Code method) openHelp() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) openMapping() (schrodinger.application.livedesign.ld_export.ExportMapManager method) openMenu() (schrodinger.application.bioluminate.ssv.toolbars.ImportToolBar method) openProject() (schrodinger.infra.phase.PhpProject method) openRingFailure() (schrodinger.infra.phase.PhpAlignCore method) openTempURL() (in module schrodinger.utils.documentation) operate() (schrodinger.pipeline.stage.Stage method) (schrodinger.pipeline.stages.canvas.Canvas2DSimilarityStage method) (schrodinger.pipeline.stages.combine.CombineStage method) (schrodinger.pipeline.stages.combine.DataFusionMergeStage method) (schrodinger.pipeline.stages.convert.ConvertStage method) (schrodinger.pipeline.stages.example.ExampleStage method) (schrodinger.pipeline.stages.filtering.ChargeFilterStage method) (schrodinger.pipeline.stages.filtering.DrugLikeSplitStage method) (schrodinger.pipeline.stages.filtering.GeneratePropsStage method) (schrodinger.pipeline.stages.filtering.LigFilterStage method) (schrodinger.pipeline.stages.filtering.MergeDuplicatesStage method) (schrodinger.pipeline.stages.filtering.SubSetStage method) (schrodinger.pipeline.stages.gencodes.RecombineStage method) (schrodinger.pipeline.stages.gencodes.RestoreTitlesStage method) (schrodinger.pipeline.stages.glide.DockingStage method) (schrodinger.pipeline.stages.glide.GlideSortStage method) (schrodinger.pipeline.stages.glide.GridgenStage method) (schrodinger.pipeline.stages.glide.MergeStage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) (schrodinger.pipeline.stages.ligprep.PostLigPrepStage method) (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) (schrodinger.pipeline.stages.phase.DBConfSitesStage method) (schrodinger.pipeline.stages.phase.DBExportStage method) (schrodinger.pipeline.stages.phase.DBManageStage method) (schrodinger.pipeline.stages.phase.PhaseShapeStage method) (schrodinger.pipeline.stages.prime.MMGBSAStage method) (schrodinger.pipeline.stages.prime.PrimeStage method) (schrodinger.pipeline.stages.pull.PullStage method) (schrodinger.pipeline.stages.qikprop.QikPropStage method) (schrodinger.pipeline.stages.qsite.QSiteStage method) (schrodinger.pipeline.stages.rmsd.RmsdStage method) (schrodinger.pipeline.stages.semiemp.SemiEmpStage method)

operater2Changed() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) operator1Changed() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) OPLS_CONVERGED_KEY (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels attribute) OPLS_ENERGY_KEY (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels attribute) opls_forcefield_names() (in module schrodinger.application.desmond.constants) OPLS_RMS_KEY (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels attribute) OPLS_VERSION (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels attribute) OPTIMIZATION (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin attribute) OptimizationAndScanMixin (class in schrodinger.application.jaguar.gui.base_panel) OptimizationFailure OptimizationTab (class in schrodinger.application.jaguar.gui.tabs.optimization_tab) OptimizationTabMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) optimize() (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.protein.assignment.ProtAssign method) (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) optimize_cluster() (schrodinger.protein.assignment.ProtAssign method) optimize_key() (in module schrodinger.application.desmond.config) (in module schrodinger.application.desmond.gconfig) optimizeGeometry() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.StructureGenome method) option_float_varargs_callback() (in module schrodinger.application.canvas.driverutils) option_string_varargs_callback() (in module schrodinger.application.canvas.driverutils) OPTION_TEXT (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) Optional (schrodinger.application.livedesign.maestro_data_types.Export3D attribute) OptionError optionfile() (schrodinger.application.licensing.flexlm.Vendor method) OPTIONS (schrodinger.application.desmond.packages.energygroup.Bulk attribute) options_file() (in module schrodinger.application.licensing.licadmin) optoelectronics_evaluator() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) OptStep (class in schrodinger.application.matsci.jaguarworkflows) Orbital (class in schrodinger.application.jaguar.results) orbital_energies() (in module schrodinger.application.jaguar.textparser) orbitalsChanged() (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) orc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orcc() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orcf1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orcf2() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orcf3() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) orchestrate() (schrodinger.application.matsci.nano.xtal.Crystal method) (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) orci() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) order (schrodinger.application.desmond.packages.msys.Bond attribute) (schrodinger.structure._StructureBond attribute) order_ring_or_chain() (in module schrodinger.structutils.assignbondorders) OrderBy (class in schrodinger.structutils.interactions.salt_bridge) OrderedDefaultDict (class in schrodinger.application.matsci.espresso.qeoutput) OrderedOctahedralSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) OrderedResidueDict (class in schrodinger.application.bioluminate.protein) OrderedSquarePlanarSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) orderInternalByName() (schrodinger.application.matsci.coarsegrain.Internals method) OrderParameter (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.application.matsci.order_parameter_mod) orders_assigned() (in module schrodinger.structutils.assignbondorders) organizeDoubleBonds() (schrodinger.application.matsci.nano.sheet.Grow method) OrganometallicCompounds (class in schrodinger.application.livedesign.maestro_data_types) ORIG_ATOM_INDEX (schrodinger.structutils.ringspear.SpearRing attribute) orig_idx_to_cur_idx() (in module schrodinger.trajectory.prody.writenmd) orig_index (schrodinger.application.desmond.packages.traj.Frame attribute) orig_index_prop (schrodinger.structutils.rmsd.ConformerRmsd attribute) orig_key() (schrodinger.utils.sea.Key method) origin (schrodinger.application.desmond.packages.msys.molfile.Grid attribute) ORIGIN (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) origin_normal (schrodinger.structutils.ringspear.SpearRing attribute) origin_to_point() (in module schrodinger.graphics3d.polyhedron) ORTHORHOMBIC_NAME (schrodinger.application.matsci.nano.xtal.CrystalSystems attribute) osc_precision (schrodinger.application.jaguar.results.JaguarResults attribute) ostream (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) other() (schrodinger.application.desmond.packages.msys.Bond method) OTHERS (schrodinger.application.matsci.desmondutils.MSJStringer attribute) OUT_EXT (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) outComFile() (schrodinger.application.macromodel.utils.ComUtil static method) outdated_server() (schrodinger.application.licensing.licadmin.LicenseResource method) Output (class in schrodinger.application.matsci.espresso.qeoutput) output (schrodinger.application.licensing.licerror.LicenseError attribute) (schrodinger.tasks.tasks_.AbstractTask attribute) output() (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) output_file (schrodinger.application.mopac.mopac_results.MopacResults attribute) (schrodinger.application.mopac.results2012.MopacResults2012 attribute) (schrodinger.application.mopac.results71.MopacResults71 attribute) output_term() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) outputChanged (schrodinger.tasks.tasks_.AbstractTask attribute) OutputFiles (schrodinger.job.jobcontrol.Job attribute) outputRequested() (schrodinger.pipeline.stage.Stage method) outputStructure() (schrodinger.protein.captermini.CapTermini method) OutputTab (class in schrodinger.application.desmond.gui) (class in schrodinger.application.jaguar.gui.tabs.output_tab) OutStruct (class in schrodinger.application.matsci.espresso.qeoutput) override_params (schrodinger.application.desmond.packages.msys.TermTable attribute) OverrideKeywords (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) overrides() (schrodinger.application.desmond.packages.msys.TermTable method) overwriteVertices() (schrodinger.application.matsci.nano.particle.Nanoparticle method) Owner (schrodinger.application.livedesign.panel_components.LRSort attribute) ownerChain() (schrodinger.models.parameters.Param method)

P

Package (class in schrodinger.application.licensing.flexlm) packFp() (schrodinger.infra.phase.PhpDatabaseFp static method) packing_fraction() (in module schrodinger.application.matsci.mlearn.features) padAlignment() (schrodinger.protein.alignment.BaseAlignment method) PADDING (schrodinger.application.matsci.desmondutils.MSJStringer attribute) PAGE_MARGIN (schrodinger.application.report2d.PicturePrinter attribute) paint_asl() (in module schrodinger.application.desmond.maestro) (schrodinger.application.desmond.maestro.Workspace method) paint_mol() (schrodinger.application.desmond.maestro.Workspace method) paintCell() (schrodinger.application.combiglide.combenumdock.createFragmentDelegate method) (schrodinger.application.combiglide.combenumdock.simpleEnumDockDelegate method) paintEvent() (schrodinger.application.bioluminate.bwidgets.RowActionItem method) (schrodinger.application.jaguar.gui.utils.WorkspaceInclusionCheckBox method) PairMarker (class in schrodinger.maestro.markers) PAIRS (schrodinger.application.matsci.rxn_path.CheckInput attribute) pairwise_align_ct() (in module schrodinger.application.ska) PairwiseAligner (class in schrodinger.protein.align) paletteChanged() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) paletteRefreshed() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) panel() (in module schrodinger.application.bioluminate.protein_report_widget) (in module schrodinger.application.livedesign.login) (in module schrodinger.application.matsci.reordergui) PanelTaskReporter (class in schrodinger.tasks.runners) Parallelepiped (class in schrodinger.application.matsci.shapes) Param (class in schrodinger.application.desmond.packages.msys) (class in schrodinger.models.parameters) param (schrodinger.application.desmond.packages.msys.Term attribute) param() (schrodinger.application.desmond.packages.msys.ParamTable method) PARAM_ORDER (schrodinger.application.matsci.cgforcefield.FFIOBond attribute) (schrodinger.application.matsci.cgforcefield.FFIOImproper attribute) (schrodinger.application.matsci.cgforcefield.FFIOParam attribute) param_value_to_dict() (in module schrodinger.models.parameters) paramDict() (schrodinger.application.bioluminate.interaction_calculator.InteractionParams method) paramid (schrodinger.application.desmond.packages.msys.Term attribute) ParamListParam (class in schrodinger.models.parameters) ParamMeta (class in schrodinger.models.parameters) ParamModel (class in schrodinger.models.parameters) params (schrodinger.application.desmond.packages.msys.ParamTable attribute) (schrodinger.application.desmond.packages.msys.TermTable attribute) ParamTable (class in schrodinger.application.desmond.packages.msys) ParamTarget (class in schrodinger.models.mappers) parent() (schrodinger.application.desmond.reorder_atom.Node method) (schrodinger.utils.sea.Sea method) parent_dir() (in module schrodinger.application.desmond.util) ParentStageData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) pargph() (in module schrodinger.application.desmond.report_helper) parse() (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) (schrodinger.application.desmond.packages.cui.LazyParser method) (schrodinger.application.jaguar.scan.Scan static method) (schrodinger.application.jaguar.textparser.TextParser method) (schrodinger.application.mopac.results2012.Mopac2012TextParser method) (schrodinger.utils.ligfilter.CriterionParser method) (schrodinger.utils.ligfilter.DefinitionParser method) parse_args() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.licensing.lmgrd_log_parser) (in module schrodinger.application.matsci.qexsd.qespresso.utils.xml2nebinput) (in module schrodinger.application.matsci.qexsd.qespresso.utils.xml2qeinput) (in module schrodinger.application.mopac.mopac_parser) (in module schrodinger.utils.installation_check) (schrodinger.application.desmond.packages.cui.CommandLine method) (schrodinger.utils.cmdline.SingleDashOptionParser method) parse_arguments() (in module schrodinger.protein.getpdb_utility) parse_basis() (in module schrodinger.application.jaguar.basis) parse_checkpoint_file() (in module schrodinger.application.desmond.starter.generator.fep_plus) parse_combined_exclusion_str() (in module schrodinger.application.matsci.coarsegrain) parse_command_line() (in module schrodinger.application.vsw.vswinput) parse_components() (in module schrodinger.application.licensing.flexlm) parse_date() (in module schrodinger.application.licensing.flexlm) parse_datetime() (in module schrodinger.application.licensing.lmgrd_log_parser) parse_ene_file() (in module schrodinger.application.matsci.desmondutils) parse_eneseq() (in module schrodinger.application.desmond.fepana) (in module schrodinger.application.desmond.packages.gdesmond_utils) parse_events() (in module schrodinger.application.licensing.lmgrd_log_parser) parse_expiration() (in module schrodinger.application.licensing.flexlm) parse_fep_data() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) parse_filter_expression() (in module schrodinger.structutils.filter) parse_geometry() (in module schrodinger.application.desmond.util) parse_gibbs_energies() (in module schrodinger.application.jaguar.utils) parse_hunt_args() (in module schrodinger.job.hunt_stub) parse_indices() (in module schrodinger.application.desmond.enhsamp) parse_it() (in module schrodinger.application.desmond.title_to_hex) parse_json() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) parse_keyword_list() (in module schrodinger.application.matsci.jobutils) parse_lambda() (in module schrodinger.application.desmond.config) parse_line() (in module schrodinger.application.licensing.flexlm) parse_lmdiag_entry() (in module schrodinger.application.licensing.licadmin) parse_lmdiag_output() (in module schrodinger.application.licensing.licadmin) parse_lmgrd_event() (in module schrodinger.application.licensing.licadmin) parse_lmgrd_lines() (in module schrodinger.application.licensing.licadmin) parse_lmgrd_log() (in module schrodinger.application.licensing.licadmin) parse_lmhostid_output() (in module schrodinger.application.licensing.licadmin) parse_lmstat_output() (in module schrodinger.application.licensing.licadmin) parse_logfile() (in module schrodinger.application.licensing.lmgrd_log_parser) parse_meta() (in module schrodinger.application.desmond.meta) parse_mexpr() (in module schrodinger.application.desmond.enhsamp) parse_prm_tag() (in module schrodinger.application.desmond.replica_sid_generator) parse_reaction_data() (in module schrodinger.analysis.reaction) parse_reagent_classes_data() (in module schrodinger.analysis.reaction) parse_res_tag() (in module schrodinger.application.desmond.fep_edge_report_maker) parse_restart_parameters_file() (in module schrodinger.application.matsci.jobutils) parse_route_data() (in module schrodinger.analysis.reaction) parse_sba() (in module schrodinger.application.desmond.simulation_block_data) parse_sbt() (in module schrodinger.application.desmond.simulation_block_test) parse_slice() (in module schrodinger.application.desmond.util) parse_timedelta() (in module schrodinger.application.licensing.lmgrd_log_parser) parse_tokens() (in module schrodinger.application.licensing.flexlm) parse_xml() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) parse_yaml() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) parseArgs() (schrodinger.application.matsci.mecp_mod.ParserWrapper method) (schrodinger.application.matsci.nano.interface_mod.ParserWrapper method) (schrodinger.application.matsci.nano.particle.ParserWrapper method) (schrodinger.application.matsci.nano.slab.ParserWrapper method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.ParserWrapper method) (schrodinger.application.matsci.nano.xtal.ParserWrapper method) (schrodinger.application.matsci.rxn_path.ParserWrapper method) parseAtomText() (schrodinger.application.matsci.reordergui.StructureListWidget method) parseBlock_F() (schrodinger.application.glide.xpdes.XpPVParser method) parseBlock_SL() (schrodinger.application.glide.xpdes.XpPVParser method) parseCanvasCsv() (schrodinger.analysis.enrichment.Calculator class method) parseDataLine() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageData method) parseEnergies() (schrodinger.application.desmond.packages.energygroup.Bulk method) parseInput() (schrodinger.analysis.enrichment.Calculator method) (schrodinger.analysis.enrichment.TitleEnrichmentCalculator method) parseLine() (schrodinger.utils.ligfilter.Criterion method) parseNode() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method) parseOptions() (schrodinger.application.canvas.cluster.CanvasFingerprintClusterCLI method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGeneratorCLI method) (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarityCLI method) parsePropertyString() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property method) Parser (class in schrodinger.application.desmond.antlr3.recognizers) ParserRuleReturnScope (class in schrodinger.application.desmond.antlr3.recognizers) ParserWrapper (class in schrodinger.application.matsci.mecp_mod) (class in schrodinger.application.matsci.nano.interface_mod) (class in schrodinger.application.matsci.nano.particle) (class in schrodinger.application.matsci.nano.slab) (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) (class in schrodinger.application.matsci.nano.xtal) (class in schrodinger.application.matsci.rxn_path) ParseSDF() (in module schrodinger.application.desmond.packages.msys) parseStr() (in module schrodinger.application.desmond.enhsamp) parseTree() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method) PARTIAL (schrodinger.application.jaguar.input.GenOptions attribute) partial_charge (schrodinger.structure._StructureAtom attribute) (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) PartiallyVisible (schrodinger.protein.sequence.Inclusion attribute) participants (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) ParticipantView (class in schrodinger.application.jaguar.gui.tabs.reaction_tab) ParticleInfo (class in schrodinger.application.matsci.coarsegrain) partition() (schrodinger.infra.fast3d.Engine method) partitionAtoms() (schrodinger.application.matsci.nano.particle.Nanoparticle method) partitionValues() (in module schrodinger.infra.phase) pass_errors (schrodinger.structure.MultiFileStructureReader attribute) passes() (schrodinger.infra.phase.PhpSiteConstrainer method) Patch (class in schrodinger.application.bioluminate.patch_utils.patch_finder) patch_count (schrodinger.surface.Surface attribute) patch_vertices (schrodinger.surface.Surface attribute) PatchAnalysis (class in schrodinger.application.bioluminate.patch_utils.patch_finder) patchesFound (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinderRunner attribute) PatchFinder (class in schrodinger.application.bioluminate.patch_utils.patch_finder) PatchFinderRunner (class in schrodinger.application.bioluminate.patch_utils.patch_finder) PatchSettings (class in schrodinger.application.bioluminate.patch_utils.settings) PatchType (class in schrodinger.application.bioluminate.patch_utils.settings) PatchTypeSettings (class in schrodinger.application.bioluminate.patch_utils.settings) path (schrodinger.application.desmond.packages.msys.IndexedFileLoader attribute) (schrodinger.application.matsci.espresso.qeinput.DataType attribute) PATH (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) path (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement attribute) path_geometry() (in module schrodinger.application.jaguar.textparser) path_structures (schrodinger.application.jaguar.output.JaguarOutput attribute) PathFailure PathModel (class in schrodinger.application.desmond.fep_gui) pathModified() (schrodinger.application.desmond.cwidget.FileEntry method) pathname() (in module schrodinger.utils.sea) (schrodinger.application.licensing.flexlm.Vendor method) (schrodinger.application.licensing.licadmin.LicenseResource method) PathTreeDict (class in schrodinger.application.livedesign.panel_components) pattern (schrodinger.application.desmond.packages.msys.SmartsPattern attribute) PATTERN (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition attribute) pattern (schrodinger.application.matsci.smartsutils.SMARTSGroupData attribute) pattern() (schrodinger.application.desmond.antlr3.treewizard.TreePatternParser method) PatternModel (class in schrodinger.ui.ligfilter) Pbc (class in schrodinger.application.desmond.packages.analysis) pbc (schrodinger.structutils.ringspear.SpearRing attribute) PBC_BOND_COLOR (schrodinger.application.matsci.nano.xtal.PBCBond attribute) PBC_BOND_COLOR_KEY (schrodinger.application.matsci.nano.xtal.PBCBond attribute) PBC_BOND_KEY (schrodinger.application.matsci.nano.xtal.PBCBond attribute) PBC_BOND_THRESHOLD (schrodinger.application.matsci.nano.xtal.PBCBond attribute) PBC_BONDING (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) pbc_ring_coords (schrodinger.structutils.ringspear.SpearRing attribute) PBCBond (class in schrodinger.application.matsci.nano.xtal) PBCBonds (class in schrodinger.application.matsci.nano.xtal) PBCMeasureMananger (class in schrodinger.trajectory.pbc_manager) PCA (class in schrodinger.trajectory.prody.pca) PDB_RES (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) PDB_STRING (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) pdbcode (schrodinger.structure._StructureAtom attribute) pdbname (schrodinger.structure._StructureAtom attribute) PDBReader (class in schrodinger.structure) pdbres (schrodinger.structure._Residue attribute) (schrodinger.structure._StructureAtom attribute) (schrodinger.structutils.analyze.Ligand attribute) PDBWriter (class in schrodinger.structure) PDOS (class in schrodinger.application.matsci.espresso.qeoutput) pearson_by_set() (in module schrodinger.application.bioluminate.escomp) Penalties (schrodinger.application.glide.xpdes.TermKeywords attribute) PENALTYWEIGHT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) peptide_name() (schrodinger.application.desmond.fep_edge_data.PRMEdgeData static method) perAtomBasisChanged() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) perAtomBasisForEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel method) PerAtomBasisRow (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets) perAtomBasisSetsPresent() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) Percent_helix() (in module schrodinger.utils.ligfilter) Percent_loop() (in module schrodinger.utils.ligfilter) Percent_strand() (in module schrodinger.utils.ligfilter) PercentScreenPlotter (class in schrodinger.analysis.enrichment) perform_transmutations() (in module schrodinger.application.matsci.enumeration) performMovement() (schrodinger.application.matsci.montecarlo.Metropolizer method) performSVD() (schrodinger.trajectory.prody.pca.PCA method) performTransmutation() (schrodinger.application.matsci.enumeration.Alchemist method) (schrodinger.application.matsci.enumeration.ElementAlchemist method) (schrodinger.application.matsci.enumeration.VacancyAlchemist method) period_start() (in module schrodinger.application.licensing.lmgrd_log_parser) periodic_callback_add() (in module schrodinger.maestro.maestro) periodic_callback_remove() (in module schrodinger.maestro.maestro) PerStrucConfigDialog (class in schrodinger.application.matsci.guibase) PerStrucSingleGpuConfigDialog (class in schrodinger.application.matsci.guibase) PhaseDB (class in schrodinger.pipeline.pipeio) PhaseFeatureMarker (class in schrodinger.application.phase.phase_markers) PhaseHypothesis (class in schrodinger.application.phase.hypothesis) PhaseHypothesisFromLigand (class in schrodinger.application.phase.hypothesis) PhaseHypothesisHybrid (class in schrodinger.application.phase.hypothesis) PhaseHypothesisInputConfig (class in schrodinger.application.phase.input) PhaseHypothesisMonitor (class in schrodinger.application.phase.pt_hypothesis) PhaseHypothesisStandard (class in schrodinger.application.phase.hypothesis) PhaseHypothesisStatic (class in schrodinger.application.phase.hypothesis) PhaseMarkers (class in schrodinger.application.phase.phase_markers) PhaseShapeStage (class in schrodinger.pipeline.stages.phase) PhaseSphere (class in schrodinger.application.phase.phase_markers) PhaseSphereMarkers (class in schrodinger.application.phase.phase_markers) PhaseTolMarkers (class in schrodinger.application.phase.phase_markers) PhaseXvolMarkers (class in schrodinger.application.phase.phase_markers) PHControlType (class in schrodinger.application.matsci.espresso.qeinput) phdb_fpreader() (in module schrodinger.application.hitexpander) phdb_mol_reader() (in module schrodinger.application.hitexpander) PhDOS (class in schrodinger.application.matsci.espresso.qeoutput) PHInputType (class in schrodinger.application.matsci.espresso.qeinput) Phob_pack (schrodinger.application.glide.xpdes.TermKeywords attribute) Phobcon_HB (schrodinger.application.glide.xpdes.TermKeywords attribute) PHONON_TEMPLATE_MAP (schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter attribute) PhononDocument (class in schrodinger.application.matsci.qexsd.qespresso.documents) PhononInputConverter (class in schrodinger.application.matsci.qexsd.qespresso.converters) PhpAlignCore (class in schrodinger.infra.phase) PhpAlignCore_makeOptions() (in module schrodinger.infra.phase) PhpAlignCoreOptions (class in schrodinger.infra.phase) PhpAtomClassDescriptions (class in schrodinger.infra.phase) PhpComplex (class in schrodinger.infra.phase) PhpConfOptions (class in schrodinger.infra.phase) PhpConfOptions_getForceFieldCommonName() (in module schrodinger.infra.phase) PhpConfOptions_getForceFieldDisplayName() (in module schrodinger.infra.phase) PhpConfOptions_getSamplingMethodDisplayName() (in module schrodinger.infra.phase) PhpDatabaseFp (class in schrodinger.infra.phase) PhpDatabaseFp_distEuclidean() (in module schrodinger.infra.phase) PhpDatabaseFp_distHamming() (in module schrodinger.infra.phase) PhpDatabaseFp_distSoergel() (in module schrodinger.infra.phase) PhpDatabaseFp_getCommonCount() (in module schrodinger.infra.phase) PhpDatabaseFp_packFp() (in module schrodinger.infra.phase) PhpDatabaseFp_simCosine() (in module schrodinger.infra.phase) PhpDatabaseFp_simDice() (in module schrodinger.infra.phase) PhpDatabaseFp_simTanimoto() (in module schrodinger.infra.phase) PhpDatabaseFp_unpackFp() (in module schrodinger.infra.phase) PhpDeltaHypo (class in schrodinger.infra.phase) PhpDeltaHypoSite (class in schrodinger.infra.phase) PhpDeNovoPharm (class in schrodinger.infra.phase) PhpException PhpExclVol (class in schrodinger.infra.phase) PhpExclVolSphere (class in schrodinger.infra.phase) PhpFastShape (class in schrodinger.infra.phase) PhpFastShapePair (class in schrodinger.infra.phase) PhpFeatureClassDescriptions (class in schrodinger.infra.phase) PhpFeatureData (class in schrodinger.infra.phase) PhpFeatureDefinition (class in schrodinger.infra.phase) PhpFeatureFinder (class in schrodinger.infra.phase) PhpFeaturePattern (class in schrodinger.infra.phase) PhpFeatureRules (class in schrodinger.infra.phase) PhpFragPair (class in schrodinger.infra.phase) PhpHiCluster (class in schrodinger.infra.phase) PhpHiClusterPair (class in schrodinger.infra.phase) PhpHypoAdaptor (class in schrodinger.infra.phase) PhpHypoOptimizer (class in schrodinger.infra.phase) PhpHypoOptimizerSettings (class in schrodinger.infra.phase) PhpIntCoord (class in schrodinger.infra.phase) PhpLicenseCoreHopping (class in schrodinger.infra.phase) PhpLicenseDBCreate (class in schrodinger.infra.phase) PhpLicenseDBSearch (class in schrodinger.infra.phase) PhpLicenseElements (class in schrodinger.infra.phase) PhpLicenseFeature (class in schrodinger.infra.phase) PhpLicenseGeneric (class in schrodinger.infra.phase) PhpLicensePartition (class in schrodinger.infra.phase) PhpLicenseQSAR (class in schrodinger.infra.phase) PhpLicenseScoring (class in schrodinger.infra.phase) PhpLicenseSelectivity (class in schrodinger.infra.phase) PhpLicenseShapeScreen (class in schrodinger.infra.phase) PhpMatchOptions (class in schrodinger.infra.phase) PhpMMconfAdaptor (class in schrodinger.infra.phase) PhpOpenRingFinder (class in schrodinger.infra.phase) PhpOptionsParser (class in schrodinger.infra.phase) PhpPackedFp (class in schrodinger.infra.phase) PhpProject (class in schrodinger.infra.phase) PhpQSAR (class in schrodinger.infra.phase) PhpQSARModel (class in schrodinger.infra.phase) PhpScreener (class in schrodinger.infra.phase) PhpSite (class in schrodinger.infra.phase) PhpSiteConstrainer (class in schrodinger.infra.phase) PhpSiteConstraint (class in schrodinger.infra.phase) PhpSiteMask (class in schrodinger.infra.phase) PhpSiteMask_getMatchLimits() (in module schrodinger.infra.phase) PhpSiteMask_resolveMaskValue() (in module schrodinger.infra.phase) PhpSiteMask_resolveMatchLimits() (in module schrodinger.infra.phase) PhpSiteMask_splitMaskValue() (in module schrodinger.infra.phase) PhpSiteMaskData (class in schrodinger.infra.phase) PhpSiteMaskGroup (class in schrodinger.infra.phase) PhpSiteWithAtoms (class in schrodinger.infra.phase) PhpSortCapperDoubleDecreasing (class in schrodinger.infra.phase) PhpSortCapperDoubleIncreasing (class in schrodinger.infra.phase) PhpStructureBus (class in schrodinger.infra.phase) PhpStructureReader (class in schrodinger.infra.phase) PhpStructureSplitter (class in schrodinger.infra.phase) PhpSubsetSplitter (class in schrodinger.infra.phase) PhpTextFileIterator (class in schrodinger.infra.phase) PhpTextFileReader (class in schrodinger.infra.phase) PhpVolCoords (class in schrodinger.infra.phase) pi_centroid (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) PI_STACK (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) pi_structure (schrodinger.structutils.interactions.pi.CationPiInteraction attribute) Picat (schrodinger.application.glide.xpdes.TermKeywords attribute) Pick3DObjectToggle (class in schrodinger.ui.picking) pick_category (schrodinger.graphics3d.arrow.MaestroArrow attribute) (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.graphics3d.torus.MaestroTorus attribute) PICK_CATEGORY() (in module schrodinger.application.phase.constants) pick_id (schrodinger.graphics3d.arrow.MaestroArrow attribute) (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.graphics3d.torus.MaestroTorus attribute) PICK_MAX_ATOMS (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker attribute) PickAtomsToggle (class in schrodinger.ui.picking) PickAtomToggle (class in schrodinger.application.desmond.fep_gui) (class in schrodinger.ui.picking) PickBondToggle (class in schrodinger.application.desmond.fep_gui) (class in schrodinger.ui.picking) pickCompleted (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker attribute) pickCompleted() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) picking_atom_start() (in module schrodinger.maestro.maestro) picking_bond_start() (in module schrodinger.maestro.maestro) picking_lasso_start() (in module schrodinger.maestro.maestro) picking_loss_notify() (in module schrodinger.maestro.maestro) picking_stop() (in module schrodinger.maestro.maestro) Picklable (class in schrodinger.application.desmond.picklejar) PicklableMetaClass (class in schrodinger.application.desmond.picklejar) PickleJar (class in schrodinger.application.desmond.picklejar) PickleState (class in schrodinger.application.desmond.picklejar) PickMixedToggle (class in schrodinger.ui.picking) PickModelClass (schrodinger.ui.picking.MaestrolessPickResidueDialog attribute) pickMolecule() (schrodinger.application.matsci.mswidgets.MdAtomSelector method) PickPairToggle (class in schrodinger.ui.picking) pickProjTableAtom() (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) PickResidueModel (class in schrodinger.ui.picking) PickResidueRow (class in schrodinger.ui.picking) PickResiduesChangedMixin (class in schrodinger.ui.picking) pickThisAtom() (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) PickTorsionToggle (class in schrodinger.ui.picking) PicturePrinter (class in schrodinger.application.report2d) PINK (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker attribute) PipeIO (class in schrodinger.pipeline.pipeio) Pipeline (class in schrodinger.pipeline.pipeline) PIPERConstraint (class in schrodinger.application.bioluminate.protein_protein_docking_shared) PIPERDistanceConstraintPair (class in schrodinger.application.bioluminate.protein_protein_docking_shared) PiPiInteraction (class in schrodinger.structutils.interactions.pi) pir (schrodinger.utils.fileutils.SeqFormat attribute) PiStackFinder (class in schrodinger.application.bioluminate.interaction_calculator) piStacksIterator() (schrodinger.application.bioluminate.interaction_calculator.PiStackFinder method) PKA_ATOM (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) pka_atom (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) PKA_ATOM_PROP (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) PKA_INVALID (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) PKA_MISSING (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) PKA_VALID (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka attribute) pl_contact_data0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) pl_contact_data1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) pl_interaction_similarity_matrix0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) pl_interaction_similarity_matrix1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) place_and_bond_atoms() (in module schrodinger.application.matsci.nano.xtal) placeAllStructsInCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) placeholderSelected (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo attribute) placeOneIniInCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) placeStructureInCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) PlanarAngle (class in schrodinger.application.desmond.packages.analysis) plot() (schrodinger.application.desmond.fep_edge_data.FEPTorsions method) plot_convergence() (in module schrodinger.application.desmond.fepana) plot_lambda_window_overlap() (in module schrodinger.application.desmond.fepana) PLOT_TYPES (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog attribute) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog attribute) PLOTALEA (schrodinger.application.mopac.results71.MopacResults71 attribute) PLOTALIE (schrodinger.application.mopac.results71.MopacResults71 attribute) plotData() (schrodinger.application.matsci.sliceplot.SlicePlot method) PLOTESP (schrodinger.application.mopac.results71.MopacResults71 attribute) Plotter (class in schrodinger.analysis.enrichment) pls (schrodinger.infra.phase.PhpQSARModel attribute) pmode() (schrodinger.utils.sea.Sea method) Point (class in schrodinger.application.matsci.rxn_path) point_group() (in module schrodinger.application.jaguar.textparser) POINT_GROUP_NAME (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) POINT_GROUP_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) point_group_used() (in module schrodinger.application.jaguar.textparser) pointInside() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) (schrodinger.application.matsci.shapes.Cylinder method) (schrodinger.application.matsci.shapes.Sphere method) points (schrodinger.protein.analysis.Report.data_set attribute) POLAR (schrodinger.protein.residue.STERIC_GROUP attribute) POLAR_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) POLAR_RESIDUE (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) POLAR_RESIDUES (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) PolarizabilitySubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) PolarSurfaceArea (class in schrodinger.application.desmond.packages.analysis) poll() (schrodinger.application.desmond.feputils.ProteinProcessManager method) Polygon (class in schrodinger.graphics3d.polygon) Polyhedron (class in schrodinger.graphics3d.polyhedron) PolymerFragment (class in schrodinger.application.matsci.amorphous) PolymerToFragments (class in schrodinger.application.matsci.amorphous) Pool (schrodinger.application.desmond.packages.traj.Source attribute) pop() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.infra.util.OneIndexedList method) (schrodinger.job.queue.PriorityQueue method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.sea.List method) pop_back() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method)

pop_errors() (schrodinger.infra.mmerr.ErrorHandler method) pop_level() (in module schrodinger.infra.mmerr) (schrodinger.infra.mmerr.ErrorHandler method) Popen() (in module schrodinger.utils.subprocess) popLocalClashes() (schrodinger.application.matsci.amorphous.PolymerToFragments method) populate_from_file() (schrodinger.application.mopac.results2012.MopacResults2012 method) populate_ppdb_from_dir() (in module schrodinger.application.matsci.espresso.ppdb) populate_with_charges() (in module schrodinger.application.matsci.clusterstruct) populateEntryTypes() (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) populateExcitedStatesType() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) populatePatternDict() (schrodinger.structutils.rmsd.ConformerRmsd method) populatePickCombo() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker method) populateTypeCombo() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatePicker method) popUpUpdated() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) port() (schrodinger.application.licensing.flexlm.Vendor method) pos (schrodinger.application.desmond.packages.msys.Atom attribute) pos() (schrodinger.application.desmond.packages.topo.DuckFrame method) (schrodinger.application.desmond.packages.traj.Frame method) PosAlign (class in schrodinger.application.desmond.packages.analysis) PoseLibrary (class in schrodinger.application.glide.glideanalysis) Positer (class in schrodinger.application.desmond.packages.staf) Position (in module schrodinger.application.desmond.packages.analysis) PositionalConstraint (class in schrodinger.application.glide.glide) positions (schrodinger.application.desmond.packages.msys.System attribute) positive (schrodinger.application.bioluminate.patch_utils.settings.PatchType attribute) POSITIVE (schrodinger.protein.residue.RESIDUE_CHARGE attribute) PosResDelegate (class in schrodinger.application.desmond.gui) PosResModel (class in schrodinger.application.desmond.gui) PosResRow (class in schrodinger.application.desmond.gui) post_process_trj() (in module schrodinger.application.desmond.process_fep_traj) postCommand() (schrodinger.job.queue.BaseJob method) postLaunch() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) (schrodinger.application.combiglide.combenumdock.InteractionEnumerationPanel method) (schrodinger.application.combiglide.combenumdock.MaterialEnumerationDialog method) PostLigPrepStage (class in schrodinger.pipeline.stages.ligprep) postProcess() (schrodinger.application.livedesign.ld_import.ImportThreadRunner method) postprocess() (schrodinger.tasks.tasks_.AbstractTask method) postProcessOptimization() (schrodinger.application.matsci.mecp_mod.MECP method) PosTrack (class in schrodinger.application.desmond.packages.analysis) postStart() (schrodinger.tasks.tasks.AbstractTask method) postTreatBuiltCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) postTreatMinimizedStructure() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) potential() (schrodinger.application.desmond.torsion_related.BondRotator method) potential_energy (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute) PotentialEnergy (class in schrodinger.application.desmond.simulation_block_test) PotGrid (class in schrodinger.application.bioluminate.escomp) PP_TYPE_PAW (schrodinger.application.matsci.espresso.utils.UPFParser attribute) PP_TYPES (schrodinger.application.matsci.espresso.utils.UPFParser attribute) pre_analyze() (in module schrodinger.application.bioluminate.patch_utils.pre_analyze) pre_score_pairs() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) pre_score_self() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) pre_treat() (schrodinger.protein.assignment.ProtAssign.changeable method) pre_treat_1() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) pre_treat_2() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) PreAnalyzer (class in schrodinger.application.bioluminate.patch_utils.patch_finder) PRECISION (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) precision (schrodinger.application.jaguar.results.BondCharge attribute) (schrodinger.application.jaguar.results.Dipole attribute) (schrodinger.application.jaguar.results.FukuiIndices attribute) (schrodinger.application.jaguar.results.Orbital attribute) (schrodinger.application.jaguar.results.ThermoCollection attribute) (schrodinger.application.jaguar.results.ThermoProp attribute) (schrodinger.application.jaguar.results.ZVariables attribute) (schrodinger.application.jaguar.scan.Scan attribute) preCommand() (schrodinger.job.queue.BaseJob method) precursors (schrodinger.analysis.reaction.RouteNode attribute) preDeepCopy() (schrodinger.application.matsci.amorphous.PolymerFragment method) PredefinedCriterion (class in schrodinger.utils.ligfilter) predict() (schrodinger.application.desmond.antlr3.dfa.DFA method) predict_correlation() (in module schrodinger.application.desmond.correlation_tau) predict_kendall_tau() (in module schrodinger.application.desmond.correlation_tau) predict_temperature() (in module schrodinger.application.desmond.predict_remd_temp) predict_temperature_ladder() (in module schrodinger.application.desmond.remd) predict_with_nreplica_and_exch() (in module schrodinger.application.desmond.remd) predict_with_temp_and_exch() (in module schrodinger.application.desmond.remd) predict_with_temp_and_nreplica() (in module schrodinger.application.desmond.remd) Preferences (class in schrodinger.utils.preferences) preflight() (schrodinger.application.jaguar.input.JaguarInput method) preoptimizeIsChecked() (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab method) prepActive() (schrodinger.application.bioluminate.protein.PrimeConfig method) prepAntibodyLoop() (schrodinger.application.bioluminate.protein.PrimeConfig method) prepare() (schrodinger.application.desmond.systype.SysType method) (schrodinger.application.desmond.systype.TyperBase static method) (schrodinger.application.desmond.systype.WatermapTyper static method) (schrodinger.application.matsci.rxn_path.ReactionCoords method) prepare_command() (schrodinger.application.desmond.rest_inp.RestInput method) prepare_for_epik() (in module schrodinger.application.prepwizard) prepare_ions() (in module schrodinger.application.desmond.move_alchem_ions) prepare_job_spec_builder() (in module schrodinger.application.matsci.jobutils) prepare_msj() (schrodinger.application.desmond.rest_inp.RestInput method) prepare_next_generation_dirs_callback() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) prepare_structure() (schrodinger.application.desmond.rest_inp.RestInput method) prepareBuildingBlocksForGrow() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) prepareInputLigands() (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) prepareOutput() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) preparePbcAndParams() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) prepareStructureForMinimization() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) prepareStructures() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) prepBldStruct() (schrodinger.application.bioluminate.protein.PrimeConfig method) prepend_mmfile_path() (in module schrodinger.application.ligprep.ionizer) prepend_path() (in module schrodinger.utils.env) prepend_schrodinger_run() (in module schrodinger.job.jobcontrol) prepEnergy() (schrodinger.application.bioluminate.protein.PrimeConfig method) prepLoop() (schrodinger.application.bioluminate.protein.PrimeConfig method) prepMinimize() (schrodinger.application.bioluminate.protein.PrimeConfig method) prepResidue() (schrodinger.application.bioluminate.protein.PrimeConfig method) preProcess() (schrodinger.tasks.tasks.AbstractTask method) preprocess() (schrodinger.tasks.tasks_.AbstractTask method) preprocess_infile() (in module schrodinger.application.jaguar.user_config) preprocessMatchAtoms() (schrodinger.application.matsci.nano.tube.NanoTube method) prepSidechain() (schrodinger.application.bioluminate.protein.PrimeConfig method) prepSidechainBB() (schrodinger.application.bioluminate.protein.PrimeConfig method) prepSidechainCBeta() (schrodinger.application.bioluminate.protein.PrimeConfig method) Pressure (class in schrodinger.application.desmond.simulation_block_test) PRESSURE (schrodinger.application.matsci.desmondutils.MSJStringer attribute) PRESSURE_KEY (schrodinger.application.matsci.espresso.qeinput.CellControlType attribute) preStart() (schrodinger.application.livedesign.ld_export.ExportThreadRunner method) PRESUMED_TS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) PRESUMED_TS_CHOICES (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) Prev (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom.NextGeomFrom attribute) preValidate() (schrodinger.tasks.tasks.AbstractTask method) prevent_overlapping_x_labels() (in module schrodinger.application.bioluminate.sliderchart) (in module schrodinger.application.desmond.mplchart) preview() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) previous() (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) PRIMARY (schrodinger.application.matsci.nano.xtal.SpaceGroups attribute) PRIMARY_OPERATIONS_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) PRIMARY_OPERS (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) PRIMARY_THIOL (schrodinger.protein.residue.SIDE_CHAIN_CHEM attribute) Prime (class in schrodinger.application.prime.input) PRIME_ANTIB_LOOP_PRED (schrodinger.application.bioluminate.protein.Refiner attribute) PRIME_LOOP_PRED (schrodinger.application.bioluminate.protein.Refiner attribute) PRIME_MINIMIZE (schrodinger.application.bioluminate.protein.Refiner attribute) PRIME_RESIDUE (schrodinger.application.bioluminate.protein.Refiner attribute) prime_search_and_scan() (schrodinger.application.desmond.torsion_related.BondRotator method) PRIME_SIDECHAIN (schrodinger.application.bioluminate.protein.Refiner attribute) PRIME_SIDECHAIN_BB (schrodinger.application.bioluminate.protein.Refiner attribute) PRIME_SIDECHAIN_CBETA (schrodinger.application.bioluminate.protein.Refiner attribute) PrimeConfig (class in schrodinger.application.bioluminate.protein) PrimeStage (class in schrodinger.pipeline.stages.prime) PrimeStructure (class in schrodinger.application.bioluminate.protein) Primitive (class in schrodinger.graphics3d.common) print_allow_adsorption_onto() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) print_attachment_points() (schrodinger.application.canvas.r_group.Data method) print_attachment_points_ct() (schrodinger.application.canvas.r_group.Data method) print_bad_jobs() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) print_deprecate() (in module schrodinger.application.watermap.watermap_inp) print_fields() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.LicenseLine method) (schrodinger.application.licensing.flexlm.Package method) (schrodinger.application.licensing.flexlm.Server method) (schrodinger.application.licensing.flexlm.Vendor method) print_if() (in module schrodinger.application.desmond.util) PRINT_INFO (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) print_job_info() (in module schrodinger.application.macromodel.paraUtils) print_pathway() (in module schrodinger.application.desmond.fepana) print_report() (in module schrodinger.application.canvas.driverutils) print_tree() (schrodinger.application.desmond.reorder_atom.Node method) print_usage() (in module schrodinger.application.desmond.simulation_block_data) (in module schrodinger.application.desmond.simulation_block_test) (schrodinger.utils.cmdline.SingleDashOptionParser method) print_val() (schrodinger.application.desmond.simulation_block_test.Test method) print_version() (in module schrodinger.utils.cmdline) printAction() (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.pipeline.StageJob method) printAllChannels() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions method) printAllSpgInfo() (schrodinger.application.matsci.nano.xtal.SpaceGroups method) printChannelDefs() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) printConstraint() (schrodinger.infra.phase.PhpSiteConstrainer method) printCrystalParams() (schrodinger.application.matsci.nano.xtal.Crystal method) printDatabaseEntry() (schrodinger.application.matsci.nano.xtal.SpaceGroup method) printDelimitedActivities() (schrodinger.infra.phase.PhpQSAR method) printDelimitedBits() (schrodinger.infra.phase.PhpQSAR method) printFailureMessage() (schrodinger.pipeline.pipeline.StageJob method) printFiltered() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) printInfo() (schrodinger.application.desmond.replica_dE.replica_container method) printInternals() (schrodinger.application.matsci.rxn_path.InternalCoords method) printJobParams() (schrodinger.application.matsci.nano.sheet.NanoSheets method) (schrodinger.application.matsci.nano.tube.NanoTubes method) printModel() (schrodinger.infra.phase.PhpQSAR method) printMultiWalledTubes() (schrodinger.application.matsci.nano.tube.NanoTubes method) printNotMinimized() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) printout() (schrodinger.application.inputconfig.InputConfig method) printParameters() (schrodinger.structutils.minimize.Minimizer method) printParams() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization method) (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.slab.Surface method) printPred() (schrodinger.infra.phase.PhpQSAR method) printProperties() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization method) printProps() (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube method) (schrodinger.application.matsci.nano.tube.NanoTube method) printRxnReprs() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) printSingleWalledTubes() (schrodinger.application.matsci.nano.tube.NanoTubes method) printStatus() (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.job.queue.JobDJ method) printSummary() (schrodinger.infra.phase.PhpHiCluster method) printSymmetryOpers() (schrodinger.application.matsci.nano.xtal.SpaceGroup method) printTree() (schrodinger.ui.ligfilter.DefinitionViewerDialog method) printvals() (in module schrodinger.infra.propedit) printVectorValues() (in module schrodinger.infra.phase) printVolOccBits() (schrodinger.infra.phase.PhpQSAR method) priority (schrodinger.application.desmond.packages.cui.LazyParser attribute) priority() (schrodinger.application.licensing.licadmin.LicenseResource method) PriorityQueue (class in schrodinger.job.queue) prm_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) PRM_STABILITY (schrodinger.application.desmond.constants.FEP_TYPES attribute) PRMEdgeData (class in schrodinger.application.desmond.fep_edge_data) PRMEdgeReportMaker (class in schrodinger.application.desmond.fep_edge_report_maker) process_attributes() (in module schrodinger.application.licensing.licadmin) process_bennett_log() (schrodinger.application.desmond.replica_dE.replica_container method) process_chunks() (in module schrodinger.application.desmond.simulation_block_test) process_docstring() (in module schrodinger.infra.epydoc_to_sphinx) process_highlights() (in module schrodinger.utils.pymol) process_hypothesis() (in module schrodinger.utils.pymol) process_loaded_model() (in module schrodinger.application.desmond.gui) process_measurements() (in module schrodinger.utils.pymol) process_option_strings() (schrodinger.utils.cmdline.SingleDashOption method) process_pending_events() (in module schrodinger.maestro.maestro) process_prj() (in module schrodinger.utils.pymol) process_row() (in module schrodinger.utils.pymol) process_salt_and_ions() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) process_sequence() (in module schrodinger.protein.helix) process_structure() (in module schrodinger.protein.pdbname) process_surface() (in module schrodinger.utils.pymol) process_type (schrodinger.application.livedesign.ld_base_classes.ImportExportThreadRunner attribute) (schrodinger.application.livedesign.ld_export.ExportThreadRunner attribute) (schrodinger.application.livedesign.ld_import.ImportThreadRunner attribute) processContextAction() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView method) processJobOutputs() (schrodinger.pipeline.stages.filtering.GeneratePropsStage method) (schrodinger.pipeline.stages.filtering.LigFilterStage method) (schrodinger.pipeline.stages.glide.DockingStage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) (schrodinger.pipeline.stages.prime.MMGBSAStage method) (schrodinger.pipeline.stages.prime.PrimeStage method) (schrodinger.pipeline.stages.qikprop.QikPropStage method) (schrodinger.pipeline.stages.qsite.QSiteStage method) (schrodinger.pipeline.stages.semiemp.SemiEmpStage method) processNext() (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) processOutput() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) processPrevPanel() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) processProducts() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) processSettings() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) processTaskMessage() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) procText() (in module schrodinger.application.desmond.enhsamp) PRODUCT (schrodinger.application.desmond.restraint.GeneratorTypes attribute) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) PRODUCT_LIKE (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) PRODUCT_NAME_BASE (schrodinger.application.matsci.rxn_channel.rxn_channel.Products attribute) PRODUCTPREFIX (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) Products (class in schrodinger.application.matsci.rxn_channel.rxn_channel) profiling() (in module schrodinger.utils.profiling) prog() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) prog_for_argparse() (in module schrodinger.application.hitexpander) progress (schrodinger.application.bioluminate.protein.PropertyCalculator attribute) progress_report_frame_number() (in module schrodinger.application.desmond.packages.analysis) proj (schrodinger.tasks.jobtasks.JobConfig attribute) projChanged (schrodinger.tasks.jobtasks.JobConfig attribute) Project (class in schrodinger.project) (schrodinger.application.livedesign.ld_base_classes.LDInputType attribute) project_close() (in module schrodinger.application.phase.phase_markers) project_close_callback_add() (in module schrodinger.maestro.maestro) project_close_callback_remove() (in module schrodinger.maestro.maestro) project_close_cancel() (in module schrodinger.maestro.maestro) project_get() (in module schrodinger.maestro.maestro) project_rename_callback_add() (in module schrodinger.maestro.maestro) project_rename_callback_remove() (in module schrodinger.maestro.maestro) project_table_get() (in module schrodinger.maestro.maestro) project_table_import() (in module schrodinger.application.livedesign.ld_import) project_table_select_only() (in module schrodinger.application.livedesign.ld_import) project_table_synchronize() (in module schrodinger.maestro.maestro) project_table_update() (in module schrodinger.maestro.maestro) project_update_callback_add() (in module schrodinger.maestro.maestro) project_update_callback_remove() (in module schrodinger.maestro.maestro) projectClosed() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) ProjectDisposition (class in schrodinger.job.launchparams) ProjectException projectModel() (schrodinger.application.phase.phase_markers.PhaseMarkers method) ProjectRow (class in schrodinger.project) projectSelected (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo attribute) ProjectSurface (class in schrodinger.project_surface) projectUpdated() (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) ProjEntry (class in schrodinger.application.jaguar.gui.input_tab_widgets) ProjEntryPka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) ProjEntryTuple (class in schrodinger.application.jaguar.gui.input_tab_widgets) ProjEntryTuplePka (class in schrodinger.application.jaguar.gui.input_tab_widgets_pka) PROJET_TABLE (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) ProjTableLikeView (class in schrodinger.application.jaguar.gui.utils) projType (schrodinger.infra.phase.PhpFragPair attribute) promoteShowToolTip() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) PROP_CMS (schrodinger.application.desmond.cms.Cms attribute) PROP_TRJ (schrodinger.application.desmond.cms.Cms attribute) prop_value (schrodinger.application.desmond.simulation_block_data.Array_Prop attribute) propagate_chain_data_from_atom() (in module schrodinger.application.matsci.amorphous) PropertiesMixin (class in schrodinger.application.jaguar.gui.base_panel) PropertiesTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) PropertiesTabBase (class in schrodinger.application.jaguar.gui.tabs.properties_tab) PropertiesTabIGO (class in schrodinger.application.jaguar.gui.tabs.properties_tab) PropertiesTableWidget (class in schrodinger.application.jaguar.gui.utils) PropertiesValidatorMixin (class in schrodinger.application.jaguar.gui.base_panel) Property (class in schrodinger.application.matsci.genetic_optimization.genetic_optimization) property (schrodinger.application.phase.hypothesis.PhaseHypothesis attribute) (schrodinger.structure.Structure attribute) (schrodinger.structure.TextualStructure attribute) (schrodinger.structure._StructureAtom attribute) (schrodinger.structure._StructureBond attribute) property_key (schrodinger.application.jaguar.utils.FreeEnergy attribute) PROPERTY_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab attribute) PropertyCalculator (class in schrodinger.application.bioluminate.protein) PropertyCriterion (class in schrodinger.utils.ligfilter) PropertyDictionary (class in schrodinger.project) PropertyMap (class in schrodinger.application.desmond.packages.msys) PropertyName (class in schrodinger.structure) PropertySelectorWithRanges (class in schrodinger.application.bioluminate.propfilter) PropertySyntaxError propertyTableSelectionChanged() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) PropFilter (class in schrodinger.structutils.filter) PropFilterDialog (class in schrodinger.application.bioluminate.propfilter) PropkaError PropKaException props (schrodinger.application.desmond.packages.msys.ParamTable attribute) (schrodinger.application.desmond.packages.msys.TermTable attribute) propType() (schrodinger.application.desmond.packages.msys.ParamTable method) PROT_ANIONS (schrodinger.structutils.interactions.salt_bridge.SaltBridgeFinder attribute) PROT_CATIONS (schrodinger.structutils.interactions.salt_bridge.SaltBridgeFinder attribute) ProtAssign (class in schrodinger.protein.assignment) ProtAssign.amide_changeable (class in schrodinger.protein.assignment) ProtAssign.amine_changeable (class in schrodinger.protein.assignment) ProtAssign.carboxyl_changeable (class in schrodinger.protein.assignment) ProtAssign.changeable (class in schrodinger.protein.assignment) ProtAssign.hbond_cluster (class in schrodinger.protein.assignment) ProtAssign.histidine_changeable (class in schrodinger.protein.assignment) ProtAssign.rotatable_changeable (class in schrodinger.protein.assignment) ProtAssign.water_changeable (class in schrodinger.protein.assignment) protein_residue() (schrodinger.application.desmond.fep_edge_data.FEPEdgeData static method) PROTEIN_SELECTIVITY (schrodinger.application.desmond.constants.FEP_TYPES attribute) protein_sequences (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) ProteinAlignment (class in schrodinger.protein.alignment) ProteinAlignmentAnnotations (class in schrodinger.protein.annotation) ProteinAlignmentAnnotations.ANNOTATION_TYPES (class in schrodinger.protein.annotation) ProteinCheckLabelSpinner (class in schrodinger.application.desmond.feputils) ProteinCheckParameters (class in schrodinger.protein.reliability) ProteinMapperMsjGenerator (class in schrodinger.application.desmond.mapper_msj_generator) ProteinProcessManager (class in schrodinger.application.desmond.feputils) ProteinProperties (class in schrodinger.application.bioluminate.patch_utils.patch_finder) ProteinReport (class in schrodinger.application.desmond.replica_sid_generator) ProteinRMSF (class in schrodinger.application.desmond.packages.analysis) ProteinSequence (class in schrodinger.protein.sequence) ProteinSequenceAnnotations (class in schrodinger.protein.annotation) ProteinSequenceAnnotations.ANNOTATION_TYPES (class in schrodinger.protein.annotation) ProtLigHbondInter (in module schrodinger.application.desmond.packages.analysis) ProtLigInter (class in schrodinger.application.desmond.packages.analysis) ProtLigPiInter (in module schrodinger.application.desmond.packages.analysis) ProtLigPolarInter (class in schrodinger.application.desmond.packages.analysis) PROTOCOL_VERSION (schrodinger.application.desmond.antlr3.debug.DebugEventListener attribute) ProtProtHbondInter (class in schrodinger.application.desmond.packages.analysis) ProtProtInter (class in schrodinger.application.desmond.packages.analysis) ProtProtPiInter (class in schrodinger.application.desmond.packages.analysis) provenance (schrodinger.application.desmond.packages.msys.System attribute) ProvidesBasisMixin (class in schrodinger.application.jaguar.gui.tabs.base_tab) ProvidesStructuresMixin (class in schrodinger.application.jaguar.gui.tabs.base_tab) PROXY_CLASS (schrodinger.application.bioluminate.antibody.search_results_table.FullTable attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) PROXY_MODEL_CLASS (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab attribute) pruneIt() (schrodinger.application.matsci.nano.slab.Surface method) Pseudo (class in schrodinger.application.desmond.cms) pseudoatom_match() (in module schrodinger.application.desmond.packages.topo) PseudopotentialsType (class in schrodinger.application.matsci.espresso.qeinput) pseudospectral() (in module schrodinger.application.jaguar.textparser) pt_entry_id (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant attribute) PT_IMPORT_TXT (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) pull_ligand() (in module schrodinger.application.glide.http_server) pullCompounds() (schrodinger.pipeline.stages.pull.PullStage method) PullStage (class in schrodinger.pipeline.stages.pull) purgeRecord() (schrodinger.job.jobcontrol.Job method) push() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.job.queue.PriorityQueue method) push_back() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) push_level() (in module schrodinger.infra.mmerr) (schrodinger.infra.mmerr.ErrorHandler method) push_ligand() (in module schrodinger.application.glide.http_server) pushpop() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) putToM2ioFile() (schrodinger.structure.Structure method) (schrodinger.structure.TextualStructure method) PW_TEMPLATE_MAP (schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter attribute) PwDocument (class in schrodinger.application.matsci.qexsd.qespresso.documents) PwInputConverter (class in schrodinger.application.matsci.qexsd.qespresso.converters) PYMOL (schrodinger.protein.sequence.Sequence.ORIGIN attribute) PymolInstance (class in schrodinger.utils.pymol) PymolScriptInstance (class in schrodinger.utils.pymol) PyStructureReaderException PYTHON_EXE (in module schrodinger.utils.sysinfo) PYTHON_MINIMIZE (schrodinger.application.bioluminate.protein.Refiner attribute)

Q

qbuttongroup_access_factory() (in module schrodinger.models.mappers) qCleanupResources() (in module schrodinger.application.bioluminate.actions.icons_rc) (in module schrodinger.application.livedesign.icons_rc) (in module schrodinger.application.matsci.controlicons_rc) QeDocument (class in schrodinger.application.matsci.qexsd.qespresso.documents) QEspressoError QikPropStage (class in schrodinger.pipeline.stages.qikprop) qInitResources() (in module schrodinger.application.bioluminate.actions.icons_rc) (in module schrodinger.application.livedesign.icons_rc) (in module schrodinger.application.matsci.controlicons_rc) qm (schrodinger.application.qsite.input.HydrogenCap attribute) qm_atoms() (in module schrodinger.application.jaguar.textparser) (in module schrodinger.application.qsite.output) qmatom (schrodinger.application.qsite.input.Cut attribute) qmmm_bend_energy() (in module schrodinger.application.qsite.output) qmmm_electrostatic_energy() (in module schrodinger.application.qsite.output) qmmm_stretch_energy() (in module schrodinger.application.qsite.output) qmmm_torsion_energy() (in module schrodinger.application.qsite.output) QMRegion (class in schrodinger.application.qsite.input) qmregion (schrodinger.application.qsite.input.QSiteInput attribute) QSiteInput (class in schrodinger.application.qsite.input) QSiteOutput (class in schrodinger.application.qsite.output) QSiteResults (class in schrodinger.application.qsite.output) QSiteStage (class in schrodinger.pipeline.stages.qsite) QSiteTextParser (class in schrodinger.application.qsite.output) qst_geometries() (in module schrodinger.application.jaguar.textparser) qst_initial_geometry() (in module schrodinger.application.jaguar.textparser) QST_SEARCH_ALONG (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute)

QuadMarker (class in schrodinger.maestro.markers) quadratic_1() (in module schrodinger.application.matsci.mecp_mod) quadratic_2() (in module schrodinger.application.matsci.mecp_mod) quadratic_3() (in module schrodinger.application.matsci.mecp_mod) Quadrilateral (class in schrodinger.graphics3d.quadrilateral) qualify() (schrodinger.pipeline.stages.filtering.DrugLikeSplitStage method) QualitySlider (class in schrodinger.application.matsci.qualityslider) query_registry() (in module schrodinger.utils.sysinfo) question() (in module schrodinger.maestro.maestro) (schrodinger.tasks.runners.AbstractTaskReporter method) (schrodinger.tasks.runners.CmdlineTaskReporter method) (schrodinger.tasks.runners.PanelTaskReporter method) (schrodinger.tasks.runners.TaskRunner method) questionRaised (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel attribute) queue_config_diffs() (in module schrodinger.utils.installation_check) queue_config_file_pairs() (in module schrodinger.utils.installation_check) queue_config_files_diff() (in module schrodinger.utils.installation_check) queue_inst_file() (in module schrodinger.utils.installation_check) queue_orig_dir() (in module schrodinger.utils.installation_check) queue_orig_file() (in module schrodinger.utils.installation_check) quick_append() (schrodinger.utils.sea.List method) QuickHelpButton (class in schrodinger.application.bioluminate.bwidgets) quickWeedAtoms() (schrodinger.structutils.ringspear.SpearRing method) quietlySelectSite() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) quit() (in module schrodinger.application.bioluminate.protein_report_widget) quotechar (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) quoting (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute)

R

r (schrodinger.graphics3d.arrow.MaestroArrow attribute) (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.graphics3d.torus.MaestroTorus attribute) (schrodinger.infra.phase.PhpExclVolSphere attribute) radius (schrodinger.application.jaguar.gui.utils.Solvent attribute) (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) (schrodinger.application.matsci.freevolume.GridRadius attribute) RADIUS (schrodinger.application.matsci.nano.tube.NanoTube attribute) radius (schrodinger.graphics3d.arrow.MaestroArrow attribute) (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.graphics3d.torus.MaestroTorus attribute) (schrodinger.structure._StructureAtom attribute) (schrodinger.structutils.ringspear.SpearRing attribute) RadiusOfGyration (in module schrodinger.application.desmond.packages.analysis) raise_main_window() (in module schrodinger.maestro.maestro) raise_voluptuous_exception() (in module schrodinger.application.jaguar.reactiq_validation) Ramachandran (class in schrodinger.application.desmond.packages.analysis) raman_activity_precision (schrodinger.application.jaguar.results.NormalMode attribute) raman_intensity_precision (schrodinger.application.jaguar.results.NormalMode attribute) RamanSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) ramp_colors (schrodinger.utils.pymol.Mapping attribute) random() (in module schrodinger.application.combiglide.combenumdock) RANDOM_ALL_TO_ON_THE_FLY_THRESH (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinitions attribute) random_choice() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) random_rotation() (in module schrodinger.application.matsci.amorphous) RANDOM_SEED (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) random_shuffle() (in module schrodinger.application.desmond.fep_mapping) random_string() (in module schrodinger.application.desmond.util) RANDOM_TYPES_CHOICES (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) randomlyRotate() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) randomlyTranslate() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) RandomSeedWidget (class in schrodinger.application.matsci.mswidgets) RandVelFrame (class in schrodinger.application.desmond.gui) range() (schrodinger.infra.mmbitset.Bitset method) RAW_AFEP (schrodinger.application.desmond.systype.DesmondTyper attribute) raw_alignment() (schrodinger.application.desmond.packages.msys.atomsel.Atomsel method) RAW_FEP (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) RAW_REGULAR (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.desmond.systype.WatermapTyper attribute) raw_val (schrodinger.utils.sea.Atom attribute) (schrodinger.utils.sea.List attribute) (schrodinger.utils.sea.Map attribute) RawInputConverter (class in schrodinger.application.matsci.qexsd.qespresso.converters) rbegin() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) RCE (class in schrodinger.application.macromodel.input) Rdf (class in schrodinger.application.desmond.packages.analysis) rdkit_reaction_from_smarts() (in module schrodinger.analysis.transformations) REACTANT (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) REACTANT_LIKE (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) REACTANT_NAME_BASE (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput attribute) ReactantMolecule (class in schrodinger.application.matsci.rxn_channel.rxn_channel) REACTANTPREFIX (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) Reactants (class in schrodinger.application.matsci.rxn_channel.rxn_channel) Reaction (class in schrodinger.analysis.reaction) reaction (schrodinger.analysis.reaction.RouteNode attribute) reaction_instance (schrodinger.analysis.reaction.RouteNode attribute) reaction_is_excluded() (in module schrodinger.analysis.reaction) reaction_is_supported() (in module schrodinger.application.jaguar.reactiq_validation) REACTIONANGLETHRESH (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) REACTIONBONDTHRESH (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) ReactionCoords (class in schrodinger.application.matsci.rxn_path) REACTIONDIHEDRALTHRESH (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) ReactionInstance (class in schrodinger.analysis.reaction) ReactionMoleculesTab (class in schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab) ReactionParticipant (class in schrodinger.application.jaguar.gui.tabs.reaction_tab) reactionParticipantAdded (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) reactionParticipantRemoved (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) reactionParticipantStructChanged (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) ReactionPath (class in schrodinger.application.matsci.rxn_path) ReactionPropertiesTab (class in schrodinger.application.jaguar.gui.tabs.reaction_properties_tab) ReactionTab (class in schrodinger.application.jaguar.gui.tabs.reaction_tab) ReactionWorkflow (class in schrodinger.application.matsci.reaction_workflow_utils) ReactionWorkflowException ReactiqConservationError ReactiqInput (class in schrodinger.application.jaguar.reactiq_input) ReactiqKeyword (class in schrodinger.application.jaguar.reactiq_keywords) ReactiqKeywordConflictError ReactiqKeywordError ReactiqKeywordException ReactiqKeywordFormatError ReactiqKeywordValueError ReactiqKeywordValueTypeError ReactiqStructureReader (class in schrodinger.application.jaguar.autots_bonding) REACTIVEATOM (schrodinger.application.matsci.rxn_path.ReactionPath attribute) ReactiveResidues (class in schrodinger.application.bioluminate.reactive_residues) reactWith() (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule method) read() (in module schrodinger.application.jaguar.input) (in module schrodinger.job.jobcontrol) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchAnalysis class method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder class method) (schrodinger.application.desmond.packages.msys.molfile.SeqFile class method) (schrodinger.application.desmond.packages.msys.molfile.StkFile class method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) (schrodinger.infra.mmgpgpu.istream method) (schrodinger.infra.mmjob.istream method) (schrodinger.infra.mmsurf.istream method) (schrodinger.project_surface.ProjectSurface class method) (schrodinger.structure.MaestroReader method) (schrodinger.structure.Structure static method) (schrodinger.surface.Surface class method) (schrodinger.utils.colorscheme.istream method) read_all_ct() (in module schrodinger.application.desmond.struc) read_asl_file() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) read_cfg() (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) read_cms() (in module schrodinger.application.desmond.packages.topo) (schrodinger.application.desmond.replica_sid_generator.FEPSimulationReport method) read_cms_and_traj() (in module schrodinger.application.desmond.packages.traj_util) read_constraints() (in module schrodinger.application.glide.glide) read_constraints_file() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint static method) read_ct() (in module schrodinger.structure) read_data_from_log_file() (in module schrodinger.application.desmond.replica_exchange_review) read_dE_file() (in module schrodinger.application.desmond.fepana) read_dE_Replicas() (schrodinger.application.desmond.replica_dE.replica_container method) read_density_from_eaf() (in module schrodinger.application.matsci.desmondutils) read_FEP_REST_energetics() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_FEPSimulation() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_keys() (in module schrodinger.utils.ligfilter) read_keywords_file() (in module schrodinger.application.glide.glide) read_keywords_file_as_dict() (in module schrodinger.application.glide.glide) read_license_file() (in module schrodinger.application.licensing.flexlm) read_LigandInfo() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_meta_cfg() (in module schrodinger.application.desmond.meta) read_mode (schrodinger.application.desmond.ffiostructure.CMSReader attribute) (schrodinger.structure.MaestroReader attribute) (schrodinger.structure.MaestroTextReader attribute) read_only (schrodinger.project.ProjectRow attribute) read_phase_subset() (in module schrodinger.infra.phase) read_protein_reliability() (in module schrodinger.application.desmond.feputils) read_ProteinInfo() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_qe_input() (schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method) read_reactions_file() (in module schrodinger.analysis.reaction) read_reagent_classes_file() (in module schrodinger.analysis.reaction) read_REST_exchanges() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) read_route_file() (in module schrodinger.analysis.reaction) read_seqres_from_ct() (in module schrodinger.structutils.analyze) read_stage_datafile() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) read_string() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) read_structures_as_conformations() (in module schrodinger.utils.cgxutils) read_table() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util) read_text() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) read_traj() (in module schrodinger.application.desmond.packages.traj) read_unique_field() (in module schrodinger.pipeline.pipeutils) read_void_file() (in module schrodinger.application.matsci.freevolume) read_volume_file() (in module schrodinger.application.matsci.freevolume) read_yaml() (in module schrodinger.application.glide.glide) readActionSelected() (schrodinger.application.desmond.gui.GuiApp method) readAgain() (schrodinger.job.jobcontrol.Job method) readAndRun() (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer class method) readColorRampFile() (schrodinger.utils.colorscheme.MM_ColorRamp method) readColorSchemeFile() (schrodinger.utils.colorscheme.ColorSchemeManager method) readCommand() (schrodinger.application.desmond.gui.GuiApp method) readConsKeywords() (schrodinger.application.glide.glide.Dock method) ReadCrdCoordinates() (in module schrodinger.application.desmond.packages.msys) readData() (in module schrodinger.infra.propedit) ReadEditMixin (class in schrodinger.application.jaguar.gui.base_panel) reader (schrodinger.structure.MultiFileStructureReader attribute) reader_class (schrodinger.structure.MultiFileStructureReader attribute) reader_open() (in module schrodinger.utils.csv_unicode) readFile() (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.structutils.filter.Filter method) (schrodinger.structutils.filter.PropFilter method) (schrodinger.structutils.filter.SmartsFilter method) ReadFileDialog (class in schrodinger.application.jaguar.gui.filedialog) readFileName() (schrodinger.structutils.filter.Filter method) readFilterCriteria() (schrodinger.ui.ligfilter.LigfilterFrame method) readFragmentLibrary() (schrodinger.application.ligprep.ionizer.Ionizer method) readFromStructure() (schrodinger.application.matsci.amorphous.BaseMoiety method) (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Monomer method) readJobsFromDatabase() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) readMapFile() (schrodinger.application.livedesign.ld_export.ExportMap method) readNewFormat() (schrodinger.pipeline.pipeline.Pipeline method) readNewFormatStage() (schrodinger.pipeline.pipeline.Pipeline method) readNewFormatVariable() (schrodinger.pipeline.pipeline.Pipeline method) readNext() (schrodinger.infra.phase.PhpTextFileReader method) ReadPDBCoordinates() (in module schrodinger.application.desmond.packages.msys) readRulesFromFile() (schrodinger.utils.colorscheme.MM_CScheme method) readSpecFile() (schrodinger.application.ligprep.ionizer.Ionizer method) readTemplateStructure() (schrodinger.application.matsci.builderwidgets.SketcherBox method) readTrj() (schrodinger.application.matsci.equilibrium_md.TrjBase method) readValueList() (schrodinger.pipeline.stages.filtering.SubSetStage method) READY (schrodinger.tasks.tasks.Status attribute) readyToRun() (schrodinger.pipeline.pipeline.StageJob method) reagent_class (schrodinger.analysis.reaction.ReagentSource attribute) ReagentClass (class in schrodinger.analysis.reaction) ReagentNode (class in schrodinger.analysis.reaction) ReagentSource (class in schrodinger.analysis.reaction) REAL_SIZE (schrodinger.application.matsci.espresso.utils.MemoryEstimator attribute) real_to_int() (in module schrodinger.application.desmond.gconfig) realSpaceGridInit() (schrodinger.application.matsci.espresso.utils.MemoryEstimator method) reassignHets() (schrodinger.application.prime.primefix.FixForPrime method) reassignResidueProperties() (schrodinger.application.matsci.amorphous.PolymerToFragments method) reassignResNums() (schrodinger.application.prime.primefix.FixForPrime method) rebuild_scripts_menu() (in module schrodinger.maestro.maestro) recalc() (schrodinger.structure._StructureChainIterator method) (schrodinger.structure._StructureMoleculeIterator method) (schrodinger.structure._StructureRingIterator method) RECEPTOR (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) receptor_b_factor (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_chain_names (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute) receptor_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_residues_interaction_ligand1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_residues_interaction_ligand2 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_sid_rmsd_backbone_lambda0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_sid_rmsd_backbone_lambda1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_sid_rmsd_ligand_lambda0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_sid_rmsd_ligand_lambda1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_sid_rmsf_backbone_lambda0 (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) receptor_sid_rmsf_backbone_lambda1 (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) receptor_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.MetalloproteinEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) receptor_title (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_total_atom (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_total_heavy (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_total_residues (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) receptor_total_residues_in_chains (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ReceptorLigandMap (class in schrodinger.application.livedesign.data_classes) ReceptorLigandPair (class in schrodinger.application.livedesign.data_classes) receptors (schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute) reciprocal_bohr_to_angstrom() (in module schrodinger.application.matsci.mecp_mod) RecognitionException recognitionException() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) RecognizerSharedState (class in schrodinger.application.desmond.antlr3.recognizers) recombine_solutions() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) recombineInputLigands() (schrodinger.pipeline.stages.glide.DockingStage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.qikprop.QikPropStage method) (schrodinger.pipeline.stages.semiemp.SemiEmpStage method) RecombineStage (class in schrodinger.pipeline.stages.gencodes) recompute_stereo() (in module schrodinger.utils.cgxutils) record (schrodinger.application.desmond.packages.timer.Timer.Args attribute) record() (schrodinger.application.desmond.antlr3.debug.RecordDebugEventListener method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) record_current_indices() (schrodinger.protein.assignment.ProtAssign method) RecordDebugEventListener (class in schrodinger.application.desmond.antlr3.debug) recover() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) recoverFromMismatchedSet() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) recoverFromMismatchedToken() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) Rectangle (class in schrodinger.application.matsci.nano.tube) recursivelySort() (schrodinger.application.matsci.coarsegrain.Internals method) redefineLatticeVecs() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) redisplayAtoms() (schrodinger.application.matsci.sliceplot.SlicePlot method) redraw (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) redraw() (in module schrodinger.maestro.maestro) (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) redraw_request() (in module schrodinger.maestro.maestro) reduce() (schrodinger.application.desmond.packages.analysis.ProteinRMSF method) (schrodinger.application.desmond.packages.analysis.ProtProtInter method) (schrodinger.application.desmond.packages.analysis.RMSF method) (schrodinger.application.desmond.packages.analysis.Ramachandran method) (schrodinger.application.desmond.packages.analysis.Rdf method) (schrodinger.application.desmond.packages.analysis.SecondaryStructure method) (schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceAreaByResidue method) (schrodinger.application.desmond.packages.analysis.VolumeMapper method) (schrodinger.application.desmond.packages.traj.Frame method) reduce_solvent() (in module schrodinger.application.desmond.packages.traj) reduce_vec() (in module schrodinger.application.desmond.packages.analysis) (schrodinger.application.desmond.packages.analysis.SmartsDirector method) (schrodinger.application.matsci.order_parameter_mod.SmartsDirector method) (schrodinger.application.matsci.order_parameter_mod.UniqueSmartsDirector method) reduce_vec_list() (in module schrodinger.application.desmond.packages.analysis) reduce_vector() (in module schrodinger.application.matsci.nano.xtal) reduced_mass_precision (schrodinger.application.jaguar.results.NormalMode attribute) reduceToSingleOperationPerIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) redundancy_tolerance (schrodinger.protein.assignment.ProtAssign.water_changeable attribute) redundant_server() (schrodinger.application.licensing.flexlm.License method) ref_asl (schrodinger.application.desmond.replica_sid_generator.AlchemAsl attribute) ref_keys (schrodinger.structutils.sitealign.SiteMatchLookup attribute) ref_solv_asl (schrodinger.application.desmond.replica_sid_generator.AlchemAsl attribute) refAtomFromCompAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) REFERENCE_FILTERS (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) ReferenceFrame (class in schrodinger.application.matsci.reordergui) ReferenceListWidget (class in schrodinger.application.matsci.reordergui) refinePrime() (schrodinger.application.bioluminate.protein.Refiner method) Refiner (class in schrodinger.application.bioluminate.protein) refresh() (in module schrodinger.application.licensing.licadmin) (schrodinger.application.licensing.licadmin.LicenseResource method) refreshMarkers (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab attribute) refreshPlot() (schrodinger.application.matsci.sliceplot.SlicePlot method) refreshRequested (schrodinger.application.livedesign.panel_components.LiveReportSelector attribute) refreshTable() (schrodinger.project.Project method) reg_xcheck() (in module schrodinger.utils.sea) regenerate_markers() (in module schrodinger.maestro.maestro) regeneratePicture() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant method) register() (schrodinger.application.desmond.image_generator.ImageGenerator method) register_file() (in module schrodinger.application.jaguar.file_logger) (schrodinger.application.jaguar.file_logger.FileLogger method) register_plugin() (in module schrodinger.application.desmond.packages.msys.molfile) reject() (schrodinger.application.bioluminate.propfilter.ValueSelectionDialog method) (schrodinger.application.canvas.r_group_dee.DEE_Backtracking method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.reordergui.ReorderAtomsDialog method) rejected() (schrodinger.ui.ligfilter.AddDefinitionDialog method) relative_path() (in module schrodinger.application.jaguar.file_logger) RELATIVE_POT_KEY (schrodinger.application.matsci.espresso.qeinput.BoundaryType attribute) RelaxFrame (class in schrodinger.application.desmond.gui) release() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) released (schrodinger.application.matsci.siteselector.siteselector.SiteRadioButton attribute) released() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) reload (schrodinger.application.jaguar.input.JaguarInput attribute) RELOAD_STRUCTURE (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) reloadTemplateList() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) relocateEtaMarkers() (schrodinger.application.matsci.builderwidgets.TMLigandRowMixin method) relocateFailedMol() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) relpath() (in module schrodinger.application.desmond.util) REMD (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) remd (schrodinger.application.desmond.config.TAG_SPECS attribute) remediate_ct() (in module schrodinger.protein.remediate) remote_command() (in module schrodinger.job.remote_command) remove() (schrodinger.application.bioluminate.sliderchart.SlidableLine method) (schrodinger.application.desmond.packages.msys.Atom method) (schrodinger.application.desmond.packages.msys.Bond method) (schrodinger.application.desmond.packages.msys.Chain method) (schrodinger.application.desmond.packages.msys.Ct method) (schrodinger.application.desmond.packages.msys.Residue method) (schrodinger.application.desmond.packages.msys.Term method) (schrodinger.application.desmond.packages.msys.TermTable method) (schrodinger.graphics3d.common.Group method) (schrodinger.job.queue.LinkedList method) (schrodinger.job.queue.RunningJobs method) (schrodinger.protein.sequence.Sequence method) (schrodinger.utils.fileutils.tempfilename method) (schrodinger.utils.preferences.Preferences method) remove_atom_property() (in module schrodinger.application.matsci.msutils) remove_basename_ext() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) remove_changeables_from_hbonders() (schrodinger.protein.assignment.ProtAssign method) remove_disulfide_bond() (in module schrodinger.protein.residue) remove_dummy_atoms() (schrodinger.protein.membrane.Membrane_Model method) remove_dupes() (in module schrodinger.structutils.smilesfilter) remove_extra_rotable_atoms() (in module schrodinger.application.desmond.r_group_asl) remove_fatal_atom_properties() (in module schrodinger.application.matsci.desmondutils) remove_file() (in module schrodinger.application.desmond.util) remove_flag() (schrodinger.application.matsci.jobutils.MultijobDriver method) remove_formal_charges() (in module schrodinger.application.jaguar.autots_bonding) remove_ghost_solvent() (in module schrodinger.application.desmond.gcmc_utils) remove_ghost_solvent_file() (in module schrodinger.application.desmond.gcmc_utils) remove_gibbs_energies() (in module schrodinger.application.jaguar.utils) remove_handlers() (in module schrodinger.utils.log) remove_input_file_paths() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) remove_last_atom_highlight() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) remove_object() (in module schrodinger.maestro.maestro) remove_option() (schrodinger.utils.cmdline.SingleDashOptionParser method) remove_pbc() (in module schrodinger.application.matsci.nano.tube) remove_plugin() (in module schrodinger.application.desmond.config) remove_ssl_ld_library_path (class in schrodinger.utils.env) remove_stale_props() (in module schrodinger.application.matsci.amorphous) remove_stereo_annotation() (in module schrodinger.structutils.smiles) remove_tag() (schrodinger.utils.sea.Sea method) remove_temp_dir() (in module schrodinger.application.desmond.mplchart) remove_unconn_core_atoms() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) remove_zero_order_bonds() (schrodinger.protein.assignment.ProtAssign method) removeAction() (schrodinger.application.bioluminate.actions.factory.Factory method) removeAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAllFeaturesForEntry() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAllGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) removeAllRefCtMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAllSeqs() (schrodinger.protein.alignment.BaseAlignment method) removeAllTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAllXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeAminoAcids() (in module schrodinger.application.desmond.automatic_analysis_generator) removeAndRenumber() (schrodinger.application.matsci.nano.particle.Nanoparticle method) removeBadOptions() (in module schrodinger.application.bioluminate.workspacelabeler) removeColorsForMissingPoints() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) removeColumn() (schrodinger.application.desmond.gui.TableModel method) removeCoordinate() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) removeDisulfideBond() (schrodinger.protein.alignment.ProteinAlignment method) removeEdge() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) removeFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeFFProperties() (schrodinger.application.matsci.builderwidgets.ItemRow method) removeFinishedPolymer() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) removeFromSequence() (schrodinger.protein.sequence.Sequence method) removeGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) removeHydrogens() (schrodinger.application.matsci.nano.tube.NanoTube method) removeIgnoredClashes() (schrodinger.application.matsci.amorphous.BuilderWithClashDetection method) removeIgnorePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) removeInternalsWithNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) removeJaguarMarker (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsTableView attribute) removeJaguarMarkerForRow() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel method) removeKey() (schrodinger.utils.ligfilter.Definition method) removeMissingPoints() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) removeNode() (schrodinger.application.matsci.amorphous.LowMemoryVolGraph method) removeOneRow() (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) removeParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) removePkaMarkers() (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) removePreviousExistingFiles() (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) removeProperties() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.StructureGenome method) removeRefCtMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeResidues() (schrodinger.protein.alignment.BaseAlignment method) removeRow() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) removeRowNumbers() (schrodinger.application.desmond.fep_gui.ResiduesModel method) removeRows() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel method) removeSelectedRows() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) removeSeq() (schrodinger.protein.alignment.BaseAlignment method) removeSeqByIndex() (schrodinger.protein.alignment.BaseAlignment method) removeSeqs() (schrodinger.protein.alignment.BaseAlignment method) removeSphere() (schrodinger.infra.phase.PhpExclVol method) removeSpheres() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) removeStruct() (schrodinger.application.combiglide.combenumdock.collectionViewerModel method) removeStructurelessResidues() (schrodinger.protein.sequence.ProteinSequence method) removeSubalignment() (schrodinger.protein.alignment.BaseAlignment method) removeSubTabMarker() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) removeTask() (schrodinger.tasks.tasks_.TaskManager method) removeTerminalGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) removeTolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeToolBar() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) removeXvolMarkers() (schrodinger.application.phase.phase_markers.PhaseMarkers method) removeXvolMarkersWithIDs() (schrodinger.application.phase.phase_markers.PhaseMarkers method) rename() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.project_surface.ProjectSurface method) (schrodinger.surface.Surface method) rename_atom_property() (in module schrodinger.application.desmond.struc) rename_cms_title() (schrodinger.application.desmond.title_to_hex.Analysis method) renameCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) renameColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) renameProperty() (in module schrodinger.infra.propedit) rend() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) renderToFile() (schrodinger.analysis.reaction.RouteRenderer method) renumber_conformer() (in module schrodinger.structutils.rmsd) renumber_residues() (in module schrodinger.protein.pdbname) renumberAtomLists() (schrodinger.application.matsci.nano.tube.NanoTubeSheet method) renumberByMolecule() (schrodinger.application.prime.primefix.FixForPrime method) renumberBySymmetry() (schrodinger.application.jaguar.rmsd.ConformerRmsdX method) (schrodinger.structutils.rmsd.ConformerRmsd method) renumberResGetM2PMap() (schrodinger.application.matsci.amorphous.PolymerToFragments method) renumberWorkingStructures() (schrodinger.application.jaguar.rmsd.ConformerRmsdX method) (schrodinger.structutils.rmsd.ConformerRmsd method) REORDER (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) reorder_atom() (in module schrodinger.application.desmond.reorder_atom) reorder_atoms() (in module schrodinger.application.desmond.fep_mapping) (in module schrodinger.structutils.build) reorder_protein_atoms_by_sequence() (in module schrodinger.structutils.build) reorder_solute() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) reorder_st() (in module schrodinger.application.desmond.fep_mapping) reorder_structures() (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) ReorderAtomFrame (class in schrodinger.application.matsci.reordergui) ReorderAtomPanel (class in schrodinger.application.matsci.reordergui) ReorderAtomsDialog (class in schrodinger.application.matsci.reordergui) reorderColorSchemes() (schrodinger.utils.colorscheme.ColorSchemeManager method) reorderSequences() (schrodinger.protein.alignment.BaseAlignment method) repair_box_vector() (in module schrodinger.application.desmond.repair_cms) REPLACE (schrodinger.job.launchparams.ProjectDisposition attribute) replace() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) replace_coords_with_zmat() (in module schrodinger.application.matsci.zmutils) REPLACE_FIT (schrodinger.job.launchparams.ProjectDisposition attribute) REPLACE_METHOD_NAME (schrodinger.models.parameters.BaseMutableParam attribute) (schrodinger.models.parameters.DictParam attribute) (schrodinger.models.parameters.ListParam attribute) (schrodinger.models.parameters.SetParam attribute) replace_slot() (in module schrodinger.application.bioluminate.actions.factory) replace_value() (schrodinger.application.matsci.jobutils.MultijobDriver method) replaceAllElements() (schrodinger.protein.sequence.Sequence method) replaceChildren() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) ReplaceOp (class in schrodinger.application.desmond.antlr3.streams) replaceResiduesWithGaps() (schrodinger.protein.alignment.BaseAlignment method) replaceSeq() (schrodinger.protein.alignment.BaseAlignment method) replaceSubalignment() (schrodinger.protein.alignment.BaseAlignment method) replica_container (class in schrodinger.application.desmond.replica_dE) replica_energy (class in schrodinger.application.desmond.replica_dE) replica_name() (in module schrodinger.application.desmond.report_helper) replicas_monitor (class in schrodinger.application.desmond.replica_dE) replicate_ct() (in module schrodinger.application.desmond.packages.topo) replot() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) repopulateSearchAlongCombo() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) Report (class in schrodinger.protein.analysis) report() (in module schrodinger.protein.assignment) (schrodinger.analysis.enrichment.Calculator method) (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_edge_report_maker.PRMEdgeReportMaker method) (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) (schrodinger.protein.analysis.Report.data_set method) Report.backbone_dihedral_data_set (class in schrodinger.protein.analysis) Report.Bfactor_data_set (class in schrodinger.protein.analysis) Report.bond_angle_data_set (class in schrodinger.protein.analysis) Report.bond_length_data_set (class in schrodinger.protein.analysis) Report.chirality_data_set (class in schrodinger.protein.analysis) Report.data_set (class in schrodinger.protein.analysis) Report.data_set.data_point (class in schrodinger.protein.analysis) Report.gamma_Bfactor_data_set (class in schrodinger.protein.analysis) Report.Gfactor_summary_data_set (class in schrodinger.protein.analysis) Report.improper_torsion_data_set (class in schrodinger.protein.analysis) Report.local_atom (class in schrodinger.protein.analysis) Report.local_protein (class in schrodinger.protein.analysis) Report.local_residue (class in schrodinger.protein.analysis) Report.missing_atoms_data_set (class in schrodinger.protein.analysis) Report.peptide_planarity_data_set (class in schrodinger.protein.analysis) Report.primex_steric_clash_data_set (class in schrodinger.protein.analysis) Report.sidechain_dihedral_data_set (class in schrodinger.protein.analysis) Report.sidechain_planarity_data_set (class in schrodinger.protein.analysis) Report.steric_clash_data_set (class in schrodinger.protein.analysis) Report2D (class in schrodinger.application.report2d) report_add_logo() (in module schrodinger.application.desmond.report_helper) report_add_ms_logo() (in module schrodinger.application.desmond.report_helper) report_data_points() (schrodinger.protein.analysis.Report.data_set method) report_t() (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) report_total_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) report_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) reportAndReturnStatus() (schrodinger.application.livedesign.ld_export.ExportThreadRunner method) reportError() (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.enhanced_sampling.mexpLexer.mexpLexer method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) reportFinalResults() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method)

ReportFrame (class in schrodinger.application.bioluminate.protein_report_widget) reportLigandsDetails() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportParameters() (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.stage.Stage method) reportProteinDetails() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportReplicaExchanges() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportReplicaPairEnergies() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportSimulationDetails() (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) reportValidation() (schrodinger.tasks.runners.TaskRunner method) (schrodinger.tasks.tasks.AbstractTask method) REPRESENTATIVE (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI attribute) representative_frames() (in module schrodinger.application.desmond.process_fep_traj) rept_file_ext (schrodinger.analysis.enrichment.Calculator attribute) REPULSION (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint attribute) requestCpus() (schrodinger.pipeline.pipeline.Pipeline method) Required (schrodinger.application.livedesign.maestro_data_types.Export3D attribute) required_login_info_set() (in module schrodinger.application.livedesign.login) requiredProduct() (schrodinger.pipeline.stage.Stage method) requiredProductRuntime() (schrodinger.pipeline.stage.Stage method) reroot() (in module schrodinger.application.desmond.reorder_atom) res_add_externals() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) res_can_be_capped() (in module schrodinger.protein.captermini) RES_MATCH_BONUS (schrodinger.protein.align.PairwiseAligner attribute) RES_MISMATCH_PENALTY (schrodinger.protein.align.PairwiseAligner attribute) res_pair (schrodinger.protein.residue.DisulfideBond attribute) RES_PROPENSITY_ANNOTATIONS (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) RES_TO_IGNORE (schrodinger.structutils.interactions.salt_bridge.SaltBridgeFinder attribute) RES_TYPES (schrodinger.application.bioluminate.patch_utils.patch_finder.Patch attribute) resBackbone() (schrodinger.application.matsci.amorphous.PolymerToFragments method) rescale_ff() (in module schrodinger.application.desmond.remd) rescale_ff_solute_tempering() (in module schrodinger.application.desmond.remd) resCapped() (schrodinger.protein.captermini.CapTermini method) rescode (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) RescodeAligner (class in schrodinger.protein.align) ResData (class in schrodinger.application.desmond.fep_edge_data) (in module schrodinger.application.bioluminate.patch_utils.patch_finder) reserve() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) reset() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.antibody.search_results_table.TableView method) (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.InputGroup method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.desmond.util.Counter method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabConsistentOrbitals method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword method) (schrodinger.application.livedesign.panel_components.AbstractExportTableModel method) (schrodinger.application.livedesign.panel_components.BaseSelectionPopup method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) (schrodinger.application.matsci.chargegui.BasisSetSelector method) (schrodinger.application.matsci.chargegui.ChargePropertySelector method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.application.matsci.clusterstructgui.DimerSpeciesSelector method) (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) (schrodinger.application.matsci.mswidgets.CompactSolventSelector method) (schrodinger.application.matsci.mswidgets.DefineASLDialog method) (schrodinger.application.matsci.mswidgets.EmbeddedSolventWidget method) (schrodinger.application.matsci.mswidgets.MultiStageArea method) (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.application.matsci.reordergui.StructurePic method) (schrodinger.application.matsci.sliceplot.SlicePlot method) (schrodinger.application.phase.featureselector.FeatureSelector method) (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) (schrodinger.models.parameters.CompoundParam method) (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) reset_colors() (in module schrodinger.application.combiglide.connection_storage) reset_solvent_resnum() (in module schrodinger.application.desmond.packages.parch) reset_tag() (schrodinger.utils.sea.Sea method) reset_tddft_excitation_energies() (in module schrodinger.application.jaguar.textparser) reset_workspace_transformations() (in module schrodinger.maestro.maestro) resetAcceptedRow() (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) resetAll() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) resetAllColorSchemeRules() (schrodinger.utils.colorscheme.ColorSchemeManager method) resetAllFeatures() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) resetAllRequested (schrodinger.tasks.runners.TaskRunner attribute) resetAnnotation() (schrodinger.protein.annotation.ProteinSequenceAnnotations method) resetAtomGroupTable() (schrodinger.application.desmond.gui.AtomGroupFrame method) resetCallNumber() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) resetColorSchemes() (schrodinger.utils.colorscheme.ColorSchemeManager method) resetData() (schrodinger.ui.ligfilter.CriteriaListModel method) resetEnsClass() (schrodinger.application.desmond.gui.EnsembleTab method) resetFiniteDiffCall() (schrodinger.application.matsci.mecp_mod.BFGS method) resetfp() (schrodinger.application.canvas.fingerprintgui.CanvasFingerprintGeneratorGUI method) resetFragDihedralPool() (schrodinger.application.matsci.amorphous.PolymerFragment method) resetFromModel() (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.MdcMiscTab method) (schrodinger.application.desmond.gui.RestraintsTab method) resetGroup() (schrodinger.utils.preferences.Preferences method) resetKey() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) resetLabelOptions() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) resetMap() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) resetMapComboBox() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) resetMaxIter() (schrodinger.application.desmond.gui.MinimizationTab method) (schrodinger.application.desmond.gui.MinimizerFrame method) resetParentProperties() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.StructureGenome method) resetPosResTable() (schrodinger.application.desmond.gui.RestraintsTab method) resetSelected() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) resetSlots() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) resetStructure() (schrodinger.application.jaguar.input.JaguarInput method) resetTable() (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) resetThermoTemp() (schrodinger.application.desmond.gui.EnsembleTab method) resetWidgets() (schrodinger.application.livedesign.panel_components.BaseSearchTreeWidgetHelper method) resid (schrodinger.application.desmond.packages.msys.Residue attribute) ResidualPotential (class in schrodinger.application.bioluminate.escomp) Residue (class in schrodinger.application.desmond.packages.msys) (class in schrodinger.protein.residue) residue (schrodinger.application.desmond.packages.msys.Atom attribute) (schrodinger.protein.sequence.StructureSequence attribute) (schrodinger.structure.Structure attribute) (schrodinger.structure.TextualStructure attribute) (schrodinger.structure._Chain attribute) (schrodinger.structure._Molecule attribute) residue() (schrodinger.application.desmond.packages.msys.System method) RESIDUE_CALCULATIONS (schrodinger.application.bioluminate.protein.PropertyCalculator attribute) RESIDUE_CHARGE (class in schrodinger.protein.residue) residue_charge (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) residue_formula() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) residue_hydrophobicity (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) residue_indices (schrodinger.application.bioluminate.protein.Consensus attribute) residue_is_nonpolar() (in module schrodinger.application.bioluminate.protein) residue_is_polar() (in module schrodinger.application.bioluminate.protein) residue_position (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) residue_structure_mae() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) residue_structure_template() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) residue_type (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) ResidueData (class in schrodinger.application.bioluminate.reactive_residues) ResidueGroups (class in schrodinger.ui.residueselector) ResidueRow (class in schrodinger.ui.picking) residues (schrodinger.application.bioluminate.protein.Consensus attribute) (schrodinger.application.desmond.packages.msys.Chain attribute) (schrodinger.application.desmond.packages.msys.System attribute) (schrodinger.protein.alignment.ResidueSelection attribute) residues_centroid_changed (schrodinger.ui.picking.PickResiduesChangedMixin attribute) residues_changed (schrodinger.ui.picking.PickResiduesChangedMixin attribute) residuesAdded (schrodinger.protein.alignment.AlignmentSignals attribute) residuesChanged (schrodinger.protein.sequence.Sequence attribute) residuesDeleted (schrodinger.protein.sequence.Sequence attribute) ResidueSelection (class in schrodinger.protein.alignment) ResiduesModel (class in schrodinger.application.desmond.fep_gui) residuesRemoved (schrodinger.protein.alignment.AlignmentSignals attribute) ResidueType (class in schrodinger.protein.residue) ResInfo (class in schrodinger.application.bioluminate.patch_utils.patch_finder) Resize() (in module schrodinger.analysis.visanalysis.volumedatautils) resize() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) resize_window() (in module schrodinger.application.desmond.util) resize_window2() (in module schrodinger.application.desmond.util) resKey() (schrodinger.application.prime.residue_interaction.InteractionReader static method) resnum (schrodinger.application.qsite.input.Cut attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.structure._Residue attribute) (schrodinger.structure._StructureAtom attribute) resolve_atomsel() (in module schrodinger.application.desmond.enhsamp) (schrodinger.application.desmond.enhsamp.FcnCall method) (schrodinger.application.desmond.enhsamp.Node method) resolve_links() (in module schrodinger.application.combiglide.combenumdock) resolveCoordsConflict() (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) resolveMaskValue() (schrodinger.infra.phase.PhpSiteMask static method) resolveMatchLimits() (schrodinger.infra.phase.PhpSiteMask static method) RESONANCE (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) resource_summary() (in module schrodinger.application.licensing.licadmin) resources() (in module schrodinger.application.licensing.licadmin) resources_from_list() (in module schrodinger.application.licensing.licadmin) resources_from_path() (in module schrodinger.application.licensing.licadmin) respaBondChanged() (schrodinger.application.desmond.gui.IntegrationTab method) ResPatchData (class in schrodinger.application.bioluminate.patch_utils.patch_finder) REST_PROPERTIES (class in schrodinger.application.desmond.constants) restart (schrodinger.application.jaguar.input.JaguarInput attribute) (schrodinger.application.jaguar.output.JaguarOutput attribute) Restart() (in module schrodinger.pipeline.pipeline) (in module schrodinger.pipeline.stage) restart() (schrodinger.pipeline.pipeline.StageJob method) restart_name() (in module schrodinger.application.jaguar.output) RESTFEPConfigDialog (class in schrodinger.application.desmond.fep_gui) RestInput (class in schrodinger.application.desmond.rest_inp) restore() (schrodinger.protein.rotamers.Rotamers method) restore_workspace (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) restore_zobs() (schrodinger.protein.assignment.ProtAssign method) restoreCurrentColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) restoreCursor() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) restoreIonCenterProps() (schrodinger.application.ligprep.ionizer.Ionizer method) restoreLabelOptions() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) restoreMasterData() (schrodinger.infra.phase.PhpProject method) restorePreviouslyIncludedEntry() (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) RestoreTitlesStage (class in schrodinger.pipeline.stages.gencodes) Restrain (class in schrodinger.application.desmond.cms) restrain_force_constant() (in module schrodinger.application.desmond.gconfig) RestraintBuilder (class in schrodinger.application.desmond.restraint) Restraints (class in schrodinger.application.desmond.packages.restrain) RestraintsTab (class in schrodinger.application.desmond.gui) Restricted (schrodinger.application.jaguar.gui.utils.SpinTreatment attribute) restToggled() (schrodinger.application.desmond.fep_gui.DesmondApp method) ResTuple (class in schrodinger.application.bioluminate.interaction_calculator) result_server_option() (in module schrodinger.tasks.jobtasks) Results (class in schrodinger.application.matsci.jaguarworkflows) (class in schrodinger.protein.reliability) (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator attribute) results (schrodinger.application.mopac.mopac_launchers.MopacLauncher attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher2012 attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher71 attribute) results() (schrodinger.application.desmond.feputils.ProteinProcessManager method) results_cache (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner attribute) RETAIN (schrodinger.application.desmond.constants.EXISTING_RESTRAINT attribute) retranslateUi() (schrodinger.application.bioluminate.propfilter_ui.Ui_Form method) (schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form method) (schrodinger.application.combiglide.combenumdock.glidePrecisionDialog method) (schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_cfc_ui.Ui_Widget method) (schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_collection_viewer_ui.Ui_Dialog method) (schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_constraints_ui.Ui_Dialog method) (schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_ui.Ui_Widget method) (schrodinger.application.desmond.desmond_advanced_tab_ui.Ui_Dialog method) (schrodinger.application.desmond.input_group_ui.Ui_Form method) (schrodinger.application.desmond.rest_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui.Ui_Dialog method) (schrodinger.application.jaguar.gui.ui.edit_dialog_ui.Ui_MainWindow method) (schrodinger.application.jaguar.gui.ui.excited_state_widget_ui.Ui_Widget method) (schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_std_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.irc_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.irc_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.multi_structures_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.optimization_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.output_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.properties_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scan_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scf_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvation_gas_phase_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvation_pka_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvation_solvent_model_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvent_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui.Ui_Widget method) (schrodinger.application.jaguar.gui.ui.theory_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.transition_state_top_ui.Ui_Form method) (schrodinger.application.livedesign.export_setup_ui.Ui_Form method) (schrodinger.application.livedesign.export_ui.Ui_Form method) (schrodinger.application.livedesign.login_ui.Ui_Dialog method) (schrodinger.application.prime.gui.ui.analyze_energy_ui.Ui_Form method) (schrodinger.application.prime.gui.ui.environment_options_ui.Ui_Form method) (schrodinger.infra.exception_handler_dir.exception_dialog_ui.Ui_Dialog method) (schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog method) (schrodinger.ui.ligfilter_ui.Ui_Form method) (schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui.Ui_Dialog method) retrieve_ent() (in module schrodinger.protein.getpdb) retrieve_frame() (schrodinger.application.desmond.packages.traj.Source method) retrieve_license_file() (in module schrodinger.application.licensing.netsuiteapi) retrieve_pdb() (in module schrodinger.protein.getpdb) RetroSynthesisNode (class in schrodinger.analysis.reaction) retrosynthesize() (in module schrodinger.analysis.reaction) retryFailure() (schrodinger.application.matsci.jaguarworkflows.RobustSubmissionJob method) (schrodinger.job.queue.JobControlJob method) ReturnCode (class in schrodinger.infra.mmcheck) retype() (schrodinger.structure._StructureAtom method) (schrodinger.structure.Structure method) REVERSE_INTERPOLATION (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) reverse_iter() (schrodinger.job.queue.LinkedList method) revert() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.infra.licensing.MMlic3AutoExitOverride method) revertCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) revertCombLib() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) reviseDatabase() (schrodinger.infra.phase.PhpProject method) reviseIonizedGroup() (schrodinger.application.ligprep.ionizer.Ionizer method) REVOLUTION (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) REVOLUTIONTHRESH (schrodinger.application.matsci.rxn_path.ReactionCoords attribute) rewind() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) rewrite() (schrodinger.application.canvas.utils.ChmCSVTools method) rewriteByIndex() (schrodinger.application.canvas.utils.ChmCSVTools method) RewriteCardinalityException RewriteEarlyExitException RewriteEmptyStreamException RewriteOperation (class in schrodinger.application.desmond.antlr3.streams) RewriteRuleElementStream (class in schrodinger.application.desmond.antlr3.tree) RewriteRuleNodeStream (class in schrodinger.application.desmond.antlr3.tree) RewriteRuleSubtreeStream (class in schrodinger.application.desmond.antlr3.tree) RewriteRuleTokenStream (class in schrodinger.application.desmond.antlr3.tree) rgb (schrodinger.application.matsci.coarsegrain.ParticleInfo attribute) rgb_float (schrodinger.structutils.color.Color attribute) (schrodinger.surface.Surface.Color attribute) RGroup (class in schrodinger.structutils.rgroup_enumerate) RgroupEnumerator (class in schrodinger.structutils.rgroup_enumerate) RgroupError RGroupException RGroupFinder (class in schrodinger.application.canvas.r_group) RGroupStructureToolTip (class in schrodinger.application.matsci.builderwidgets) rhl1() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) rhl2() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) right_click_callback_add() (in module schrodinger.maestro.maestro) right_click_callback_remove() (in module schrodinger.maestro.maestro) ring (schrodinger.structure.Structure attribute) (schrodinger.structure.TextualStructure attribute) ring_atoms() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) ring_indexes (schrodinger.structutils.ringspear.Spear attribute) ring_size (schrodinger.structutils.ringspear.SpearRing attribute) ringbondcount() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method) rl_pair_items (schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute) rl_pairs (schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute) rmKwargs() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property static method) rms_structures() (in module schrodinger.application.jaguar.autots_rmsd) RMSD (class in schrodinger.application.desmond.packages.analysis) rmsd_matrix() (in module schrodinger.application.desmond.packages.analysis) rmsd_precision (schrodinger.application.jaguar.output.JaguarOutput attribute) RmsdStage (class in schrodinger.pipeline.stages.rmsd) RMSDSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) (class in schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) RMSF (class in schrodinger.application.desmond.packages.analysis) RobustSubmissionJob (class in schrodinger.application.matsci.jaguarworkflows) rollback() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) rolmp2() (in module schrodinger.application.jaguar.textparser) rosen() (in module schrodinger.application.matsci.mecp_mod) Rot_bonds (schrodinger.application.glide.xpdes.TermKeywords attribute) Rotamers (class in schrodinger.protein.rotamers) rotamers (schrodinger.protein.rotamers.Rotamers attribute) rotatable_bonds_iterator() (in module schrodinger.structutils.analyze) ROTATE (schrodinger.application.matsci.montecarlo.Metropolizer attribute) rotate_double_bonds() (in module schrodinger.application.matsci.nano.util) rotate_structure() (in module schrodinger.structutils.transform) rotateNanoSheet() (schrodinger.application.matsci.nano.tube.NanoSheet method) rotateProteinToMembrane() (schrodinger.protein.membrane.Membrane_Model method) rotateRigidBodyCell() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) rotateTube() (schrodinger.application.matsci.nano.tube.NanoTube method) rotation_matrix (schrodinger.structutils.ringspear.SpearRing attribute) rotation_points_add() (in module schrodinger.maestro.maestro) rotation_points_remove() (in module schrodinger.maestro.maestro) rotational_strength_precision (schrodinger.application.jaguar.results.NormalMode attribute) RotationError rotomers() (schrodinger.application.matsci.amorphous.TorsionAngler method) ROUGH_CUT_DISTANCE (in module schrodinger.structutils.ringspear) round() (schrodinger.application.matsci.mswidgets.SliderchartVLClass method) roundup() (in module schrodinger.application.matsci.msutils) RouteNode (class in schrodinger.analysis.reaction) RouteRenderer (class in schrodinger.analysis.reaction) row_charge (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry attribute) ROW_CLASS (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) (schrodinger.application.livedesign.panel_components.AbstractExportTableModel attribute) (schrodinger.application.phase.featureselector.FeatureModel attribute) (schrodinger.application.phase.phase_widgets.HypothesisModel attribute) (schrodinger.ui.picking.PickResidueModel attribute) row_number (schrodinger.project.ProjectRow attribute) RowActionItem (class in schrodinger.application.bioluminate.bwidgets) rowCount() (schrodinger.application.bioluminate.antibody.search_results_table.FrameworkModel method) (schrodinger.application.bioluminate.propfilter.CriteriaListModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.desmond.fep_gui.PathModel method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.ui.chooseligand.ChooseLigandModel method) (schrodinger.ui.ligfilter.CriteriaListModel method) (schrodinger.ui.ligfilter.PatternModel method) rowGetExpanded() (schrodinger.infra.table.Table method) rowGetVisible() (schrodinger.infra.table.Table method) RowProxy (class in schrodinger.utils.pymol) rowSetExpanded() (schrodinger.infra.table.Table method) rowSetVisible() (schrodinger.infra.table.Table method) rowsForEid() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) rrho() (schrodinger.application.macromodel.utils.ComUtil method) rsh_put_cmd() (in module schrodinger.job.remote_command) rsh_test() (in module schrodinger.job.remote_command) RSI (schrodinger.maestro.markers.Icons attribute) rsqrScramble (schrodinger.infra.phase.PhpQSARModel attribute) RULE (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.desmond.systype.TyperBase attribute) (schrodinger.application.desmond.systype.WatermapTyper attribute) rulePostProcessing() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) RuleReturnScope (class in schrodinger.application.desmond.antlr3.recognizers) run() (in module schrodinger.application.licensing.licadmin) (schrodinger.analysis.reaction.Synthesizer method) (schrodinger.application.bioluminate.interaction_calculator.InteractionCalculator class method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinderRunner method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) (schrodinger.application.canvas.r_group_dee.SimulatedAnnealing method) (schrodinger.application.desmond.rest_inp.RestInput method) (schrodinger.application.desmond.starter.starter.Starter method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.desmond.util.TestSuite method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel method) (schrodinger.application.matsci.order_parameter_mod.OrderParameter method) (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) (schrodinger.application.mopac.mopac_launchers.MopacLauncher method) (schrodinger.application.mopac.mopac_launchers.MopacLauncher2012 method) (schrodinger.application.mopac.mopac_launchers.MopacLauncher71 method) (schrodinger.application.mopac.structure_launchers.StructureLauncher method) (schrodinger.application.report2d.PicturePrinter method) (schrodinger.application.watermap.watermap_inp.WaterMapInput method) (schrodinger.infra.fast3d.Engine method) (schrodinger.infra.fast3d.SingleConformerEngine method) (schrodinger.infra.fast3d.Volumizer method) (schrodinger.job.app.App method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobDJ method) (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.pipeline.stage.Stage method) (schrodinger.protein.align.AbstractAligner method) (schrodinger.protein.align.BasicAligner method) (schrodinger.protein.align.PairwiseAligner method) (schrodinger.protein.align.RescodeAligner method) (schrodinger.protein.align.SuperpositionAligner method) (schrodinger.structutils.analyze.MissingLoopFinder method) (schrodinger.utils.installation_check.TestJob method) run_align() (in module schrodinger.application.ska) run_analysis() (schrodinger.protein.analysis.Report.steric_clash_data_set method) run_apbs() (in module schrodinger.application.desmond.fep_net_charge) run_bennett() (in module schrodinger.application.desmond.fepana) run_bennett_orig() (in module schrodinger.application.desmond.fepana) run_check() (in module schrodinger.protein.reliability) run_cleanup() (in module schrodinger.application.mopac.utils) run_conformational_search() (in module schrodinger.application.matsci.reaction_workflow_utils) run_desmond() (in module schrodinger.application.desmond.packages.gdesmond_utils) run_hmc() (schrodinger.application.desmond.torsion_related.BondRotator method) run_installation_check() (in module schrodinger.utils.installation_check) run_jobs_with_update_logging() (in module schrodinger.application.matsci.textlogger) run_kwargs (schrodinger.application.jaguar.input.JaguarInput attribute) run_lmdiag() (in module schrodinger.application.licensing.licadmin) run_lmstat() (in module schrodinger.application.licensing.licadmin) run_multiple_inputs() (in module schrodinger.application.bioluminate.escomp) run_phase_database_job() (in module schrodinger.pipeline.stages.phase) run_postmortem() (in module schrodinger.utils.installation_check) run_propka() (in module schrodinger.application.bioluminate.run_propka) (schrodinger.protein.assignment.ProtAssign method) run_protein_reliability() (in module schrodinger.application.desmond.feputils) run_quick_check() (in module schrodinger.protein.reliability) run_requested (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) run_rga() (in module schrodinger.application.desmond.fep_mapping) run_system_builder() (in module schrodinger.application.matsci.desmondutils) run_test_jobs() (in module schrodinger.utils.installation_check) run_workflows() (in module schrodinger.application.matsci.jaguarworkflows) runAddJob() (schrodinger.pipeline.stages.phase.DBManageStage method) runCanvasKPLS() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS method) runCluFile() (schrodinger.application.macromodel.utils.CluUtil method) runEditedInput() (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) runIt() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS method) (schrodinger.application.matsci.genetic_optimization.genetic_optimization.ClassEvaluator method) (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.matsci.mecp_mod.MECP method) (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.particle.Nanoparticle method) (schrodinger.application.matsci.nano.slab.Surface method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) (schrodinger.application.matsci.nano.surfaces_interfaces_mod.SurfacesInterfaces method) (schrodinger.application.matsci.rxn_path.ReactionPath method) runJMSWF() (schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow method) runJob() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) runJobDJ() (schrodinger.pipeline.stage.Stage method) runJobs() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) runMain() (schrodinger.application.livedesign.ld_export.ExportThreadRunner method) (schrodinger.application.livedesign.ld_import.ImportThreadRunner method) (schrodinger.tasks.tasks.BaseFunctionTask method) RunMode (class in schrodinger.tasks.jobtasks) RUNNING (schrodinger.tasks.tasks.Status attribute) (schrodinger.tasks.tasks_.Status attribute) RunningJobs (class in schrodinger.job.queue) runpKa() (schrodinger.application.bioluminate.protein.PropertyCalculator method) runPrimeLoopPrediction() (schrodinger.application.bioluminate.protein.Refiner method) runPrimeMinimization() (schrodinger.application.bioluminate.protein.Refiner method) runPrimeResidue() (schrodinger.application.bioluminate.protein.Refiner method) runPrimeSidechain() (schrodinger.application.bioluminate.protein.Refiner method) runPrimeSidechainBB() (schrodinger.application.bioluminate.protein.Refiner method) runPrimeSidechainCBeta() (schrodinger.application.bioluminate.protein.Refiner method) runPythonMinimize() (schrodinger.application.bioluminate.protein.Refiner method) runRefinement() (schrodinger.application.bioluminate.protein.Refiner method) runSingleStruc() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) runsLocally() (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) runSuperposition() (schrodinger.application.matsci.rxn_path.ReactionCoords method) runTabValidation() (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) RuntimeParametersError RuntimeParametersKeyError runTransmutations() (schrodinger.application.matsci.enumeration.Alchemist method) (schrodinger.application.matsci.enumeration.StructureAlchemist method) runXCluFile() (schrodinger.application.macromodel.utils.CluUtil method) rxn_coord_precision (schrodinger.application.jaguar.results.JaguarResults attribute) RXN_REPRESENTATION_KEY (schrodinger.application.matsci.rxn_channel.rxn_channel.Products attribute) RXNCOORD (schrodinger.application.matsci.rxn_path.ReactionPath attribute) RXNINDEX (schrodinger.application.matsci.rxn_path.ReactionPath attribute)

S

s_min_eval() (in module schrodinger.application.jaguar.textparser) SA_LOWEST_BOND_STRETCH (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_LOWEST_HESSIAN (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_LOWEST_NON_TORSIONAL (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_RP_PATH (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SA_USER (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) SAction (class in schrodinger.application.bioluminate.actions.factory) SALT_BRIDGE (schrodinger.application.bioluminate.interaction_calculator.Interactions attribute) SaltBridgeFinder (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.structutils.interactions.salt_bridge) same_feature_definitions() (in module schrodinger.infra.phase) same_host() (in module schrodinger.utils.licutils) SAME_LENGTH_THRESH (schrodinger.application.matsci.nano.xtal.CheckInput attribute) SAME_STRUCTURE (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) SAME_VECTOR_THRESH (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) sameSizeAndThreshold() (schrodinger.application.bioluminate.patch_utils.settings.PatchSettings method) SAMPLE_DATA (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) SAMPLE_DEFAULT (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) sampleActives() (schrodinger.infra.phase.PhpProject method) SampleRingsStage (class in schrodinger.pipeline.stages.macromodel) sanitize() (schrodinger.protein.sequence.Sequence method) sanitize_for_viparr() (schrodinger.application.desmond.cms.Cms method) sanityCheckParentAndChildIndexes() (schrodinger.application.desmond.antlr3.tree.BaseTree method) sasa (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) Save() (in module schrodinger.application.desmond.packages.msys) save() (schrodinger.application.desmond.report_helper.NumberedCanvas method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) (schrodinger.infra.phase.PhpHypoAdaptor method) save_2d_annotated_img() (in module schrodinger.application.desmond.report_helper) save_to_disk() (in module schrodinger.application.livedesign.ld_import) saveAs() (schrodinger.application.jaguar.input.JaguarInput method) saveAsBatch() (schrodinger.application.jaguar.input.JaguarInput method) SaveCCP4File() (in module schrodinger.analysis.visanalysis.volumedataio) saveConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) saveCurrentCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) saveCurrentColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) saveCurrentCombLibDef() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) SaveDesmondFilesWidget (class in schrodinger.application.matsci.mswidgets) SaveDMS() (in module schrodinger.application.desmond.packages.msys) saveExportMap() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) saveFeatureDef() (schrodinger.infra.phase.PhpProject method) saveFeatureDefToFile() (schrodinger.infra.phase.PhpProject method) saveFeatureEquiv() (schrodinger.infra.phase.PhpProject method) saveFeatureFreq() (schrodinger.infra.phase.PhpProject method) saveFeatureRadii() (schrodinger.infra.phase.PhpProject method) saveFeatureTol() (schrodinger.infra.phase.PhpProject method) saveFind() (schrodinger.infra.phase.PhpProject method) saveIonCenterProps() (schrodinger.application.ligprep.ionizer.Ionizer method) saveLabelOptions() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) saveLocalStructs() (schrodinger.application.matsci.amorphous.PolymerToFragments method) SaveMAE() (in module schrodinger.application.desmond.packages.msys) saveMasterData() (schrodinger.infra.phase.PhpProject method) SaveMol2() (in module schrodinger.application.desmond.packages.msys) saveNewMapping() (schrodinger.application.livedesign.ld_export.ExportMapManager method) savePalette() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) SavePDB() (in module schrodinger.application.desmond.packages.msys) savePlot() (schrodinger.analysis.enrichment.Calculator method) savePropAndCms() (schrodinger.application.matsci.equilibrium_md.EquilibriumMdBase method) saveQsar() (schrodinger.infra.phase.PhpProject method) saveSettings() (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) saveSiteMasks() (schrodinger.infra.phase.PhpProject method) saveTemplate() (schrodinger.application.matsci.builderwidgets.SketcherBox method) saveTorsionConstraint() (schrodinger.application.matsci.espresso.qeinput.FreePositionsType static method) SaveVisFile() (in module schrodinger.analysis.visanalysis.volumedataio) SbcUtil (class in schrodinger.application.macromodel.utils) Scaffold (class in schrodinger.application.matsci.amorphous) ScaffoldError scalar_search_wolfe1() (schrodinger.application.matsci.mecp_mod.BFGS method) scale_vertices() (in module schrodinger.graphics3d.polyhedron) scaleActivity() (schrodinger.infra.phase.PhpProject method) Scan (class in schrodinger.application.jaguar.scan) SCAN (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin attribute) scan_collection_dir() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) scan_coordinates() (in module schrodinger.application.jaguar.textparser) scan_step (schrodinger.application.jaguar.output.JaguarOutput attribute) SCANANGLE (schrodinger.maestro.markers.Icons attribute) SCANATOM (schrodinger.maestro.markers.Icons attribute) ScanCoordinateColumns (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanCoordinateData (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanCoordinatesDelegate (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanCoordinatesModel (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanCoordinatesProxyModel (class in schrodinger.application.jaguar.gui.tabs.scan_tab) scanCount() (schrodinger.application.jaguar.input.JaguarInput method) SCANDIST (schrodinger.maestro.markers.Icons attribute) ScanTab (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanTabMarkerMixin (class in schrodinger.application.jaguar.gui.base_panel) ScanTabNextGeom (class in schrodinger.application.jaguar.gui.tabs.scan_tab) ScanTabNextGeom.NextGeomFrom (class in schrodinger.application.jaguar.gui.tabs.scan_tab) scf_FAIL (schrodinger.application.mopac.results71.MopacResults71 attribute) scf_OK (schrodinger.application.mopac.results71.MopacResults71 attribute) scfe() (in module schrodinger.application.jaguar.textparser) ScfIteration (class in schrodinger.application.jaguar.results) ScfTab (class in schrodinger.application.jaguar.gui.tabs.scf_tab) ScfTabConsistentOrbitals (class in schrodinger.application.jaguar.gui.tabs.scf_tab) ScfTabIGO (class in schrodinger.application.jaguar.gui.tabs.scf_tab) SCHEMES (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar attribute) ScholarStructureItem (class in schrodinger.application.desmond.fep_scholar_util) schrod_port() (schrodinger.application.licensing.licadmin.LicenseResource method) SchrodImageGenerator (class in schrodinger.application.desmond.image_generator) schrodinger (module) SCHRODINGER (schrodinger.application.desmond.envir.CONST attribute) schrodinger.analysis (module) schrodinger.analysis.cluster (module) schrodinger.analysis.enrichment (module) schrodinger.analysis.reaction (module) schrodinger.analysis.transformations (module) schrodinger.analysis.visanalysis (module) schrodinger.analysis.visanalysis.vdaxis (module) schrodinger.analysis.visanalysis.vdcoordinateframe (module) schrodinger.analysis.visanalysis.vdexception (module) schrodinger.analysis.visanalysis.volumedata (module) schrodinger.analysis.visanalysis.volumedataio (module) schrodinger.analysis.visanalysis.volumedatastructureutils (module) schrodinger.analysis.visanalysis.volumedatautils (module) schrodinger.application (module) schrodinger.application.aacg (module) schrodinger.application.aacg.utils (module) schrodinger.application.bindingsite (module) schrodinger.application.bindingsite.atomtyping (module) schrodinger.application.bindingsite.cavutils (module) schrodinger.application.bindingsite.common (module) schrodinger.application.bindingsite.intfield (module) schrodinger.application.bioluminate (module) schrodinger.application.bioluminate.actions (module) schrodinger.application.bioluminate.actions.configs (module) schrodinger.application.bioluminate.actions.factory (module) schrodinger.application.bioluminate.actions.icons (module) schrodinger.application.bioluminate.actions.icons_rc (module) schrodinger.application.bioluminate.antibody (module) schrodinger.application.bioluminate.antibody.search_results_table (module) schrodinger.application.bioluminate.antibody.utils (module) schrodinger.application.bioluminate.bwidgets (module) schrodinger.application.bioluminate.escomp (module) schrodinger.application.bioluminate.interaction_calculator (module) schrodinger.application.bioluminate.patch_utils (module) schrodinger.application.bioluminate.patch_utils.patch_finder (module) schrodinger.application.bioluminate.patch_utils.pre_analyze (module) schrodinger.application.bioluminate.patch_utils.settings (module) schrodinger.application.bioluminate.propfilter (module) schrodinger.application.bioluminate.propfilter_ui (module) schrodinger.application.bioluminate.propka_parse (module) schrodinger.application.bioluminate.protein (module) schrodinger.application.bioluminate.protein_protein_docking_shared (module) schrodinger.application.bioluminate.protein_report_widget (module) schrodinger.application.bioluminate.protein_structure_quality_ui (module) schrodinger.application.bioluminate.reactive_residues (module) schrodinger.application.bioluminate.run_propka (module) schrodinger.application.bioluminate.sliderchart (module) schrodinger.application.bioluminate.ssv (module) schrodinger.application.bioluminate.ssv.toolbars (module) schrodinger.application.bioluminate.ssv.viewer (module) schrodinger.application.bioluminate.surfcomp (module) schrodinger.application.bioluminate.validate_imported_modules (module) schrodinger.application.bioluminate.workspacelabeler (module) schrodinger.application.canvas (module) schrodinger.application.canvas.base (module) schrodinger.application.canvas.cluster (module) schrodinger.application.canvas.clustergui (module) schrodinger.application.canvas.driverutils (module) schrodinger.application.canvas.fingerprint (module) schrodinger.application.canvas.fingerprintgui (module) schrodinger.application.canvas.r_group (module) schrodinger.application.canvas.r_group_dee (module) schrodinger.application.canvas.similarity (module) schrodinger.application.canvas.similaritygui (module) schrodinger.application.canvas.topo_descriptors (module) schrodinger.application.canvas.utils (module) schrodinger.application.combiglide (module) schrodinger.application.combiglide.combenumdock (module) schrodinger.application.combiglide.combenumdock_dir (module) schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_cfc_ui (module) schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_collection_viewer_ui (module) schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_constraints_ui (module) schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_ui (module) schrodinger.application.combiglide.connection_storage (module) schrodinger.application.combiglide.corehop (module) schrodinger.application.combiglide.packages (module) schrodinger.application.combiglide.utils (module) schrodinger.application.desmond (module) schrodinger.application.desmond.ana (module) schrodinger.application.desmond.antlr3 (module) schrodinger.application.desmond.antlr3.compat (module) schrodinger.application.desmond.antlr3.constants (module) schrodinger.application.desmond.antlr3.debug (module) schrodinger.application.desmond.antlr3.dfa (module) schrodinger.application.desmond.antlr3.exceptions (module) schrodinger.application.desmond.antlr3.extras (module) schrodinger.application.desmond.antlr3.recognizers (module) schrodinger.application.desmond.antlr3.streams (module) schrodinger.application.desmond.antlr3.tokens (module) schrodinger.application.desmond.antlr3.tree (module) schrodinger.application.desmond.antlr3.treewizard (module) schrodinger.application.desmond.automatic_analysis_generator (module) schrodinger.application.desmond.autopartition (module) schrodinger.application.desmond.bennett (module) schrodinger.application.desmond.cmdline (module) schrodinger.application.desmond.cms (module) schrodinger.application.desmond.cns_io (module) schrodinger.application.desmond.config (module) schrodinger.application.desmond.constants (module) schrodinger.application.desmond.correlation_tau (module) schrodinger.application.desmond.cwidget (module) schrodinger.application.desmond.deltaE (module) schrodinger.application.desmond.depictor (module) schrodinger.application.desmond.desmond_advanced_tab_ui (module) schrodinger.application.desmond.enhanced_sampling (module) schrodinger.application.desmond.enhanced_sampling.FcnTypes (module) schrodinger.application.desmond.enhanced_sampling.mexpLexer (module) schrodinger.application.desmond.enhanced_sampling.mexpParser (module) schrodinger.application.desmond.enhsamp (module) schrodinger.application.desmond.envir (module) schrodinger.application.desmond.event_analysis (module) schrodinger.application.desmond.event_analysis.pl_image_tools (module) schrodinger.application.desmond.fep_constants (module) schrodinger.application.desmond.fep_edge_data (module) schrodinger.application.desmond.fep_edge_report_maker (module) schrodinger.application.desmond.fep_gui (module) schrodinger.application.desmond.fep_mapping (module) schrodinger.application.desmond.fep_net_charge (module) schrodinger.application.desmond.fep_reporter (module) schrodinger.application.desmond.fep_scholar_msj_generator (module) schrodinger.application.desmond.fep_scholar_rules (module) schrodinger.application.desmond.fep_scholar_util (module) schrodinger.application.desmond.fep_struc (module) schrodinger.application.desmond.fep_util (module) schrodinger.application.desmond.fepana (module) schrodinger.application.desmond.feputils (module) schrodinger.application.desmond.ffiostructure (module) schrodinger.application.desmond.frag_snap (module) schrodinger.application.desmond.gaussian_filter (module) schrodinger.application.desmond.gchart (module) schrodinger.application.desmond.gcmc_utils (module) schrodinger.application.desmond.gconfig (module) schrodinger.application.desmond.gui (module) schrodinger.application.desmond.icon (module) schrodinger.application.desmond.image_generator (module) schrodinger.application.desmond.input_group_ui (module) schrodinger.application.desmond.maestro (module) schrodinger.application.desmond.mapper_msj_generator (module) schrodinger.application.desmond.measurement (module) schrodinger.application.desmond.memory_estimate (module) schrodinger.application.desmond.meta (module) schrodinger.application.desmond.move_alchem_ions (module) schrodinger.application.desmond.mplchart (module) schrodinger.application.desmond.packages (module) schrodinger.application.desmond.packages.analysis (module) schrodinger.application.desmond.packages.cui (module) schrodinger.application.desmond.packages.energygroup (module) schrodinger.application.desmond.packages.enhanced_sampling (module) schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes (module) schrodinger.application.desmond.packages.gdesmond_utils (module) schrodinger.application.desmond.packages.msys (module) schrodinger.application.desmond.packages.msys.atomsel (module) schrodinger.application.desmond.packages.msys.groups (module) schrodinger.application.desmond.packages.msys.molfile (module) schrodinger.application.desmond.packages.msys.posre (module) schrodinger.application.desmond.packages.parch (module) schrodinger.application.desmond.packages.restrain (module) schrodinger.application.desmond.packages.staf (module) schrodinger.application.desmond.packages.timer (module) schrodinger.application.desmond.packages.topo (module) schrodinger.application.desmond.packages.traj (module) schrodinger.application.desmond.packages.traj_util (module) schrodinger.application.desmond.packages.viparr (module) schrodinger.application.desmond.packages.viparr1 (module) schrodinger.application.desmond.packages.viparr1.plugins (module) schrodinger.application.desmond.packages.viparr1.systest (module) schrodinger.application.desmond.packages.viparr1.systest.systest (module) schrodinger.application.desmond.packages.viparr1.viparr (module) schrodinger.application.desmond.packages.viparr1.viparr.elements (module) schrodinger.application.desmond.packages.viparr1.viparr.isomorph (module) schrodinger.application.desmond.packages.viparr1.viparr.version (module) schrodinger.application.desmond.packages.viparr1.viparr.viparr (module) schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge (module) schrodinger.application.desmond.packages.viparr1.viparr.viparr_plugins_util (module) schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue (module) schrodinger.application.desmond.packages.viparr1.viparr.viparr_util (module) schrodinger.application.desmond.picklejar (module) schrodinger.application.desmond.platforms (module) schrodinger.application.desmond.predict_remd_temp (module) schrodinger.application.desmond.process_fep_traj (module) schrodinger.application.desmond.r_group_asl (module) schrodinger.application.desmond.remd (module) schrodinger.application.desmond.reorder_atom (module) schrodinger.application.desmond.repair_cms (module) schrodinger.application.desmond.replica_dE (module) schrodinger.application.desmond.replica_exchange_review (module) schrodinger.application.desmond.replica_sid_generator (module) schrodinger.application.desmond.report_helper (module) schrodinger.application.desmond.rest_inp (module) schrodinger.application.desmond.rest_tab_ui (module) schrodinger.application.desmond.restraint (module) schrodinger.application.desmond.simulation_block_data (module) schrodinger.application.desmond.simulation_block_test (module) schrodinger.application.desmond.smarts (module) schrodinger.application.desmond.starter (module) schrodinger.application.desmond.starter.generator (module) schrodinger.application.desmond.starter.generator.fep_plus (module) schrodinger.application.desmond.starter.starter (module) schrodinger.application.desmond.starter.ui (module) schrodinger.application.desmond.starter.ui.cmdline (module) schrodinger.application.desmond.starter.ui.fep_plus (module) schrodinger.application.desmond.struc (module) schrodinger.application.desmond.system_builder_inp (module) schrodinger.application.desmond.system_builder_util (module) schrodinger.application.desmond.systype (module) schrodinger.application.desmond.title_to_hex (module) schrodinger.application.desmond.torsion_related (module) schrodinger.application.desmond.util (module) schrodinger.application.desmond.xvfbwrapper (module) schrodinger.application.epik (module) schrodinger.application.ffbuilder (module) schrodinger.application.ffbuilder.utils (module) schrodinger.application.glide (module) schrodinger.application.glide.ensemble_selection (module) schrodinger.application.glide.glide (module) schrodinger.application.glide.glideanalysis (module) schrodinger.application.glide.gui (module) schrodinger.application.glide.http_client (module) schrodinger.application.glide.http_server (module) schrodinger.application.glide.packages (module) schrodinger.application.glide.poseviewconvert (module) schrodinger.application.glide.utils (module) schrodinger.application.glide.xpdes (module) schrodinger.application.hitexpander (module) schrodinger.application.inputconfig (module) schrodinger.application.jaguar (module) schrodinger.application.jaguar.autots_bonding (module) schrodinger.application.jaguar.autots_constants (module) schrodinger.application.jaguar.autots_exceptions (module) schrodinger.application.jaguar.autots_rmsd (module) schrodinger.application.jaguar.basis (module) schrodinger.application.jaguar.check_headers (module) schrodinger.application.jaguar.chirality (module) schrodinger.application.jaguar.constants (module) schrodinger.application.jaguar.exceptions (module) schrodinger.application.jaguar.file_logger (module) schrodinger.application.jaguar.global_macros (module) schrodinger.application.jaguar.gui (module) schrodinger.application.jaguar.gui.base_panel (module) schrodinger.application.jaguar.gui.basis_selector (module) schrodinger.application.jaguar.gui.edit_dialog (module) schrodinger.application.jaguar.gui.filedialog (module) schrodinger.application.jaguar.gui.input_tab_widgets (module) schrodinger.application.jaguar.gui.input_tab_widgets_hb (module) schrodinger.application.jaguar.gui.input_tab_widgets_pka (module) schrodinger.application.jaguar.gui.tabs (module) schrodinger.application.jaguar.gui.tabs.base_tab (module) schrodinger.application.jaguar.gui.tabs.coordinates (module) schrodinger.application.jaguar.gui.tabs.input_sub_tabs (module) schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab (module) schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set (module) schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints (module) schrodinger.application.jaguar.gui.tabs.input_tab (module) schrodinger.application.jaguar.gui.tabs.irc_tab (module) schrodinger.application.jaguar.gui.tabs.molecule_tab (module) schrodinger.application.jaguar.gui.tabs.multi_structure_tab (module) schrodinger.application.jaguar.gui.tabs.optimization_tab (module) schrodinger.application.jaguar.gui.tabs.output_tab (module) schrodinger.application.jaguar.gui.tabs.properties_tab (module) schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab (module) schrodinger.application.jaguar.gui.tabs.reaction_properties_tab (module) schrodinger.application.jaguar.gui.tabs.reaction_tab (module) schrodinger.application.jaguar.gui.tabs.scan_tab (module) schrodinger.application.jaguar.gui.tabs.scf_tab (module) schrodinger.application.jaguar.gui.tabs.solvation_tab (module) schrodinger.application.jaguar.gui.tabs.sub_tab_widgets (module) schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets (module) schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets (module) schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets (module) schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector (module) schrodinger.application.jaguar.gui.tabs.theory_tab (module) schrodinger.application.jaguar.gui.tabs.transition_state_tab (module) schrodinger.application.jaguar.gui.theory_tab_widgets (module) schrodinger.application.jaguar.gui.ui (module) schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui (module) schrodinger.application.jaguar.gui.ui.edit_dialog_ui (module) schrodinger.application.jaguar.gui.ui.excited_state_widget_ui (module) schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui (module) schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui (module) schrodinger.application.jaguar.gui.ui.input_std_bottom_ui (module) schrodinger.application.jaguar.gui.ui.input_sub_tabs (module) schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui (module) schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui (module) schrodinger.application.jaguar.gui.ui.input_top_ui (module) schrodinger.application.jaguar.gui.ui.irc_bottom_ui (module) schrodinger.application.jaguar.gui.ui.irc_top_ui (module) schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui (module) schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui (module) schrodinger.application.jaguar.gui.ui.molecule_top_ui (module) schrodinger.application.jaguar.gui.ui.multi_structures_ui (module) schrodinger.application.jaguar.gui.ui.optimization_tab_ui (module) schrodinger.application.jaguar.gui.ui.output_tab_ui (module) schrodinger.application.jaguar.gui.ui.properties_tab_ui (module) schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui (module) schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui (module) schrodinger.application.jaguar.gui.ui.reaction_tab_ui (module) schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui (module) schrodinger.application.jaguar.gui.ui.scan_tab_ui (module) schrodinger.application.jaguar.gui.ui.scf_tab_ui (module) schrodinger.application.jaguar.gui.ui.solvation_gas_phase_ui (module) schrodinger.application.jaguar.gui.ui.solvation_pka_ui (module) schrodinger.application.jaguar.gui.ui.solvation_solvent_model_ui (module) schrodinger.application.jaguar.gui.ui.solvent_tab_ui (module) schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui (module) schrodinger.application.jaguar.gui.ui.theory_tab_ui (module) schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui (module) schrodinger.application.jaguar.gui.ui.transition_state_top_ui (module) schrodinger.application.jaguar.gui.utils (module) schrodinger.application.jaguar.input (module) schrodinger.application.jaguar.jaguar_diff (module) schrodinger.application.jaguar.jaguar_keyword_utils (module) schrodinger.application.jaguar.keywordDB (module) schrodinger.application.jaguar.mmjag (module) schrodinger.application.jaguar.output (module) schrodinger.application.jaguar.reactiq_input (module) schrodinger.application.jaguar.reactiq_input_constants (module) schrodinger.application.jaguar.reactiq_keywords (module) schrodinger.application.jaguar.reactiq_validation (module) schrodinger.application.jaguar.results (module) schrodinger.application.jaguar.rmsd (module) schrodinger.application.jaguar.scan (module) schrodinger.application.jaguar.structure_isomorphism (module) schrodinger.application.jaguar.textparser (module) schrodinger.application.jaguar.user_config (module) schrodinger.application.jaguar.utils (module) schrodinger.application.jaguar.validation (module) schrodinger.application.licensing (module) schrodinger.application.licensing.flexlm (module) schrodinger.application.licensing.licadmin (module) schrodinger.application.licensing.licerror (module) schrodinger.application.licensing.lmgrd_log_parser (module) schrodinger.application.licensing.netsuiteapi (module) schrodinger.application.ligprep (module) schrodinger.application.ligprep.ionizer (module) schrodinger.application.livedesign (module) schrodinger.application.livedesign.data_classes (module) schrodinger.application.livedesign.export_controller (module) schrodinger.application.livedesign.export_setup_ui (module) schrodinger.application.livedesign.export_ui (module) schrodinger.application.livedesign.icons_rc (module) schrodinger.application.livedesign.import_controller (module) schrodinger.application.livedesign.ld_base_classes (module) schrodinger.application.livedesign.ld_export (module) schrodinger.application.livedesign.ld_folder_tree (module) schrodinger.application.livedesign.ld_import (module) schrodinger.application.livedesign.ld_utils (module) schrodinger.application.livedesign.login (module) schrodinger.application.livedesign.login_ui (module) schrodinger.application.livedesign.maestro_data_types (module) schrodinger.application.livedesign.panel_components (module) schrodinger.application.livedesign.upload_utils (module) schrodinger.application.macromodel (module) schrodinger.application.macromodel.apps (module) schrodinger.application.macromodel.input (module) schrodinger.application.macromodel.packages (module) schrodinger.application.macromodel.paraUtils (module) schrodinger.application.macromodel.tools (module) schrodinger.application.macromodel.utils (module) schrodinger.application.matsci (module) schrodinger.application.matsci.amorphous (module) schrodinger.application.matsci.atomicsymbols (module) schrodinger.application.matsci.atomicsymbolsgui (module) schrodinger.application.matsci.bandshape_utils (module) schrodinger.application.matsci.basiselements (module) schrodinger.application.matsci.buildcomplex (module) schrodinger.application.matsci.builderwidgets (module) schrodinger.application.matsci.cgforcefield (module) schrodinger.application.matsci.cgforcefieldgui (module) schrodinger.application.matsci.chargegui (module) schrodinger.application.matsci.clusterstruct (module) schrodinger.application.matsci.clusterstructgui (module) schrodinger.application.matsci.coarsegrain (module) schrodinger.application.matsci.controlicons_rc (module) schrodinger.application.matsci.desmondutils (module) schrodinger.application.matsci.elementalprops (module) schrodinger.application.matsci.enumeration (module) schrodinger.application.matsci.equilibrium_md (module) schrodinger.application.matsci.espresso (module) schrodinger.application.matsci.espresso.ppdb (module) schrodinger.application.matsci.espresso.qeinput (module) schrodinger.application.matsci.espresso.qeoutput (module) schrodinger.application.matsci.espresso.utils (module) schrodinger.application.matsci.freevolume (module) schrodinger.application.matsci.genetic_optimization (module) schrodinger.application.matsci.genetic_optimization.genetic_optimization (module) schrodinger.application.matsci.guibase (module) schrodinger.application.matsci.jaguar_multistage_workflow_utils (module) schrodinger.application.matsci.jaguarworkflows (module) schrodinger.application.matsci.jobdirdlg (module) schrodinger.application.matsci.jobutils (module) schrodinger.application.matsci.mecp_mod (module) schrodinger.application.matsci.mlearn (module) schrodinger.application.matsci.mlearn.base (module) schrodinger.application.matsci.mlearn.features (module) schrodinger.application.matsci.montecarlo (module) schrodinger.application.matsci.msutils (module) schrodinger.application.matsci.mswidgets (module) schrodinger.application.matsci.nano (module) schrodinger.application.matsci.nano.check (module) schrodinger.application.matsci.nano.constants (module) schrodinger.application.matsci.nano.interface_mod (module) schrodinger.application.matsci.nano.particle (module) schrodinger.application.matsci.nano.plane (module) schrodinger.application.matsci.nano.sheet (module) schrodinger.application.matsci.nano.slab (module) schrodinger.application.matsci.nano.surfaces_interfaces_mod (module) schrodinger.application.matsci.nano.tube (module) schrodinger.application.matsci.nano.util (module) schrodinger.application.matsci.nano.xtal (module) schrodinger.application.matsci.optoelectronics (module) schrodinger.application.matsci.order_parameter_mod (module) schrodinger.application.matsci.parserutils (module) schrodinger.application.matsci.property_names (module) schrodinger.application.matsci.qexsd (module) schrodinger.application.matsci.qexsd.qespresso (module) schrodinger.application.matsci.qexsd.qespresso.cards (module) schrodinger.application.matsci.qexsd.qespresso.converters (module) schrodinger.application.matsci.qexsd.qespresso.documents (module) schrodinger.application.matsci.qexsd.qespresso.exceptions (module) schrodinger.application.matsci.qexsd.qespresso.options (module) schrodinger.application.matsci.qexsd.qespresso.utils (module) schrodinger.application.matsci.qexsd.qespresso.utils.logger (module) schrodinger.application.matsci.qexsd.qespresso.utils.mapping (module) schrodinger.application.matsci.qexsd.qespresso.utils.xml2nebinput (module) schrodinger.application.matsci.qexsd.qespresso.utils.xml2qeinput (module) schrodinger.application.matsci.qexsd.qespresso.xsdtypes (module) schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree (module) schrodinger.application.matsci.qexsd.qespresso.xsdtypes.exceptions (module) schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument (module) schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema (module) schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes (module) schrodinger.application.matsci.qexsd.utils (module) schrodinger.application.matsci.qualityslider (module) schrodinger.application.matsci.reaction_workflow_utils (module) schrodinger.application.matsci.reorder (module) schrodinger.application.matsci.reordergui (module) schrodinger.application.matsci.rxn_channel (module) schrodinger.application.matsci.rxn_channel.rxn_channel (module) schrodinger.application.matsci.rxn_path (module) schrodinger.application.matsci.shapes (module) schrodinger.application.matsci.siteselector (module) schrodinger.application.matsci.siteselector.siteselector (module) schrodinger.application.matsci.sliceplot (module) schrodinger.application.matsci.smartsutils (module) schrodinger.application.matsci.smartsutilsgui (module) schrodinger.application.matsci.spectra (module) schrodinger.application.matsci.swap_fragments_utils (module) schrodinger.application.matsci.textlogger (module) schrodinger.application.matsci.zmutils (module) schrodinger.application.medchem (module) schrodinger.application.medchem.property (module) schrodinger.application.mopac (module) schrodinger.application.mopac.exceptions (module) schrodinger.application.mopac.mopac_backend (module) schrodinger.application.mopac.mopac_launchers (module) schrodinger.application.mopac.mopac_parser (module) schrodinger.application.mopac.mopac_results (module) schrodinger.application.mopac.mopac_startup (module) schrodinger.application.mopac.results2012 (module) schrodinger.application.mopac.results71 (module) schrodinger.application.mopac.structure_launchers (module) schrodinger.application.mopac.utils (module) schrodinger.application.phase (module) schrodinger.application.phase.constants (module) schrodinger.application.phase.create_xvol (module) schrodinger.application.phase.featureselector (module) schrodinger.application.phase.hypothesis (module) schrodinger.application.phase.hypothesis_binding_modes (module) schrodinger.application.phase.input (module) schrodinger.application.phase.packages (module) schrodinger.application.phase.phase_markers (module) schrodinger.application.phase.phase_widgets (module) schrodinger.application.phase.pt_hypothesis (module) schrodinger.application.pldb (module) schrodinger.application.pldb.packages (module) schrodinger.application.prepwizard (module) schrodinger.application.prime (module) schrodinger.application.prime.gui (module) schrodinger.application.prime.gui.analyze_energy (module) schrodinger.application.prime.gui.ui (module) schrodinger.application.prime.gui.ui.analyze_energy_ui (module) schrodinger.application.prime.gui.ui.environment_options_ui (module) schrodinger.application.prime.input (module) schrodinger.application.prime.primefix (module) schrodinger.application.prime.residue_interaction (module) schrodinger.application.qsite (module) schrodinger.application.qsite.input (module) schrodinger.application.qsite.output (module) schrodinger.application.report2d (module) schrodinger.application.ska (module) schrodinger.application.utils (module) schrodinger.application.vsw (module) schrodinger.application.vsw.input (module) schrodinger.application.vsw.pipeutils (module) schrodinger.application.vsw.stages (module) schrodinger.application.vsw.stages.combine (module) schrodinger.application.vsw.stages.convert (module) schrodinger.application.vsw.stages.filtering (module) schrodinger.application.vsw.stages.gencodes (module) schrodinger.application.vsw.stages.glide (module) schrodinger.application.vsw.stages.macromodel (module) schrodinger.application.vsw.stages.phase (module) schrodinger.application.vsw.stages.prime (module) schrodinger.application.vsw.stages.pull (module) schrodinger.application.vsw.stages.qikprop (module) schrodinger.application.vsw.stages.qsite (module) schrodinger.application.vsw.stages.rmsd (module) schrodinger.application.vsw.stages.semiemp (module) schrodinger.application.vsw.vswinput (module) schrodinger.application.watermap (module) schrodinger.application.watermap.utils (module) schrodinger.application.watermap.watermap_inp (module) schrodinger.application.watermap.watermap_scoring (module) schrodinger.graphics3d (module) schrodinger.graphics3d.arrow (module) schrodinger.graphics3d.box (module) schrodinger.graphics3d.common (module) schrodinger.graphics3d.gridbox (module) schrodinger.graphics3d.lines (module) schrodinger.graphics3d.polygon (module) schrodinger.graphics3d.polyhedron (module) schrodinger.graphics3d.quadrilateral (module) schrodinger.graphics3d.sphere (module) schrodinger.graphics3d.torus (module) schrodinger.infra (module) schrodinger.infra.epydoc_to_sphinx (module) schrodinger.infra.exception_handler (module) schrodinger.infra.exception_handler_dir (module) schrodinger.infra.exception_handler_dir.exception_dialog (module) schrodinger.infra.exception_handler_dir.exception_dialog_ui (module) schrodinger.infra.fast3d (module) schrodinger.infra.licensing (module) schrodinger.infra.mm (module) schrodinger.infra.mmbitset (module) schrodinger.infra.mmcheck (module) schrodinger.infra.mmerr (module) schrodinger.infra.mmgpgpu (module) schrodinger.infra.mmim (module) schrodinger.infra.mminit (module) schrodinger.infra.mmjob (module) schrodinger.infra.mmkv (module) schrodinger.infra.mmlist (module) schrodinger.infra.mmobject (module) schrodinger.infra.mmproj (module) schrodinger.infra.mmreflect (module) schrodinger.infra.mmsurf (module) schrodinger.infra.phase (module) schrodinger.infra.propedit (module) schrodinger.infra.structure (module) schrodinger.infra.table (module) schrodinger.infra.util (module) schrodinger.job (module) schrodinger.job.app (module) schrodinger.job.host_check (module) schrodinger.job.hunt_stub (module) schrodinger.job.jobcontrol (module) schrodinger.job.launchapi (module) schrodinger.job.launcher (module) schrodinger.job.launchparams (module) schrodinger.job.queue (module) schrodinger.job.remote_command (module) schrodinger.job.util (module) schrodinger.maestro (module) schrodinger.maestro.commands (module) schrodinger.maestro.maestro (module) schrodinger.maestro.markers (module) schrodinger.models (module) schrodinger.models.json (module) schrodinger.models.mappers (module) schrodinger.models.parameters (module) schrodinger.pipeline (module) schrodinger.pipeline.input (module) schrodinger.pipeline.pipeio (module) schrodinger.pipeline.pipeline (module) schrodinger.pipeline.pipeutils (module) schrodinger.pipeline.stage (module) schrodinger.pipeline.stages (module) schrodinger.pipeline.stages.canvas (module) schrodinger.pipeline.stages.combine (module) schrodinger.pipeline.stages.convert (module) schrodinger.pipeline.stages.example (module) schrodinger.pipeline.stages.filtering (module) schrodinger.pipeline.stages.gencodes (module) schrodinger.pipeline.stages.glide (module) schrodinger.pipeline.stages.ligprep (module) schrodinger.pipeline.stages.macromodel (module) schrodinger.pipeline.stages.phase (module) schrodinger.pipeline.stages.prime (module) schrodinger.pipeline.stages.pull (module) schrodinger.pipeline.stages.qikprop (module) schrodinger.pipeline.stages.qsite (module) schrodinger.pipeline.stages.rmsd (module) schrodinger.pipeline.stages.semiemp (module) schrodinger.project (module) schrodinger.project_surface (module) schrodinger.protein (module) schrodinger.protein.align (module) schrodinger.protein.alignment (module) schrodinger.protein.analysis (module) schrodinger.protein.analysis_params (module) schrodinger.protein.annotation (module) schrodinger.protein.assignment (module) schrodinger.protein.captermini (module) schrodinger.protein.constants (module) schrodinger.protein.findhets (module) schrodinger.protein.getpdb (module) schrodinger.protein.getpdb_utility (module) schrodinger.protein.helix (module) schrodinger.protein.membrane (module) schrodinger.protein.pdbname (module) schrodinger.protein.reliability (module) schrodinger.protein.remediate (module) schrodinger.protein.residue (module) schrodinger.protein.rotamers (module) schrodinger.protein.sequence (module) schrodinger.Qt (module) schrodinger.Qt.PyQt5 (module) schrodinger.Qt.PyQt5.QtCore (module) schrodinger.Qt.PyQt5.QtGui (module) schrodinger.Qt.PyQt5.QtNetwork (module) schrodinger.Qt.PyQt5.QtOpenGL (module) schrodinger.Qt.PyQt5.QtPrintSupport (module) schrodinger.Qt.PyQt5.QtSvg (module) schrodinger.Qt.PyQt5.QtTest (module) schrodinger.Qt.PyQt5.QtWidgets (module) schrodinger.structure (module) schrodinger.structutils (module) schrodinger.structutils.analyze (module) schrodinger.structutils.assignbondorders (module) schrodinger.structutils.build (module) schrodinger.structutils.color (module) schrodinger.structutils.createfragments (module) schrodinger.structutils.filter (module) schrodinger.structutils.interactionfp (module) schrodinger.structutils.interactions (module) schrodinger.structutils.interactions.hbond (module) schrodinger.structutils.interactions.pi (module) schrodinger.structutils.interactions.salt_bridge (module) schrodinger.structutils.interactions.ssbond (module) schrodinger.structutils.interactions.steric_clash (module) schrodinger.structutils.io (module) schrodinger.structutils.measure (module) schrodinger.structutils.minimize (module) schrodinger.structutils.pbc_tools (module) schrodinger.structutils.rgroup_enumerate (module) schrodinger.structutils.ringspear (module) schrodinger.structutils.rmsd (module) schrodinger.structutils.shuffle (module) schrodinger.structutils.sitealign (module) schrodinger.structutils.smiles (module) schrodinger.structutils.smilesfilter (module) schrodinger.structutils.sort (module) schrodinger.structutils.structalign (module) schrodinger.structutils.transform (module) schrodinger.surface (module) schrodinger.tasks (module) schrodinger.tasks.jobtasks (module) schrodinger.tasks.runners (module) schrodinger.tasks.tasks (module) schrodinger.tasks.tasks_ (module) schrodinger.thirdparty (module) schrodinger.thirdparty.rdkit_adapter (module) schrodinger.trajectory (module) schrodinger.trajectory.pbc_manager (module) schrodinger.trajectory.prody (module) schrodinger.trajectory.prody.crosscorrelation (module) schrodinger.trajectory.prody.ensemble (module) schrodinger.trajectory.prody.mode (module) schrodinger.trajectory.prody.modeset (module) schrodinger.trajectory.prody.nma (module) schrodinger.trajectory.prody.pca (module) schrodinger.trajectory.prody.test_arrow (module) schrodinger.trajectory.prody.writenmd (module) schrodinger.ui (module) schrodinger.ui.chooseligand (module) schrodinger.ui.ligfilter (module) schrodinger.ui.ligfilter_definition_dialog_ui (module) schrodinger.ui.ligfilter_ui (module) schrodinger.ui.picking (module) schrodinger.ui.picking_dir (module) schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui (module) schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui (module) schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui (module) schrodinger.ui.residueselector (module) schrodinger.utils (module) schrodinger.utils.cgxutils (module) schrodinger.utils.cmdline (module) schrodinger.utils.colorscheme (module) schrodinger.utils.config (module) schrodinger.utils.csv_unicode (module) schrodinger.utils.documentation (module) schrodinger.utils.env (module) schrodinger.utils.fileutils (module) schrodinger.utils.imputils (module) schrodinger.utils.installation_check (module) schrodinger.utils.license (module) schrodinger.utils.licutils (module) schrodinger.utils.ligfilter (module) schrodinger.utils.log (module) schrodinger.utils.maestro_scripts_path (module) schrodinger.utils.mmutil (module) schrodinger.utils.moduleproxy (module) schrodinger.utils.multifpfile (module) schrodinger.utils.pandasutils (module) schrodinger.utils.preferences (module) schrodinger.utils.profiling (module) schrodinger.utils.pymol (module) schrodinger.utils.scollections (module) schrodinger.utils.sea (module) schrodinger.utils.sshconfig (module) schrodinger.utils.subproc (module) schrodinger.utils.subprocess (module) schrodinger.utils.sysinfo (module) schrodinger.utils.units (module) SCHRODINGER_UTILITIES (schrodinger.application.desmond.envir.CONST attribute) SchrodStruc (class in schrodinger.application.desmond.fep_struc) scisol_enabled() (in module schrodinger.application.desmond.fep_gui) SCISSORS (schrodinger.maestro.markers.Icons attribute) score_combination() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_donor_acceptor() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_donor_donor() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_exhaustively() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_ligand() (in module schrodinger.application.watermap.watermap_scoring) score_mapping() (schrodinger.application.jaguar.structure_isomorphism.AutoTSAtomMapper method) (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) score_pair() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) score_sequentially() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) screen() (schrodinger.infra.phase.PhpScreener method) SCREEN_PARAM_KEY (schrodinger.application.matsci.espresso.qeinput.HybridType attribute) script_dir() (in module schrodinger.application.jaguar) scrollToItemWithPath() (schrodinger.application.livedesign.panel_components.LDSelectionTreeView method) SDReader (class in schrodinger.structure) SDWriter (class in schrodinger.structure) se_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) se_tot_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) Sea (class in schrodinger.utils.sea) sea_filter() (in module schrodinger.utils.sea) search() (schrodinger.structutils.analyze.AslLigandSearcher method) SEARCH_ALONG_VALUES (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) search_antibody() (in module schrodinger.application.bioluminate.antibody.utils) search_for_free_display() (schrodinger.application.desmond.xvfbwrapper.Xvfb method) SEARCH_LST (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) SEARCH_QST (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) SEARCH_STANDARD (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) searchAlongChanged() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) SearchForDataPointsWithin() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) SearchForDataPointsWithinL() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) searchMethodChanged() (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) searchTextChanged() (schrodinger.application.livedesign.panel_components.BaseSearchTreeWidgetHelper method) second (schrodinger.application.desmond.packages.msys.Bond attribute) (schrodinger.infra.mmgpgpu.SwigIntIntPair attribute) (schrodinger.infra.mmjob.SwigIntIntPair attribute) (schrodinger.infra.mmsurf.SwigIntIntPair attribute) (schrodinger.utils.colorscheme.SwigIntIntPair attribute) SECOND_SEP (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition attribute) SECONDARY_SORT_COLUMNS (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel attribute) secondary_structure (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.structure._Residue attribute) (schrodinger.structure._StructureAtom attribute) secondary_structures (schrodinger.protein.sequence.ProteinSequence attribute) SecondaryStructure (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.protein.sequence) sectionDefined() (schrodinger.application.jaguar.input.JaguarInput method) SEED (schrodinger.application.matsci.desmondutils.MSJStringer attribute) seek() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.structure.MaestroReader method) segid (schrodinger.application.desmond.packages.msys.Chain attribute) select() (schrodinger.application.desmond.packages.msys.System method) (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) select_atom() (schrodinger.application.desmond.cms.Cms method) select_atom_comp() (schrodinger.application.desmond.cms.Cms method) select_surf_asl() (in module schrodinger.utils.pymol) SELECT_TEXT (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) selectAddRows() (schrodinger.infra.table.Table method) selectAll() (schrodinger.ui.residueselector.MutationSelectorFrame method) selectArr() (schrodinger.application.desmond.packages.msys.System method) selectAtom() (schrodinger.application.desmond.packages.msys.Residue method) (schrodinger.application.matsci.reordergui.ComparisonFrame method) (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.application.matsci.reordergui.StructurePic method) selectAtomGroupAsl() (schrodinger.application.desmond.gui.AtomGroupFrame method) selectChain() (schrodinger.application.desmond.packages.msys.System method) selectCt() (schrodinger.application.desmond.packages.msys.System method) selected (schrodinger.application.jaguar.gui.input_tab_widgets.UseFrom attribute) (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite attribute) SELECTED (schrodinger.utils.pandasutils.WhichRows attribute) selected_atoms_get() (in module schrodinger.maestro.maestro) selected_atoms_get_asl() (in module schrodinger.maestro.maestro) selected_atoms_get_smarts() (in module schrodinger.maestro.maestro) SELECTED_COLOR (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) selected_rows (schrodinger.project.EntryGroup attribute) (schrodinger.project.Project attribute) selected_sequences (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) selectedFeaturesCount() (schrodinger.application.phase.featureselector.FeatureModel method) selectedIndex() (schrodinger.application.matsci.reordergui.ReferenceFrame method) selectedOption() (schrodinger.application.jaguar.gui.filedialog.FileDialogWithExtraCombo method) selectFirstAllowedPropertyRow() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) selectIds() (schrodinger.application.desmond.packages.msys.System method) SelectingFilteredListWidget (class in schrodinger.application.bioluminate.propfilter) selectionChanged (schrodinger.application.phase.featureselector.FeatureSelector attribute) selectionChanged() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) (schrodinger.application.livedesign.panel_components.LDSelectionTreeView method) selectionChangedCallback() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) selectionCommand() (schrodinger.application.jaguar.gui.utils.ProjTableLikeView method) selectNewAssay() (schrodinger.application.livedesign.panel_components.AssaySelectionPopup method) selectOnly() (schrodinger.project.ProjectRow method) selectOnlyByEntry() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) selectOnlyBySeqs() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) SELECTORS (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog attribute) selectPattern() (schrodinger.ui.ligfilter.LigfilterFrame method) selectPlaceholderItem() (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) selectPosResAsl() (schrodinger.application.desmond.gui.RestraintsTab method) selectPredefined() (schrodinger.ui.ligfilter.LigfilterFrame method) selectProperty() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) selectRefAtom() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) selectResidue() (schrodinger.application.desmond.packages.msys.Chain method) selectResidueCheckbox() (schrodinger.ui.residueselector.MutationSelectorFrame method) selectRows() (schrodinger.infra.table.Table method) (schrodinger.project.Project method) semanticPredicate() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) SemiEmpStage (class in schrodinger.pipeline.stages.semiemp) send_maestro_settings() (in module schrodinger.utils.pymol) sendemail() (in module schrodinger.maestro.maestro) sendHostsToUse() (schrodinger.pipeline.pipeline.StageJob method) sendMessage() (schrodinger.job.jobcontrol.Job method) sendVersionCheck() (schrodinger.utils.pymol.PymolInstance method) separate_complex() (in module schrodinger.application.livedesign.ld_utils) seq (in module schrodinger.application.desmond.packages.msys.molfile) seq_align_match() (in module schrodinger.structutils.analyze) seq_annotations (schrodinger.protein.alignment.BaseAlignment attribute) (schrodinger.protein.alignment.ProteinAlignment attribute) SeqFile (class in schrodinger.application.desmond.packages.msys.molfile) SeqFile.Reader (class in schrodinger.application.desmond.packages.msys.molfile) SeqFormat (class in schrodinger.utils.fileutils) Sequence (class in schrodinger.protein.sequence) sequence (schrodinger.protein.annotation.SequenceAnnotations attribute) Sequence.ORIGIN (class in schrodinger.protein.sequence) sequence_logo (schrodinger.protein.annotation.ProteinAlignmentAnnotations attribute) (schrodinger.protein.annotation.ProteinAlignmentAnnotations.ANNOTATION_TYPES attribute) SequenceAnnotations (class in schrodinger.protein.annotation) sequenceContextCallback() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) sequenceCopied (schrodinger.protein.sequence.Sequence attribute) SequenceDockWidget (class in schrodinger.application.bioluminate.ssv.viewer) SequenceElement (class in schrodinger.protein.residue) SequenceFileDialog (class in schrodinger.application.bioluminate.bwidgets) sequenceNameChanged (schrodinger.protein.alignment.AlignmentSignals attribute) sequenceResiduesChanged (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesAboutToBeInserted (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesAboutToBeRemoved (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesAboutToBeReordered (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesImported (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) sequencesInserted (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesRemoved (schrodinger.protein.alignment.AlignmentSignals attribute) sequencesReordered (schrodinger.protein.alignment.AlignmentSignals attribute) sequenceStructureChanged (schrodinger.protein.alignment.AlignmentSignals attribute) sequenceVisibilityChanged (schrodinger.protein.alignment.AlignmentSignals attribute) serial_split() (in module schrodinger.application.macromodel.tools) SerializationError serialize() (schrodinger.application.desmond.picklejar.PickleJar static method) serialize_conformations() (in module schrodinger.utils.cgxutils) SerializeMAE() (in module schrodinger.application.desmond.packages.msys) serializeNode() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) serializeToken() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) Series (class in schrodinger.application.desmond.enhsamp) series() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) Server (class in schrodinger.application.licensing.flexlm) server_host() (schrodinger.application.licensing.flexlm.License method) server_host_and_port() (schrodinger.application.licensing.licadmin.LicenseResource method) server_hostid() (schrodinger.application.licensing.licadmin.LicenseResource method) server_hostids() (schrodinger.application.licensing.licadmin.LicenseResource method) server_hostnames() (schrodinger.application.licensing.licadmin.LicenseResource method) server_hostport() (schrodinger.application.licensing.flexlm.License method) server_log() (in module schrodinger.application.licensing.licadmin) server_pathname() (schrodinger.application.licensing.licadmin.LicenseResource method) server_version() (schrodinger.application.licensing.licadmin.LicenseResource method) ServerInfo (class in schrodinger.application.licensing.licadmin) set() (schrodinger.application.matsci.builderwidgets.StructureLabel method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.utils.colorscheme.MM_Color method) (schrodinger.utils.colorscheme.MM_Colormap method) (schrodinger.utils.preferences.Preferences method) set_active_databases() (in module schrodinger.application.bioluminate.antibody.utils) set_all_databases() (in module schrodinger.application.bioluminate.antibody.utils) set_angle_potential_type() (in module schrodinger.application.matsci.coarsegrain) set_antibody_scheme() (in module schrodinger.application.bioluminate.antibody.utils) set_as_coarse_grain() (in module schrodinger.application.matsci.coarsegrain) set_atom_coarse_grain_properties() (in module schrodinger.application.matsci.coarsegrain) set_atom_group() (schrodinger.application.desmond.cms.Cms method) set_atom_group_from_asl() (schrodinger.application.desmond.cms.Cms method) set_atom_reference_coordinates() (in module schrodinger.application.desmond.struc) set_atom_type() (schrodinger.application.jaguar.structure_isomorphism.AutoTSAtomMapper method) (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) set_boolean_flag() (in module schrodinger.application.matsci.qexsd.qespresso.options) set_box_buffer_width() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator static method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) set_color() (schrodinger.application.desmond.torsion_related.TorsionPotential method) set_colors() (in module schrodinger.maestro.maestro) set_coords() (in module schrodinger.maestro.maestro) set_coords1() (in module schrodinger.maestro.maestro) set_coords2() (in module schrodinger.maestro.maestro) set_coul_correction() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) set_count() (schrodinger.application.mopac.results71.MopacResults71 method) set_ct_reference_coordinates() (in module schrodinger.application.desmond.struc) set_current_application_panel_callback() (in module schrodinger.maestro.maestro) set_default_template_file() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) set_deletable() (schrodinger.application.desmond.maestro.NewEntry method) set_docking_configuration() (in module schrodinger.maestro.maestro) set_e_and_g() (in module schrodinger.application.matsci.mecp_mod) set_encoded_restraints() (in module schrodinger.application.desmond.restraint) set_entry_id() (in module schrodinger.maestro.maestro) set_entry_property() (in module schrodinger.application.phase.phase_markers) set_exception_handler() (in module schrodinger.infra.exception_handler) set_excluded_volume_visible() (in module schrodinger.application.phase.phase_markers) set_expires() (schrodinger.application.licensing.licadmin.LicenseFeature method) set_feature_tolerance_visible() (in module schrodinger.application.phase.phase_markers) set_ff() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) set_file_logger() (in module schrodinger.application.licensing.flexlm) set_final_structure() (schrodinger.application.mopac.mopac_results.MopacResults method) (schrodinger.application.mopac.results2012.MopacResults2012 method) (schrodinger.application.mopac.results71.MopacResults71 method) set_freestyle_site_type() (in module schrodinger.application.phase.phase_markers) set_freezing_atommass() (in module schrodinger.application.desmond.remd) set_from_atom() (schrodinger.application.canvas.r_group.TempAtom method) set_globalMax() (schrodinger.application.desmond.replica_dE.replica_container method) set_globalMin() (schrodinger.application.desmond.replica_dE.replica_container method) set_globals() (in module schrodinger.infra.mm) set_glow_color() (in module schrodinger.maestro.maestro) set_group() (in module schrodinger.application.livedesign.ld_import) set_hostid() (schrodinger.application.licensing.licadmin.LicenseFeature method) set_hotregion() (in module schrodinger.application.desmond.r_group_asl) set_ibrav_to_zero() (in module schrodinger.application.matsci.qexsd.qespresso.options) set_id() (schrodinger.application.desmond.fep_struc.Struc method) set_is_glowing() (in module schrodinger.maestro.maestro) set_lambda_hopping() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) set_lambda_windows() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) set_lattice_properties() (in module schrodinger.application.matsci.nano.xtal) set_lda_plus_u_flag() (in module schrodinger.application.matsci.qexsd.qespresso.options) set_ligand_from() (schrodinger.application.desmond.torsion_related.TorsionPotential method) set_ligand_to() (schrodinger.application.desmond.torsion_related.TorsionPotential method) set_logger() (in module schrodinger.application.licensing.flexlm) (in module schrodinger.application.matsci.qexsd.qespresso.utils.logger) set_mag_hubbu() (in module schrodinger.application.matsci.espresso.utils) set_marker_properties() (in module schrodinger.application.matsci.builderwidgets) set_match_atom() (schrodinger.application.desmond.fep_scholar_util.FEPScholarMapper method) set_material() (in module schrodinger.maestro.maestro) set_method() (schrodinger.application.mopac.mopac_results.MopacResults method) (schrodinger.application.mopac.results2012.MopacResults2012 method) (schrodinger.application.mopac.results71.MopacResults71 method) set_nactive_gids() (schrodinger.application.desmond.cms.Cms method) set_neighbor_atoms_basis_set() (in module schrodinger.application.matsci.clusterstruct) set_net_charge_box() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) set_nonbond_potential_type() (in module schrodinger.application.matsci.coarsegrain) set_nresamples() (schrodinger.application.desmond.bennett.CalcBAR method) set_obj_param_value() (in module schrodinger.models.parameters) set_option() (in module schrodinger.application.matsci.jobutils) set_original_index_property() (in module schrodinger.application.desmond.packages.topo) set_output() (schrodinger.application.desmond.bennett.CalcBAR method) set_output_file() (schrodinger.application.mopac.mopac_results.MopacResults method) (schrodinger.application.mopac.results2012.MopacResults2012 method) (schrodinger.application.mopac.results71.MopacResults71 method) set_parameter() (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method) set_parent() (schrodinger.utils.sea.Sea method) set_path() (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter method) set_pbc_properties() (in module schrodinger.application.matsci.nano.xtal) set_physical_properties() (in module schrodinger.application.matsci.nano.xtal) set_pick_category() (in module schrodinger.maestro.maestro) set_pick_id() (in module schrodinger.maestro.maestro) set_pka_marker (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesViewPka attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) set_pmode() (schrodinger.utils.sea.Sea method) set_polyhedron_style() (in module schrodinger.maestro.maestro) set_project_command() (in module schrodinger.maestro.maestro) set_prompt_mode_for_next_export() (in module schrodinger.maestro.maestro) set_prop_list() (schrodinger.application.canvas.r_group.Data method) set_properties_and_write_structure() (in module schrodinger.application.matsci.mecp_mod) set_property_labels_visible() (in module schrodinger.application.phase.phase_markers) set_radius() (in module schrodinger.maestro.maestro) set_rbpotential() (schrodinger.application.desmond.torsion_related.TorsionPotential method) set_readonly() (schrodinger.application.desmond.maestro.NewEntry method) set_reference_ligand_visible() (in module schrodinger.application.phase.phase_markers) set_relative_restrain_scaling() (in module schrodinger.application.desmond.gconfig) set_representation() (in module schrodinger.application.matsci.nano.particle) set_representation_bond() (in module schrodinger.application.matsci.nano.xtal) set_restrain() (schrodinger.application.desmond.cms.Cms method) set_return_code() (schrodinger.application.mopac.results71.MopacResults71 method) set_rightclick_on_pick_category() (in module schrodinger.maestro.maestro) set_seed() (schrodinger.application.desmond.bennett.CalcBAR method) set_server_refresh() (in module schrodinger.application.licensing.licadmin) set_sh_file_flags() (in module schrodinger.tasks.jobtasks) set_solute_structure() (schrodinger.trajectory.prody.ensemble.Ensemble method) set_solvate() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) set_sort_index() (schrodinger.application.licensing.flexlm.Feature method) set_source_path() (in module schrodinger.application.matsci.jobutils) set_starts() (schrodinger.application.licensing.licadmin.LicenseFeature method) set_status() (schrodinger.application.mopac.results2012.MopacResults2012 method) set_structure_file() (in module schrodinger.application.jaguar.file_logger) set_subjob_msj() (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.VacuumMsjGenerator method) set_title() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) set_title_to_stoichiometry() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) set_tokens() (schrodinger.application.licensing.licadmin.LicenseFeature method) set_tree_index() (in module schrodinger.application.desmond.reorder_atom) set_up_logger() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) set_user_states() (schrodinger.protein.assignment.ProtAssign method) set_val() (schrodinger.application.desmond.simulation_block_test.Test method) set_value() (schrodinger.utils.sea.Map method) set_what_td_calculation() (in module schrodinger.application.matsci.qexsd.qespresso.options) set_workspace_bounding_box() (in module schrodinger.maestro.maestro) set_zob_to_sob() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) setAcceptableContraintEids() (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) setActions() (schrodinger.application.bioluminate.actions.factory.Factory method) setActive() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) setActiveCoord() (schrodinger.application.jaguar.input.JaguarInput method) setActivity() (schrodinger.infra.phase.PhpProject method) setActivityMissing() (schrodinger.infra.phase.PhpProject method) setAddAlchemicalIons() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setADProjectedPointsChecked() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) setAlignCutoff() (schrodinger.infra.phase.PhpMatchOptions method) setAlignPenalty() (schrodinger.infra.phase.PhpMatchOptions method) setAlignWeight() (schrodinger.infra.phase.PhpMatchOptions method) setAllAssayData() (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) setAllData() (schrodinger.ui.ligfilter.CriteriaListModel method) setAllExcludes() (schrodinger.infra.phase.PhpFeatureDefinition method) setAllIncludes() (schrodinger.infra.phase.PhpFeatureDefinition method) setAllLocks() (schrodinger.protein.alignment.BaseAlignment method) setAllowedPrograms() (schrodinger.application.matsci.jobdirdlg.NewJobDirDialog method) (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) setAllPairs() (schrodinger.application.matsci.coarsegrain.Internals method) setAllTransBackbone() (schrodinger.application.matsci.amorphous.Monomer method) setAlpha() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) setAmideSamplingMethod() (schrodinger.infra.phase.PhpMMconfAdaptor method) setAngleNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setAngles() (schrodinger.application.matsci.coarsegrain.Internals method) setAntibodyNumberingToolBarVisible() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) setAppendConfs() (schrodinger.infra.phase.PhpConfOptions method) setAppendLogs() (schrodinger.job.launcher.Launcher method) setArea() (schrodinger.application.matsci.shapes.Face method) setAsFragment() (schrodinger.application.matsci.amorphous.BaseMoiety method) (schrodinger.application.matsci.amorphous.Cascader method) (schrodinger.application.matsci.amorphous.Monomer method) setAsl() (schrodinger.maestro.markers.Marker method) setASL() (schrodinger.utils.colorscheme.MM_CSchemeRule method) setAsuAtomsFalse() (schrodinger.application.matsci.nano.xtal.Crystal method) setAsWorkspace() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView method) setAtomBondTyping() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) setAtomicBasis() (schrodinger.application.jaguar.input.JaguarInput method) setAtomList() (schrodinger.infra.phase.PhpFeaturePattern method) setAtomNum() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) setAtomProps() (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell method) setAtomRNumbers() (schrodinger.application.matsci.builderwidgets.SketcherBox method) setAttributes() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property method) setBackboneAndSideGroup() (schrodinger.application.matsci.amorphous.PolymerToFragments method) setBacktrackingLevel() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) setBaroMethod() (schrodinger.application.desmond.gui.EnsembleTab method) setBaroStyle() (schrodinger.application.desmond.gui.EnsembleTab method) setBaseName() (schrodinger.application.matsci.nano.interface_mod.Interface method) setBasic() (schrodinger.application.matsci.coarsegrain.Internals method) setBasis() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) setBasisFromText() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) setBeta() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) setBindingSiteASL() (schrodinger.protein.reliability.ProteinCheckParameters method) setBindingSiteAtoms() (schrodinger.structutils.sitealign.BindingSiteAligner method) setBlankBasisAllowed() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) setBoltzmannDistribution() (schrodinger.application.matsci.amorphous.EnergySurface method) setBondNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setBondOrder() (schrodinger.structutils.assignbondorders.AssignBondOrders method) setBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setBoundaryCondition() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setBoundingRect() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) setCell() (schrodinger.application.desmond.packages.msys.System method) setCGBondLengths() (in module schrodinger.application.matsci.coarsegrain) setChanged() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) setChannel() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setChannelAttrs() (schrodinger.application.matsci.rxn_channel.rxn_channel.ChannelDefinition method) setChargeConstraints() (schrodinger.application.jaguar.input.JaguarInput method) setCharPositionInLine() (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setCharStream() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) setChecked() (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) setCheckedData() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) setChild() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setChildIndex() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setChorusProperties() (schrodinger.application.matsci.nano.xtal.Crystal method) setClassKwargsAttr() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property method) setClickable() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) setColor() (schrodinger.utils.colorscheme.MM_CSchemeRule method) setColoring() (schrodinger.surface.Surface method) setColormap() (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) setColorModeAction() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) setColorName() (schrodinger.utils.colorscheme.MM_CSchemeRule method) setColorRGB() (schrodinger.structure._StructureAtom method) setColors() (schrodinger.graphics3d.sphere.MaestroSphere method) (schrodinger.graphics3d.torus.MaestroTorus method) setColorSchemeChanged() (schrodinger.utils.colorscheme.ColorSchemeManager method) setColorSchemeRuleASL() (schrodinger.utils.colorscheme.ColorSchemeManager method) setColorSchemeRuleColor() (schrodinger.utils.colorscheme.ColorSchemeManager method) setColorSchemeRuleDescription() (schrodinger.utils.colorscheme.ColorSchemeManager method) setColumns() (schrodinger.application.desmond.gui.TableModel method) setCombiningRule() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) setComblibDir() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) setCommandLine() (schrodinger.job.launchapi.TaskSpecificationBuilder method) setCompStr() (schrodinger.utils.ligfilter.Criterion method) setConfig() (schrodinger.tasks.runners.JobTaskRunner method) setConfOptions() (schrodinger.infra.phase.PhpScreener method) setConfs() (schrodinger.trajectory.prody.ensemble.Ensemble method) setConnectionFile() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConnectionMaxLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConnectionMinLink() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConnectionName() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConnectionSize() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setConstants() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) setConstraint() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.infra.phase.PhpSiteConstraint method) setCoordinates() (schrodinger.infra.phase.PhpSite method) setCoords() (schrodinger.graphics3d.sphere.MaestroSphere method) (schrodinger.graphics3d.torus.MaestroTorus method) (schrodinger.trajectory.prody.ensemble.Ensemble method) setCoorGenMode() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) setCovariance() (schrodinger.trajectory.prody.pca.PCA method) setCrystalSymmetry() (schrodinger.application.matsci.nano.xtal.Crystal method) setCTSource() (schrodinger.infra.phase.PhpFeatureFinder method) setCurrentChoice() (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) setCurrentColorSchemeName() (schrodinger.utils.colorscheme.ColorSchemeManager method) setCurrentMmJagData() (schrodinger.application.jaguar.gui.utils.EnhancedComboBox method) setCurrentSpecies() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) setCustomName() (schrodinger.tasks.runners.TaskRunner method) setCustomTemplateDir() (schrodinger.application.matsci.builderwidgets.SketcherBox method) setCVals() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) setData() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.desmond.fep_gui.ResiduesModel method) (schrodinger.application.desmond.fep_gui.StrucListModel method) (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesModelPka method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) (schrodinger.application.jaguar.gui.tabs.theory_tab.ComboRadioSelector method) (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionComboBox method) (schrodinger.application.livedesign.panel_components.LiveReportSelector method) (schrodinger.application.matsci.amorphous.TorsionAngler method) (schrodinger.infra.phase.PhpSiteMaskData method) (schrodinger.pipeline.pipeio.Grid method) (schrodinger.pipeline.pipeio.PhaseDB method) (schrodinger.pipeline.pipeio.Structures method) (schrodinger.pipeline.pipeio.Text method) setDataRow() (schrodinger.infra.phase.PhpFeatureData method) setDataValue() (schrodinger.infra.phase.PhpFeatureData method) setDebug() (schrodinger.infra.phase.PhpFastShape method) (schrodinger.infra.table.Table static method) (schrodinger.project.Project static method) setDebugLevel() (schrodinger.job.launchparams.LaunchParameters method) setDebugListener() (schrodinger.application.desmond.antlr3.debug.DebugParser method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) setdefault() (schrodinger.utils.scollections.IdentityDict method) setDefaultBasis() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) setDefaultCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) setDefaultColorScheme() (schrodinger.utils.colorscheme.ColorSchemeManager method) setDefaultDataRow() (schrodinger.infra.phase.PhpFeatureData method) setDefaultDataValue() (schrodinger.infra.phase.PhpFeatureData method) setDefaultLimits() (schrodinger.infra.phase.PhpComplex method) setDefaults() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) (schrodinger.application.livedesign.panel_components.LiveDesignProjectsCombo method) (schrodinger.application.matsci.guibase.MultiDesmondJobApp method) (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) (schrodinger.infra.phase.PhpSite method) (schrodinger.models.mappers.MapperMixin method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) setDefaultText() (schrodinger.application.livedesign.panel_components.AssaySelectionPopup method) setDeleteAfterIncorporation() (schrodinger.job.launchparams.LaunchParameters method) setDeltaDist() (schrodinger.infra.phase.PhpMatchOptions method) setDeltasToNeighboringCells() (schrodinger.application.matsci.nano.xtal.PBCBond method) (schrodinger.application.matsci.nano.xtal.PBCBonds method) setDensityIncreaseAllowed() (schrodinger.application.matsci.amorphous.AmorphousCellBuilder method) setDescription() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) (schrodinger.utils.colorscheme.MM_CScheme method) (schrodinger.utils.colorscheme.MM_CSchemeRule method) setDesiredNumberOfConformers() (schrodinger.infra.fast3d.Engine method) setDetached() (schrodinger.job.launchparams.LaunchParameters method) setDihedralNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setDihedrals() (schrodinger.application.matsci.coarsegrain.Internals method) setDirective() (schrodinger.application.jaguar.input.JaguarInput method) setDisplayedEids() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) setDistanceCell() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setDistanceMatrixCallback() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) setDmatrix() (schrodinger.infra.phase.PhpHiCluster method) setDriverReservesCores() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setEditOff() (schrodinger.infra.phase.PhpFeaturePattern method) setEditOn() (schrodinger.infra.phase.PhpFeaturePattern method) setEditorData() (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.TempItemDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BasisSetDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBoxDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeSelectorDelegate method) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopUpDelegate method) setEigens() (schrodinger.trajectory.prody.nma.NMA method) (schrodinger.trajectory.prody.pca.PCA method) setElements() (schrodinger.application.matsci.espresso.qeinput.StructureType method) setEnabled() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) setEnabledExceptSimulationTime() (schrodinger.application.desmond.gui.MdGroup method) (schrodinger.application.desmond.gui.SimOptionsFrame method) setEnableOptimization() (schrodinger.infra.phase.PhpMMconfAdaptor method) setEnergiesAndForces() (schrodinger.application.matsci.mecp_mod.MECPStep method) setEnergiesAndForcesData() (schrodinger.application.matsci.mecp_mod.MECPStep method) setEnergyWindow() (schrodinger.infra.phase.PhpConfOptions method) setEntryID() (schrodinger.graphics3d.common.Primitive method) setErrorStatus() (schrodinger.application.livedesign.ld_base_classes.ImportExportThreadRunner method) setExcitedStateCheckBoxText() (schrodinger.application.jaguar.gui.theory_tab_widgets.ExcitedStateWidget method) setExcludeLocation() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setExcludePattern() (schrodinger.infra.phase.PhpFeatureDefinition method) setExhaustiveMatching() (schrodinger.infra.phase.PhpMatchOptions method) setExportData() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) setExportGlobal() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) setExtendDistance() (schrodinger.infra.phase.PhpFeatureDefinition method) (schrodinger.infra.phase.PhpFeaturePattern method) setFeatureComment() (schrodinger.infra.phase.PhpFeatureDefinition method) setFeatureDefinitions() (schrodinger.infra.phase.PhpFeatureFinder method) setFeatureName() (schrodinger.infra.phase.PhpFeatureDefinition method) setFeatureNumber() (schrodinger.infra.phase.PhpFeatureDefinition method) setFeatures() (schrodinger.application.phase.featureselector.FeatureSelector method) setFeatureSelection() (schrodinger.application.phase.phase_markers.PhaseMarkers method) setFeatureType() (schrodinger.infra.phase.PhpFeatureDefinition method) setFFType() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) setFile() (schrodinger.application.combiglide.combenumdock.createFragmentDelegate method) (schrodinger.application.combiglide.combenumdock.simpleEnumDockDelegate method) setFileName() (schrodinger.utils.colorscheme.MM_CScheme method) setFilter() (schrodinger.analysis.enrichment.FingerprintFromFileGenerator method) setFixed() (schrodinger.application.macromodel.utils.SbcUtil method) setFloatable() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) setFloatableMovable() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) setFloatableMovableClosable() (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget method) setForceField() (schrodinger.infra.phase.PhpConfOptions method) (schrodinger.infra.phase.PhpMMconfAdaptor method) setFormalCharge() (schrodinger.structutils.assignbondorders.AssignBondOrders method) setFragDihedralPool() (schrodinger.application.matsci.amorphous.PolymerFragment method) setFragmentCollection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) setFragType() (schrodinger.infra.phase.PhpSite method) setFrozen() (schrodinger.application.macromodel.utils.SbcUtil method) setFrozenAtoms() (schrodinger.infra.phase.PhpMMconfAdaptor method) setFullSystemSpecified() (schrodinger.application.desmond.fep_gui.DesmondApp method) setGaps() (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.protein.sequence.Sequence method) setGeometry() (schrodinger.infra.phase.PhpFeaturePattern method) setGidOffset() (schrodinger.application.desmond.packages.staf.Positer method) setGlowColor() (schrodinger.graphics3d.common.Primitive method) setGroup() (schrodinger.infra.phase.PhpProject method) (schrodinger.infra.phase.PhpSiteMaskGroup method) setGuiState() (schrodinger.application.desmond.gui.SimOptionsFrame method) setHbondParameters() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setHKL() (schrodinger.application.matsci.nano.interface_mod.Interface method) setHost() (schrodinger.job.jobcontrol.Host method) setHostList() (schrodinger.job.queue.JobDJ method) setHostname() (schrodinger.job.launchparams.LaunchParameters method) setHydrophobicityWindowPadding() (schrodinger.protein.alignment.ProteinAlignment method) setHypoID() (schrodinger.infra.phase.PhpHypoAdaptor method) setIgnorePair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setImpropers() (schrodinger.application.matsci.coarsegrain.Internals method) setIncludeAcceptor() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeAromatic() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeBackbone() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeCharged() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeContact() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncluded() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) setIncludedExcludedNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setIncludeDonor() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludedVolumeCutoff() (schrodinger.infra.phase.PhpMatchOptions method) setIncludedVolumeWeight() (schrodinger.infra.phase.PhpMatchOptions method) setIncludeHydrophobic() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludePattern() (schrodinger.infra.phase.PhpFeatureDefinition method) setIncludePolar() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setIncludeSidechain() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setInitiatorResidue() (schrodinger.application.matsci.amorphous.PolymerToFragments method) setInput() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.pipeline.stage.Stage method) setInputDirectory() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) setInputFile() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setInputFiles() (schrodinger.job.launchapi.JobSpecificationBuilder method) setInputSelector() (schrodinger.application.jaguar.gui.basis_selector.BasisSelector method) setInputStream() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setInTemplates() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.matsci.mecp_mod.MECPStep method) setInteractionCutoff() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setInterfaceLatticeProperties() (schrodinger.application.matsci.nano.interface_mod.Interface method) setInterfaceProperties() (schrodinger.application.matsci.nano.interface_mod.Interface method) setInternals() (schrodinger.application.matsci.coarsegrain.Internals method) setInvertFilter() (schrodinger.analysis.enrichment.FingerprintFromFileGenerator method) setIonLocation() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setIsGlowing() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.graphics3d.common.Primitive method) setIsInfinite() (schrodinger.application.matsci.nano.interface_mod.Interface method) setIsoelectricPointWindowPadding() (schrodinger.protein.alignment.ProteinAlignment method) setItemChecked() (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) setItemDelegateForColumn() (schrodinger.application.jaguar.gui.utils.ProjTableLikeView method) setItemEnabled() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) setItems() (schrodinger.ui.ligfilter.PatternModel method) setItemsEnabled() (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) setItemsTooltip() (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) setItemTooltip() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) setItUp() (schrodinger.application.matsci.textlogger.GetLogger method) setJaguarKwargs() (schrodinger.application.matsci.mecp_mod.MECP method) setJaguarValue() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) setJaguarValues() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) setJobData() (schrodinger.application.matsci.mecp_mod.MECPStep method) setJobDJOptions() (schrodinger.pipeline.stage.Stage method) setJobname() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) setJobName() (schrodinger.job.app.App method) setJobname() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.JobSpecificationBuilder method) (schrodinger.job.launchparams.LaunchParameters method)

setJobOptions() (schrodinger.pipeline.stage.Stage method) setJobUsesTPP() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setKeyword() (schrodinger.application.mopac.structure_launchers.StructureLauncher method) setKeywords() (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.qualityslider.KeywordEdit method) (schrodinger.application.matsci.qualityslider.QualitySlider method) setLabel() (schrodinger.application.matsci.reordergui.StructureFrame method) setLabelPixmap() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) setLabelsVisible() (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) setLabelTooltip() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) setLastRewriteTokenIndex() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) setLatticeProperties() (schrodinger.application.matsci.nano.interface_mod.Interface method) (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) setLaunchDirectory() (schrodinger.job.launchparams.LaunchParameters method) setLayerLabelSize() (schrodinger.application.matsci.sliceplot.SlicePlot method) setLayerWidgetStates() (schrodinger.application.matsci.sliceplot.SlicePlot method) setLigandCleanupOptions() (schrodinger.structutils.minimize.Minimizer method) setLigRange() (schrodinger.application.glide.glide.Dock method) setLimits() (schrodinger.infra.phase.PhpComplex method) setLine() (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setLinkage() (schrodinger.application.canvas.cluster.CanvasFingerprintCluster method) setLinkageType() (schrodinger.infra.phase.PhpHiCluster method) setLiveReportDefaults() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) setLocalStructAtomIds() (schrodinger.application.matsci.amorphous.PolymerToFragments method) setLockedColumns() (schrodinger.protein.alignment.BaseAlignment method) setLongName() (schrodinger.utils.colorscheme.MM_CScheme method) setLRName() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) setMaestroProjectDisposition() (schrodinger.job.launchparams.LaunchParameters method) setMaestroProjectName() (schrodinger.job.launchparams.LaunchParameters method) setMaestroViewname() (schrodinger.job.launchparams.LaunchParameters method) setMainProduct() (schrodinger.pipeline.stage.Stage method) setMarkerHighlighting (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView attribute) setMaskValue() (schrodinger.infra.phase.PhpSite method) setMatchOptions() (schrodinger.infra.phase.PhpScreener method) setMaxConformations() (schrodinger.infra.phase.PhpMMconfAdaptor method) setMaxConfs() (schrodinger.infra.phase.PhpConfOptions method) setMaxReport() (schrodinger.infra.phase.PhpMatchOptions method) setMembrane() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMembranePatch() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMembranize() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMetric() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) setMetricCB() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) setMinSites() (schrodinger.infra.phase.PhpMatchOptions method) setMMFepioMapModeOption() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setMMFepioRetainAngleOption() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setModel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) (schrodinger.application.livedesign.panel_components.ExportTableView method) (schrodinger.models.mappers.AbstractParamMapper method) (schrodinger.models.mappers.MapperMixin method) setModelClass() (schrodinger.models.mappers.AbstractParamMapper method) setModelData() (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.TempItemDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBoxDelegate method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinatesDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeSelectorDelegate method) (schrodinger.application.livedesign.panel_components.AssaySelectionPopUpDelegate method) setMoleculeCompletion() (schrodinger.application.matsci.nano.particle.Nanoparticle method) setMultiplePatternCriterionState() (schrodinger.ui.ligfilter.LigfilterFrame method) setMultiplePredefinedCriterionState() (schrodinger.ui.ligfilter.LigfilterFrame method) setMultiplePropCriterionState() (schrodinger.ui.ligfilter.LigfilterFrame method) setMustMatch() (schrodinger.infra.phase.PhpProject method) setName() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) (schrodinger.utils.colorscheme.MM_Color method) setNanoparticleProperties() (schrodinger.application.matsci.nano.particle.Nanoparticle method) setNeedRebuildColorSchemes() (schrodinger.utils.colorscheme.ColorSchemeManager method) setNegativeIon() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setNeutralize() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setNoLaunch() (schrodinger.job.launcher.Launcher method) setNonAngleNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setNonAngleNonDihedralNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setNonBonds() (schrodinger.application.matsci.coarsegrain.Internals method) setNonUniqueIds() (schrodinger.analysis.enrichment.FingerprintFromFileGenerator method) setNormal() (schrodinger.application.matsci.shapes.Face method) setNormalAngle() (schrodinger.application.matsci.nano.slab.Surface method) setNRequired() (schrodinger.application.glide.glide.Dock method) setNumberOfProcessorsManyNodes() (schrodinger.job.launchparams.LaunchParameters method) setNumberOfProcessorsOneNode() (schrodinger.job.launchparams.LaunchParameters method) setNumberOfSubjobs() (schrodinger.job.launchparams.LaunchParameters method) setNumClusters() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) setNumConfsPerRotBond() (schrodinger.infra.phase.PhpMMconfAdaptor method) setOneAmassLine() (in module schrodinger.application.matsci.qexsd.qespresso.options) setOpcdArgs() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.SbcUtil method) setOperatorNames() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization method) setOplsaaVersion() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setOPLSDir() (schrodinger.job.launchparams.LaunchParameters method) setOption() (schrodinger.structure._BaseWriter method) (schrodinger.structure.SDWriter method) (schrodinger.structure.StructureWriter method) setOptions() (schrodinger.infra.phase.PhpMMconfAdaptor method) (schrodinger.pipeline.pipeline.Pipeline method) (schrodinger.structutils.minimize.Minimizer method) setOrigin() (schrodinger.application.matsci.nano.xtal.Crystal method) (schrodinger.protein.sequence.Sequence method) setOriginalName() (schrodinger.utils.colorscheme.MM_CScheme method) setOutput() (schrodinger.pipeline.stage.Stage method) setOutputFile() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setOutputFiles() (schrodinger.job.launchapi.JobSpecificationBuilder method) setOutputName() (schrodinger.pipeline.stage.Stage method) setOverride() (schrodinger.application.desmond.packages.msys.TermTable method) setPanel() (schrodinger.tasks.runners.PanelTaskReporter method) setPanelOptions() (schrodinger.application.jaguar.gui.base_panel.AutomaticJobnameMixin method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.matsci.reordergui.ReorderAtomPanel method) (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) setParallelization() (schrodinger.application.matsci.mecp_mod.MECP method) SetParam (class in schrodinger.models.parameters) setParameters() (schrodinger.application.matsci.nano.slab.Surface method) setParamMapper() (schrodinger.models.parameters.ParamModel method) setParent() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setPathtoBranchingAtom() (schrodinger.application.matsci.amorphous.PolymerToFragments method) setPattern() (schrodinger.infra.phase.PhpFeaturePattern method) setPatternID() (schrodinger.infra.phase.PhpFeaturePattern method) setPatternOptions() (schrodinger.ui.ligfilter.LigfilterFrame method) setPattyHandle() (schrodinger.infra.phase.PhpFeaturePattern method) setPBCBonds() (schrodinger.application.matsci.nano.xtal.PBCBonds method) setPerAtom() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) setPerAtomBasisModel() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) setPermitted() (schrodinger.infra.phase.PhpSite method) setPharmSet() (schrodinger.infra.phase.PhpProject method) setPickAtom() (schrodinger.ui.picking.PickMixedToggle method) setPickBond() (schrodinger.ui.picking.PickMixedToggle method) setPixmap() (schrodinger.application.desmond.feputils.LabelSpinner method) setpKaData() (schrodinger.application.bioluminate.protein.PropertyCalculator method) setPlotType() (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) setPosition() (schrodinger.application.bioluminate.sliderchart.SlidableHLine method) (schrodinger.application.bioluminate.sliderchart.SlidableVLine method) setPositions() (schrodinger.application.desmond.packages.msys.System method) setPositiveIon() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setPrecision() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) setPrimitiveCell() (schrodinger.application.matsci.espresso.qeinput.StructureType method) setProgramName() (schrodinger.job.app.App method) (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setProhibited() (schrodinger.infra.phase.PhpSite method) setProjCoords() (schrodinger.infra.phase.PhpSite method) setProjectedOnly() (schrodinger.infra.phase.PhpSite method) setProjectedType() (schrodinger.infra.phase.PhpFeaturePattern method) setProjectedTypeOff() (schrodinger.infra.phase.PhpFeatureDefinition method) setProjectedTypeOn() (schrodinger.infra.phase.PhpFeatureDefinition method) setProperties() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) setPropertyLabelVisible() (schrodinger.application.phase.phase_markers.PhaseMarkers method) setProtein() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) setQsarSet() (schrodinger.infra.phase.PhpProject method) setRad() (schrodinger.infra.phase.PhpSite method) setReactionInstance() (schrodinger.analysis.reaction.RouteNode method) setReactiveInds() (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule method) setReactiveMolecules() (schrodinger.application.matsci.rxn_channel.rxn_channel.Reactants method) setReceptorStructure() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) setRefCtTitle() (schrodinger.infra.phase.PhpHypoAdaptor method) setReferenceSeq() (schrodinger.protein.alignment.BaseAlignment method) setRelativeEnergy() (schrodinger.infra.phase.PhpMMconfAdaptor method) setResidueConnectivity() (schrodinger.application.matsci.amorphous.PolymerToFragments method) setResidues() (schrodinger.application.bioluminate.protein.Refiner method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method) setRGBColors() (schrodinger.graphics3d.sphere.MaestroSphere method) setRightClickHandler() (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) setRightClickOnGObject() (schrodinger.graphics3d.common.Primitive method) setRingsForOneMol() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) setRootLoggerForPyEvolve() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.GeneticOptimization method) setRotatableBond() (schrodinger.application.matsci.amorphous.PolymerToFragments method) setRow() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) setRows() (schrodinger.application.desmond.gui.AtomGroupModel method) (schrodinger.application.desmond.gui.PosResModel method) setRules() (schrodinger.utils.colorscheme.MM_CScheme method) setSaltNegativeIon() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSaltPositiveIon() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSamplingMethod() (schrodinger.infra.phase.PhpConfOptions method) (schrodinger.infra.phase.PhpMMconfAdaptor method) setSasOptions() (schrodinger.infra.phase.PhpFeatureDefinition method) setSaveAllJobOutput() (schrodinger.job.launchparams.LaunchParameters method) setScanCoordinate() (schrodinger.application.jaguar.input.JaguarInput method) setSCFGS() (schrodinger.application.matsci.mecp_mod.MECP method) setScoreInPlace() (schrodinger.infra.phase.PhpMatchOptions method) setSelected() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphere method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) setSelectedFeatures() (schrodinger.application.phase.featureselector.FeatureSelector method) (schrodinger.application.phase.phase_widgets.FeatureMatchCombo method) setSelectedMutations() (schrodinger.ui.residueselector.MutationSelectorComboBox method) (schrodinger.ui.residueselector.MutationSelectorFrame method) (schrodinger.ui.residueselector.MutationSelectorLineEdit method) setSelectedValues() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) setSelection() (schrodinger.application.phase.phase_markers.PhaseMarkers method) setSelectorEnabled() (schrodinger.application.jaguar.gui.tabs.theory_tab.DFTComboRadioSelector method) setShiftLeft() (schrodinger.application.matsci.siteselector.siteselector.CoordinationSite method) setShortName() (schrodinger.utils.colorscheme.MM_CScheme method) setShownRow() (schrodinger.application.desmond.fep_gui.StrucListModel method) setSiteClickable() (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector method) setSiteMatches() (schrodinger.structutils.sitealign.BindingSiteAligner method) setSiteNumber() (schrodinger.infra.phase.PhpSite method) setSites() (schrodinger.application.matsci.coarsegrain.Internals method) setSiteSimilarity() (schrodinger.infra.phase.PhpSite method) setSiteStatusOff() (schrodinger.infra.phase.PhpSite method) setSiteStatusOn() (schrodinger.infra.phase.PhpSite method) setSiteType() (schrodinger.infra.phase.PhpSite method) setSiteTypeChar() (schrodinger.infra.phase.PhpSite method) setSize() (schrodinger.infra.mmkv.MMKVArgList method) setSketcherStructure() (schrodinger.application.matsci.builderwidgets.SketcherBox method) setSlotOrder() (schrodinger.application.matsci.buildcomplex.ComplexBuilder method) setSolute() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSoluteAlignment() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSoluteCoords() (schrodinger.trajectory.prody.ensemble.Ensemble method) setSolvate() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSolvent() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setSource() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) setSourceModel() (schrodinger.application.bioluminate.antibody.search_results_table.FullProxyModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabProxyModel method) setSphereRadius() (schrodinger.infra.phase.PhpExclVol method) setSphereRadiusAndCoords() (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) setSphereXYZ() (schrodinger.infra.phase.PhpExclVol method) setSpinMult() (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) setStageOptions() (schrodinger.pipeline.pipeline.Pipeline method) setStatus() (schrodinger.infra.phase.PhpSite method) (schrodinger.tasks.tasks.AbstractTask method) setStatusIncorporated() (schrodinger.job.jobcontrol.Job method) setStderr() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setStdout() (schrodinger.job.launchapi.JobSpecificationArgsBuilder method) (schrodinger.job.launchapi.TaskSpecificationBuilder method) setStdOutErrFile() (schrodinger.job.launcher.Launcher method) setStrainedAdsorptionLatticeProperties() (schrodinger.application.matsci.nano.interface_mod.Interface method) setStructure() (schrodinger.application.desmond.fep_scholar_util.FEPStructureObject method) (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) (schrodinger.application.matsci.chargegui.BasisSetSelector method) (schrodinger.application.matsci.espresso.qeinput.KpointsType method) (schrodinger.application.matsci.mecp_mod.JaguarJobs method) (schrodinger.application.matsci.reordergui.ReferenceFrame method) (schrodinger.application.matsci.reordergui.StructureFrame method) (schrodinger.application.matsci.reordergui.StructureListWidget method) (schrodinger.application.matsci.reordergui.StructurePic method) (schrodinger.project.ProjectRow method) (schrodinger.protein.sequence.Sequence method) (schrodinger.structutils.minimize.Minimizer method) setStructureAndUpdateBorder() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) setStructureFile() (schrodinger.application.qsite.input.QSiteInput method) setStructureMonitorFile() (schrodinger.job.launcher.Launcher method) setStructureOutput() (schrodinger.pipeline.input.Writer method) setStructureOutputFile() (schrodinger.job.launcher.Launcher method) setStructureOutputFileBE() (schrodinger.job.app.App method) setStructureOutputFileFE() (schrodinger.job.app.App method) setStructureProperties() (schrodinger.application.matsci.nano.xtal.Crystal method) setStructures() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) setStructureSelectorsEnabled() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) setStructureType() (schrodinger.application.matsci.espresso.qeinput.PseudopotentialsType method) setStyle() (schrodinger.graphics3d.polyhedron.Polyhedron method) (schrodinger.structure._StructureBond method) setSubs() (schrodinger.application.macromodel.utils.SbcUtil method) setSubTabMarkerHighlighting() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) setSubTabsVisible() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) setSurfaceProperties() (schrodinger.application.matsci.nano.slab.Surface method) setTemplateResource() (schrodinger.application.licensing.licadmin.LocalServerProcess method) setTemporaryPixmap() (schrodinger.application.desmond.feputils.LabelSpinner method) setter (schrodinger.models.mappers.AccessType attribute) setText() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.application.desmond.cwidget.EntryField method) (schrodinger.application.desmond.cwidget.FileEntry method) (schrodinger.application.desmond.fep_gui.CustomGPUComboBox method) (schrodinger.application.livedesign.panel_components.AssaySelectionLineEdit method) (schrodinger.maestro.markers.AtomMarker method) setThermoMethod() (schrodinger.application.desmond.gui.EnsembleTab method) setTimeLimit() (schrodinger.infra.phase.PhpMatchOptions method) Setting (class in schrodinger.application.jaguar.keywordDB) SETTING_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) SETTINGS (schrodinger.application.matsci.desmondutils.MSJStringer attribute) SETTINGS_ONLY (schrodinger.application.jaguar.gui.filedialog.ReadFileDialog attribute) SETTINGS_VARS (schrodinger.maestro.markers.AtomMarker attribute) SettingsParamMapper (class in schrodinger.models.mappers) setTitle() (schrodinger.trajectory.prody.mode.Vector method) (schrodinger.trajectory.prody.nma.NMA method) setTokenBoundaries() (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.debug.TraceDebugEventListener method) (schrodinger.application.desmond.antlr3.tree.CommonTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) setTokenIndex() (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) setTokenSource() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) setTokenStartIndex() (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) setTokenStopIndex() (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) setTokenStream() (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) setTokenTypeChannel() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) setTol() (schrodinger.infra.phase.PhpSite method) setToolBars() (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow method) setTPP() (schrodinger.job.launchparams.LaunchParameters method) setTransparency() (schrodinger.surface.Surface method) setTreatHydrogens() (schrodinger.infra.phase.PhpExclVol method) setTreeAdaptor() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) setTreeNodeStream() (schrodinger.application.desmond.antlr3.tree.TreeParser method) setTvalueFilterOff() (schrodinger.infra.phase.PhpQSAR method) setTvalueFilterOn() (schrodinger.infra.phase.PhpQSAR method) setType() (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tokens.CommonToken method) (schrodinger.application.desmond.antlr3.tokens.Token method) (schrodinger.application.desmond.antlr3.tree.BaseTreeAdaptor method) (schrodinger.application.desmond.antlr3.tree.TreeAdaptor method) (schrodinger.infra.phase.PhpFeaturePattern method) setTypeSimilarity() (schrodinger.infra.phase.PhpFeaturePattern method) setUniformDistribution() (schrodinger.application.matsci.amorphous.EnergySurface method) setUniqueIdsOnly() (schrodinger.analysis.enrichment.FingerprintFromFileGenerator method) setUniqueNavigationNodes() (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) setUnknownTokenBoundaries() (schrodinger.application.desmond.antlr3.tree.CommonTree method) setup() (in module schrodinger.infra.epydoc_to_sphinx) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.SimOptionsFrame method) (schrodinger.application.glide.glide.ConstraintGroup method) (schrodinger.application.glide.http_server.GlideHTTPHandler method) (schrodinger.application.jaguar.gui.base_panel.AutomaticJobnameMixin method) (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel method) (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.ExcitedStateValidatorMixin method) (schrodinger.application.jaguar.gui.base_panel.InputMultiplicityMixin method) (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) (schrodinger.application.jaguar.gui.base_panel.MarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) (schrodinger.application.jaguar.gui.base_panel.MultiStructurePanelMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) (schrodinger.application.jaguar.gui.base_panel.OptimizationTabMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.PropertiesValidatorMixin method) (schrodinger.application.jaguar.gui.base_panel.ReadEditMixin method) (schrodinger.application.jaguar.gui.base_panel.ScanTabMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabBase method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.ESPSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PolarizabilitySubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTabIGO method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTabNoOptimized method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab method) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab method) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin method) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab method) (schrodinger.application.livedesign.panel_components.AssaySelectionPopup method) (schrodinger.application.livedesign.panel_components.BaseSelectionPopup method) (schrodinger.application.livedesign.panel_components.EndpointSelectionPopup method) (schrodinger.application.livedesign.panel_components.LiveReportSelectionPopup method) (schrodinger.application.macromodel.input.ConfSearch method) (schrodinger.application.macromodel.input.EmbraceConfSearch method) (schrodinger.application.macromodel.input.EmbraceMinimization method) (schrodinger.application.macromodel.input.EnergyListing method) (schrodinger.application.macromodel.input.Minimization method) (schrodinger.application.macromodel.input.Minta method) (schrodinger.application.macromodel.input.RCE method) (schrodinger.application.matsci.guibase.MultiDesmondJobApp method) (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) (schrodinger.job.queue.BaseJob method) (schrodinger.protein.assignment.ProtAssign method) (schrodinger.ui.ligfilter.LigfilterFrame method) (schrodinger.ui.residueselector.MutationSelectorPopUp method) setup_alchem_properties() (in module schrodinger.application.desmond.replica_sid_generator) (schrodinger.application.desmond.replica_sid_generator.FEPReport method) setup_arrow() (in module schrodinger.trajectory.prody.test_arrow) setup_atom() (in module schrodinger.trajectory.prody.writenmd) setup_local_static() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) setup_local_static_alt() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) setup_md_job() (in module schrodinger.application.matsci.equilibrium_md) setup_project_close() (in module schrodinger.application.phase.phase_markers) setup_protein() (schrodinger.protein.analysis.Report method) setup_protein_health_button() (in module schrodinger.application.desmond.feputils) setup_protein_warning() (in module schrodinger.application.desmond.feputils) setup_xtal() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) setupAset() (schrodinger.application.macromodel.utils.ComUtil method) setupCheckboxes() (schrodinger.ui.residueselector.MutationSelectorFrame method) setUpFast3D() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) setupFind() (schrodinger.infra.phase.PhpProject method) setupGPGPUTable() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) setupGravity() (schrodinger.application.matsci.montecarlo.Metropolizer method) setupHostLayout() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) setUpInputFiles() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) setUpIterationLaunchDir() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) setUpJaguarJobs() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) setupJobs() (schrodinger.pipeline.stages.filtering.GeneratePropsStage method) (schrodinger.pipeline.stages.filtering.LigFilterStage method) (schrodinger.pipeline.stages.glide.DockingStage method) (schrodinger.pipeline.stages.glide.GridgenStage method) (schrodinger.pipeline.stages.ligprep.LigPrepStage method) (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) (schrodinger.pipeline.stages.prime.MMGBSAStage method) (schrodinger.pipeline.stages.prime.PrimeStage method) (schrodinger.pipeline.stages.qikprop.QikPropStage method) (schrodinger.pipeline.stages.qsite.QSiteStage method) (schrodinger.pipeline.stages.semiemp.SemiEmpStage method) setupJson() (schrodinger.application.glide.glide.Dock method) (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.glide.glide.Gridgen method) setUpLaunchDir() (schrodinger.application.matsci.mecp_mod.JaguarJobs method) setupLayout() (schrodinger.application.livedesign.panel_components.BaseLiveReportSelectionPopup method) (schrodinger.application.livedesign.panel_components.BaseSearchTreeWidgetHelper method) setupLDClient() (schrodinger.application.livedesign.login.LiveDesignLoginDialog method) setUpMaeWriter() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) (schrodinger.application.matsci.mecp_mod.MECP method) setupMappingWidgets() (schrodinger.application.livedesign.ld_export.AbstractExportPanel method) setUpMembrane() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyOptions method) setupQsar() (schrodinger.infra.phase.PhpProject method) setupQSiteJob() (schrodinger.pipeline.stages.qsite.QSiteStage method) setupStatusBar() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) setupSubHostCombo() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.fep_gui.GPUAndCPURESTFEPConfigDialog method) setupSubHostLayout() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) setupTacticity() (schrodinger.application.matsci.amorphous.Monomer method) setupTaskMessagingSignals() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) setupTaskWidget() (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel method) setupUi() (schrodinger.application.bioluminate.propfilter_ui.Ui_Form method) (schrodinger.application.bioluminate.protein_structure_quality_ui.Ui_Form method) (schrodinger.application.combiglide.combenumdock.glidePrecisionDialog method) (schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_cfc_ui.Ui_Widget method) (schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_collection_viewer_ui.Ui_Dialog method) (schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_constraints_ui.Ui_Dialog method) (schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_ui.Ui_Widget method) (schrodinger.application.desmond.desmond_advanced_tab_ui.Ui_Dialog method) (schrodinger.application.desmond.input_group_ui.Ui_Form method) (schrodinger.application.desmond.rest_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui.Ui_Dialog method) (schrodinger.application.jaguar.gui.ui.edit_dialog_ui.Ui_MainWindow method) (schrodinger.application.jaguar.gui.ui.excited_state_widget_ui.Ui_Widget method) (schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_std_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.input_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.irc_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.irc_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.molecule_top_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.multi_structures_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.optimization_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.output_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.properties_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.reaction_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scan_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.scf_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvation_gas_phase_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvation_pka_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvation_solvent_model_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.solvent_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui.Ui_Widget method) (schrodinger.application.jaguar.gui.ui.theory_tab_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui.Ui_Form method) (schrodinger.application.jaguar.gui.ui.transition_state_top_ui.Ui_Form method) (schrodinger.application.livedesign.export_setup_ui.Ui_Form method) (schrodinger.application.livedesign.export_ui.Ui_Form method) (schrodinger.application.livedesign.login_ui.Ui_Dialog method) (schrodinger.application.prime.gui.ui.analyze_energy_ui.Ui_Form method) (schrodinger.application.prime.gui.ui.environment_options_ui.Ui_Form method) (schrodinger.infra.exception_handler_dir.exception_dialog_ui.Ui_Dialog method) (schrodinger.ui.ligfilter_definition_dialog_ui.Ui_Dialog method) (schrodinger.ui.ligfilter_ui.Ui_Form method) (schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui.Ui_Dialog method) (schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui.Ui_Dialog method) setupViewer() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) setupWidgets() (schrodinger.application.livedesign.panel_components.BaseLiveReportSelectionPopup method) (schrodinger.application.livedesign.panel_components.BaseSearchTreeWidgetHelper method) setUseAlchemicalWater() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setUseAtomTypes() (schrodinger.infra.phase.PhpMatchOptions method) setUsedHosts() (schrodinger.pipeline.pipeline.StageJob method) setUsedOff() (schrodinger.infra.phase.PhpFeaturePattern method) setUsedOn() (schrodinger.infra.phase.PhpFeaturePattern method) setUseHardAlignCutoff() (schrodinger.infra.phase.PhpMatchOptions method) setUseNDDOForCharges() (schrodinger.infra.phase.PhpMMconfAdaptor method) setValidator() (schrodinger.application.desmond.cwidget.EntryField method) setValue() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword method) (schrodinger.models.mappers.AttrTarget method) (schrodinger.models.mappers.ParamTarget method) (schrodinger.models.mappers.Target method) (schrodinger.models.parameters.CompoundParam method) setValues() (schrodinger.application.jaguar.input.JaguarInput method) (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) setVdwScalingFactor() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setVectorCutoff() (schrodinger.infra.phase.PhpMatchOptions method) setVectorWeight() (schrodinger.infra.phase.PhpMatchOptions method) setVelocities() (schrodinger.application.desmond.packages.msys.System method) setVerbosity() (schrodinger.infra.phase.PhpMMconfAdaptor method) setVisible() (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.matsci.chargegui.ChargePropertySelector method) (schrodinger.maestro.markers.Marker method) setVolumeCutoff() (schrodinger.infra.phase.PhpMatchOptions method) setVolumeWeight() (schrodinger.infra.phase.PhpMatchOptions method) setVsliderPosition() (schrodinger.application.matsci.mswidgets.SliderchartVLClass method) setWaitCursor() (schrodinger.application.matsci.builderwidgets.ItemRow method) (schrodinger.application.matsci.jobdirdlg.NewJobDirFrame method) setWeight() (schrodinger.trajectory.prody.ensemble.Ensemble method) setWeights() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_selector.ChargeSelectorLineEdit method) setWriteG96File() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteMaeffFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteMaeFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteOneMaeFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWritePdbFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteTopFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setWriteXyzFile() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) setX() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) setXCoord() (schrodinger.infra.phase.PhpSite method) setXP() (schrodinger.infra.phase.PhpSite method) setXvolSelected() (schrodinger.application.phase.phase_markers.PhaseMarkers method) setXY() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) setXYZ() (schrodinger.structure.Structure method) setXYZCoords() (schrodinger.graphics3d.sphere.MaestroSphere method) setY() (schrodinger.application.bioluminate.sliderchart.SliderPlot method) setYCoord() (schrodinger.infra.phase.PhpSite method) setZCoord() (schrodinger.infra.phase.PhpSite method) ShadowData (class in schrodinger.application.matsci.cgforcefield) shared_tags (schrodinger.analysis.transformations.TransformsRepository attribute) SHEET_OUT_MAE_NAME (schrodinger.application.matsci.nano.constants.Constants attribute) shell() (in module schrodinger.job.remote_command) short() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.LicenseLine method) (schrodinger.application.licensing.flexlm.Package method) short_code (schrodinger.protein.residue.Residue attribute) SHORT_FINGERPRINT_TYPES (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator attribute) short_hash (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) SHORT_HERMANN_MAUGUIN_SYMBOL (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) SHORT_NAME (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) SHORT_NAME_TAG (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) shorthost() (in module schrodinger.application.licensing.flexlm) (in module schrodinger.application.licensing.licadmin) (in module schrodinger.utils.licutils) shortname (schrodinger.project.Project attribute) shouldRelax() (schrodinger.application.desmond.gui.RelaxFrame method) show() (schrodinger.application.canvas.clustergui.ClusterStatisticsPlotDialog method) (schrodinger.application.canvas.clustergui.DendrogramPlotDialog method) (schrodinger.application.canvas.clustergui.DistanceMatrixPlotDialog method) (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) (schrodinger.application.phase.phase_markers.PhaseFeatureMarker method) (schrodinger.application.phase.phase_markers.PhaseSphereMarkers method) (schrodinger.graphics3d.common.Group method) (schrodinger.graphics3d.common.Primitive method) (schrodinger.graphics3d.gridbox.GridBox method) (schrodinger.maestro.markers.Marker method) (schrodinger.surface.Surface method) show_about_utilities() (in module schrodinger.utils.documentation) show_attached_hydrogen() (in module schrodinger.application.desmond.depictor) show_canvas_user_manual() (in module schrodinger.utils.documentation) show_contact_info() (in module schrodinger.utils.documentation) SHOW_DIELECTRIC (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab attribute) show_docking_panels_window() (in module schrodinger.maestro.maestro) show_elements_task_tutorial() (in module schrodinger.utils.documentation) show_elements_visualization_tutorial() (in module schrodinger.utils.documentation) show_entry() (schrodinger.application.desmond.maestro.Workspace method) show_hex_id_title_id_map() (in module schrodinger.application.desmond.title_to_hex) show_knime_workflows() (in module schrodinger.utils.documentation) show_knowledge_base() (in module schrodinger.utils.documentation) show_known_issues() (in module schrodinger.utils.documentation) show_legal_notice() (in module schrodinger.utils.documentation) show_maestro_training_videos() (in module schrodinger.utils.documentation) show_manuals_index() (in module schrodinger.utils.documentation) show_message() (in module schrodinger.utils.documentation) show_new_features() (in module schrodinger.utils.documentation) show_new_maestro_features() (in module schrodinger.utils.documentation) show_object() (in module schrodinger.maestro.maestro) show_only() (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) show_only_entry() (schrodinger.application.desmond.maestro.Workspace method) show_phase_hover_markers() (in module schrodinger.application.phase.phase_markers) show_python_api() (in module schrodinger.utils.documentation) show_python_overview() (in module schrodinger.utils.documentation) show_python_search() (in module schrodinger.utils.documentation) show_script_center() (in module schrodinger.utils.documentation) show_tool_tip (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel attribute) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) show_topic() (in module schrodinger.utils.documentation) show_workspace_phase_markers() (in module schrodinger.application.phase.phase_markers) showAllFeatures() (schrodinger.application.phase.phase_markers.PhaseMarkers method) showAllFeaturesForEntry() (schrodinger.application.phase.phase_markers.PhaseMarkers method) showAllJaguarMarkers() (schrodinger.application.jaguar.gui.base_panel.MarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) showDendrogramPlot() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) showDescription() (schrodinger.application.matsci.cgforcefieldgui.CGForceFieldSelector method) showDistanceMatrixPlot() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) showEvent() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) (schrodinger.application.matsci.sliceplot.SlicePlot method) showFeature() (schrodinger.application.phase.phase_markers.PhaseMarkers method) showLabels() (schrodinger.application.bioluminate.workspacelabeler.WorkspaceLabeler method) (schrodinger.application.glide.gui.GlideWorkspaceMarkers method) showLaunchStatus() (schrodinger.application.matsci.guibase.MultiJobApp method) showMainWindow() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) showMoleculeWidgetForParticipant() (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) showNC() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) showPage() (schrodinger.application.desmond.report_helper.NumberedCanvas method) showProteinHealthReport() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) showScheme() (schrodinger.application.bioluminate.ssv.toolbars.AntibodyNumberingToolBar method) showStatisticsPlot() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) showSubwidgets() (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) showToolTip() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesView method) showtype() (in module schrodinger.application.desmond.enhanced_sampling.FcnTypes) (in module schrodinger.application.desmond.enhsamp) (in module schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) showUnavailable() (schrodinger.application.livedesign.panel_components.ColumnSelectionProxyModel method) shrinkRowHeight() (schrodinger.application.jaguar.gui.utils.PropertiesTableWidget method) shuffle_structs() (in module schrodinger.structutils.shuffle) ShuffleException Shuffler (class in schrodinger.structutils.shuffle) shutdown_request() (schrodinger.application.glide.http_server.GlideHTTPServer method) shutdown_server() (schrodinger.application.glide.http_client.HTTPClient method) SIDE_CHAIN_CHEM (class in schrodinger.protein.residue) side_chain_chem (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) sidechain_dihedral_atomnames (in module schrodinger.protein.analysis_params) sidechain_dihedrals (in module schrodinger.protein.analysis_params) SIDECHAIN_INTERACTION (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) SIDECHAIN_POS (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator attribute) sidechains() (schrodinger.protein.getpdb_utility.Code method) sig_n (schrodinger.application.jaguar.results.JaguarResults attribute) sig_neg_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sig_neg_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sig_neg_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sig_p (schrodinger.application.jaguar.results.JaguarResults attribute) sig_pos_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sig_pos_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sig_pos_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sig_tot_alea_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sig_tot_alie_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sig_tot_esp_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) signal (schrodinger.models.mappers.AccessType attribute) signature() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) signedExpComp() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) sigtot (schrodinger.application.jaguar.results.JaguarResults attribute) silentlySetItems() (schrodinger.application.matsci.builderwidgets.TemplateCombo method) silentlyTryToSelectText() (schrodinger.application.matsci.builderwidgets.TemplateCombo method) simBuser() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simCosine() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.infra.phase.PhpDatabaseFp static method) simDice() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.infra.phase.PhpDatabaseFp static method) simDixon() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simEuclidean() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simHamann() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simHamming() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) SIMILARITY_METRICS (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity attribute) simKulczynski() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simMatching() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simMcConnaughey() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simMinMax() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simModifiedTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) SimOptionsFrame (class in schrodinger.application.desmond.gui) simPatternDifference() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simPearson() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simPetke() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simpleEnumDockDelegate (class in schrodinger.application.combiglide.combenumdock) SimpleSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) (class in schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) SimplifiedSequenceViewer (class in schrodinger.application.bioluminate.ssv.viewer) simplify_structure() (in module schrodinger.application.jaguar.autots_bonding) simRogersTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simShape() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simSimpson() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simSize() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simSoergel() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simTanimoto() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) (schrodinger.infra.phase.PhpDatabaseFp static method) simTversky() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) SIMULATE (schrodinger.application.matsci.desmondutils.MSJStringer attribute) simulate() (schrodinger.application.matsci.montecarlo.Metropolizer method) SimulatedAnnealing (class in schrodinger.application.canvas.r_group_dee) simulateTreeConstruction() (schrodinger.application.desmond.antlr3.debug.DebugTreeAdaptor method) simVariance() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) simYule() (schrodinger.application.canvas.similarity.CanvasFingerprintSimilarity method) Single (schrodinger.structure.BondType attribute) SINGLE_DISPLACEMENT_TYPE (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) single_point() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) single_point_cluster() (schrodinger.protein.assignment.ProtAssign method) SINGLE_PRECISION (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) SINGLE_STRUC (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) SingleConformerEngine (class in schrodinger.infra.fast3d) SingleDashOption (class in schrodinger.utils.cmdline) SingleDashOptionParser (class in schrodinger.utils.cmdline) SingleFilter (class in schrodinger.structutils.filter) SingleGpuDesmondGuiConfigDialog (class in schrodinger.application.desmond.gui) SinglePropFilter (class in schrodinger.structutils.filter) SingleSmartsFilter (class in schrodinger.structutils.filter) singleton() (in module schrodinger.application.desmond.depictor) Site (class in schrodinger.application.desmond.cms) site (schrodinger.infra.phase.PhpSiteWithAtoms attribute) site() (schrodinger.application.desmond.cms.Cms method) site_matches (schrodinger.structutils.sitealign.BindingSiteAligner attribute) siteDeselected() (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog method) siteIndices (schrodinger.infra.phase.PhpSiteConstraint attribute) (schrodinger.infra.phase.PhpSiteMaskGroup attribute) SiteMatchLookup (class in schrodinger.structutils.sitealign) siteNumber (schrodinger.infra.phase.PhpDeltaHypoSite attribute) (schrodinger.infra.phase.PhpSiteMaskData attribute) sitePicked() (schrodinger.application.matsci.siteselector.siteselector.SiteRadioButton method) SiteRadioButton (class in schrodinger.application.matsci.siteselector.siteselector) siteSelected() (schrodinger.application.matsci.siteselector.siteselector.SiteSelectionDialog method) SiteSelectionDialog (class in schrodinger.application.matsci.siteselector.siteselector) SiteStatusOff (schrodinger.infra.phase.PhpSite attribute) SiteStatusOn (schrodinger.infra.phase.PhpSite attribute) siteToStrings() (schrodinger.infra.phase.PhpProject method) siteType (schrodinger.infra.phase.PhpDeltaHypoSite attribute) (schrodinger.infra.phase.PhpSiteMaskData attribute) siteTypes (schrodinger.infra.phase.PhpSiteConstraint attribute) siteUnpicked() (schrodinger.application.matsci.siteselector.siteselector.SiteRadioButton method) size (schrodinger.analysis.reaction.ReagentSource attribute) SIZE (schrodinger.application.matsci.siteselector.siteselector.LinearSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedOctahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.OrderedSquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.SquarePlanarSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TetrahedralSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalBipyramidalSiteSelector attribute) (schrodinger.application.matsci.siteselector.siteselector.TrigonalPlanarSiteSelector attribute) size() (schrodinger.analysis.reaction.ReagentClass method) (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.IntStream method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.packages.msys.Graph method) (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmbitset.Bitset method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.infra.phase.PhpSortCapperDoubleDecreasing method) (schrodinger.infra.phase.PhpSortCapperDoubleIncreasing method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) sizeHint() (schrodinger.application.desmond.fep_scholar_util.FEPStructureObject method) (schrodinger.application.jaguar.gui.utils.PropertiesTableWidget method) sizeHintForColumn() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabTableView method) SketchDialog (class in schrodinger.application.matsci.builderwidgets) SketcherBox (class in schrodinger.application.matsci.builderwidgets) sketchStructure() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) Skip (class in schrodinger.application.matsci.genetic_optimization.genetic_optimization) skip() (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.packages.msys.molfile.FrameIter method) skip_if() (in module schrodinger.infra.util) skipCM1A() (schrodinger.infra.fast3d.Volumizer method) skipinitialspace (schrodinger.application.canvas.utils.chm_bluebird attribute) (schrodinger.application.canvas.utils.chm_excel attribute) skipOffTokenChannels() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) skipOffTokenChannelsReverse() (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) Slab (class in schrodinger.application.matsci.shapes) SLAB_THRESHOLD (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) SliceParams (class in schrodinger.application.desmond.packages.energygroup) SlicePlot (class in schrodinger.application.matsci.sliceplot) sliceProp() (in module schrodinger.infra.propedit) SlidableHLine (class in schrodinger.application.bioluminate.sliderchart) SlidableLine (class in schrodinger.application.bioluminate.sliderchart) SlidableVLine (class in schrodinger.application.bioluminate.sliderchart) SliderchartVLClass (class in schrodinger.application.matsci.mswidgets) SliderPlot (class in schrodinger.application.bioluminate.sliderchart) slot() (schrodinger.models.mappers.Target method) slugify() (in module schrodinger.application.jaguar.file_logger) sm_geometry() (in module schrodinger.application.jaguar.textparser) SMAGGLASS (schrodinger.maestro.markers.Icons attribute) SMALL (schrodinger.protein.residue.STERIC_GROUP attribute) SMALL_MOLECULE (schrodinger.application.desmond.constants.FEP_TYPES attribute) SmallMoleculeReport (class in schrodinger.application.desmond.replica_sid_generator) smarts() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) SMARTS_KWARG (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) SMARTS_NONUNIQUE_BONDS (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) SMARTS_UNIQUE_PAIR (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) SMARTS_UNIQUE_TRIPLE_NORMAL (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) SmartsCriterion (class in schrodinger.utils.ligfilter) SmartsDirector (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.application.matsci.order_parameter_mod) SmartsException SmartsFilter (class in schrodinger.structutils.filter) SMARTSGroupData (class in schrodinger.application.matsci.smartsutils) SMARTSGroupError SMARTSNameValidator (class in schrodinger.application.matsci.smartsutilsgui) SmartsPattern (class in schrodinger.application.desmond.packages.msys) smiles() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) smiles2image() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) smiles2mol() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) smiles2svg() (schrodinger.application.desmond.image_generator.SchrodImageGenerator method) SmilesCsvReader (class in schrodinger.structure) SmilesCsvWriter (class in schrodinger.structure) SmilesErrorHandler (class in schrodinger.structutils.smilesfilter) SmilesGenerateError SmilesGenerator (class in schrodinger.structutils.smiles) SmilesReader (class in schrodinger.structure) SmilesStructure (class in schrodinger.structure) SmilesWriter (class in schrodinger.structure) smoothColors() (schrodinger.surface.Surface method) Sn2Failure sn_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sn_tot_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sol_charge (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_forward (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_forward_analytical_std (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_forward_bootstrap_std (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_forward_df_per_replica (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_forward_dg (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_forward_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_reverse (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_reverse_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_sliding (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_delta_g_sliding_err (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_end_time_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_ensemble (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_ff (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_rest_exchanges (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_result (schrodinger.application.desmond.fep_edge_data.FEPTorsions attribute) sol_salt_info (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_salt_molecules (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_sid_number_of_frames (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_sid_snapshot_times_ps (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_sid_trajectory_interval_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_sim_time (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_start_time_ns (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_temperature (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_timestep_interval (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_timestep_list (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_total_atoms (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_total_replicas (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sol_total_waters (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) solid (schrodinger.surface.Style attribute) (schrodinger.surface.Surface.Style attribute) solute_asl (schrodinger.trajectory.prody.ensemble.Ensemble attribute) solution_phase() (in module schrodinger.application.jaguar.textparser) SOLVATION (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget attribute) solvation() (in module schrodinger.application.jaguar.textparser) solvation_charge (schrodinger.structure._StructureAtom attribute) solvation_job() (in module schrodinger.application.jaguar.textparser) SolvationTab (class in schrodinger.application.jaguar.gui.tabs.solvation_tab) SolvationTabNoOptimized (class in schrodinger.application.jaguar.gui.tabs.solvation_tab) Solvent (class in schrodinger.application.jaguar.gui.utils) SOLVENT_EXPOSURE_TENDENCY (class in schrodinger.protein.residue) solvent_fullsystem_ct (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) SOLVENT_HOTREGION (schrodinger.application.desmond.constants.REST_PROPERTIES attribute) SOLVENT_MODELS (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) SolventAccessibleSurfaceArea (class in schrodinger.application.desmond.packages.analysis) SolventAccessibleSurfaceAreaByResidue (class in schrodinger.application.desmond.packages.analysis) SolventDialog (class in schrodinger.application.matsci.mswidgets) SolventError solventKeywordsChanged() (schrodinger.application.matsci.mswidgets.CompactSolventSelector method) solventModelChanged() (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab method) SolventPkaTab (class in schrodinger.application.jaguar.gui.tabs.solvation_tab) SOLVENTS (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab attribute) SolventTab (class in schrodinger.application.jaguar.gui.tabs.solvation_tab) solventTypeChanged() (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab method) sort() (schrodinger.application.bioluminate.protein_report_widget.DataModel method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.protein.alignment.BaseAlignment method) (schrodinger.structutils.sort.StructureFileSorter method) sort_atoms() (in module schrodinger.application.desmond.automatic_analysis_generator) sort_atoms_by_dist() (in module schrodinger.application.matsci.nano.xtal) sort_by_centroid_distance() (in module schrodinger.application.jaguar.autots_rmsd) sort_file() (in module schrodinger.structutils.sort) sort_file_in_memory() (in module schrodinger.structutils.sort) sort_index() (schrodinger.application.licensing.flexlm.Feature method) sort_key() (schrodinger.structutils.analyze.Ligand method) sort_posre() (in module schrodinger.application.desmond.cms) SORT_ROLE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel attribute) sortBondableAtomsByGroups() (schrodinger.structutils.assignbondorders.AssignBondOrders method) sortByProperties() (schrodinger.application.glide.glideanalysis.PoseLibrary method) sorted() (schrodinger.application.desmond.packages.msys.System method) sorted_hosts() (in module schrodinger.job.jobcontrol) sorted_hypo_structures() (in module schrodinger.application.phase.hypothesis) sortEntryCheck() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) sortFirstThreeOfGroup() (schrodinger.structutils.assignbondorders.AssignBondOrders method) sortInterTitle() (schrodinger.application.glide.glideanalysis.PoseLibrary method) sortIntraTitle() (schrodinger.application.glide.glideanalysis.PoseLibrary method) sortPoses() (schrodinger.application.glide.glideanalysis.PoseLibrary method) sortRows() (schrodinger.infra.table.Table method) Source (class in schrodinger.application.desmond.packages.traj) source() (schrodinger.application.desmond.packages.traj.Frame method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesProxyModel method) source_color (schrodinger.surface.ColorBy attribute) (schrodinger.surface.Surface.ColorBy attribute) source_index (schrodinger.structutils.rgroup_enumerate.RGroup attribute) SPACE_GROUP (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) SPACE_GROUP_ID (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) SPACE_GROUP_ID_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) SPACE_GROUP_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) SPACE_GROUP_SETTING (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) SpaceGroup (class in schrodinger.application.matsci.nano.xtal) SpaceGroups (class in schrodinger.application.matsci.nano.xtal) SpatialHash (class in schrodinger.application.desmond.packages.msys) Spear (class in schrodinger.structutils.ringspear) spear_indexes (schrodinger.structutils.ringspear.Spear attribute) SpearRing (class in schrodinger.structutils.ringspear) Spec (class in schrodinger.application.ligprep.ionizer) spec_description (schrodinger.job.launchapi.JobSpecificationKeyError attribute) (schrodinger.job.launchapi.RuntimeParametersKeyError attribute) (schrodinger.job.launchapi.SpecificationKeyError attribute) (schrodinger.job.launchapi.TaskSpecificationKeyError attribute) SPEC_TEMPLACE_MAP (schrodinger.application.matsci.qexsd.qespresso.converters.TD_spctInConverter attribute) specialStateTransition() (schrodinger.application.desmond.antlr3.dfa.DFA method) SPECIES (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) (schrodinger.application.bioluminate.antibody.search_results_table.SplitColumns attribute) species_changed (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector attribute) speciesChanged() (schrodinger.application.matsci.clusterstructgui.MonomerSpeciesSelector method) SpeciesData (class in schrodinger.application.matsci.clusterstruct) SpecificationKeyError SpectatorMoleculeError SPECTRUM_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) SPECTRUM_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) SpectrumDocument (class in schrodinger.application.matsci.qexsd.qespresso.documents) Sphere (class in schrodinger.application.matsci.shapes) (class in schrodinger.graphics3d.sphere) SPHERE_COLOR (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) (schrodinger.application.phase.phase_markers.PhaseTolMarkers attribute) (schrodinger.application.phase.phase_markers.PhaseXvolMarkers attribute) SPHERE_OPACITY (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) (schrodinger.application.phase.phase_markers.PhaseTolMarkers attribute) (schrodinger.application.phase.phase_markers.PhaseXvolMarkers attribute) sphere_overlap_volume() (in module schrodinger.structutils.interactions.steric_clash) SPHERE_RADII (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) SPHERE_RESOLUTION (schrodinger.application.phase.phase_markers.PhaseSphereMarkers attribute) SphereCore (class in schrodinger.graphics3d.sphere) SPIN_LSDA_ID (schrodinger.application.matsci.espresso.qeinput.SpinType attribute) SPIN_MULT (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) spin_mult (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) SPIN_MULT (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) spin_mult (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) SPIN_NON_LSDA_ID (schrodinger.application.matsci.espresso.qeinput.SpinType attribute) spin_splitting_precision (schrodinger.application.jaguar.results.JaguarResults attribute) spin_splitting_score() (in module schrodinger.application.jaguar.textparser) SpinExcitedStateController (class in schrodinger.application.jaguar.gui.theory_tab_widgets) SpinTreatment (class in schrodinger.application.jaguar.gui.utils) spinTreatmentChanged (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget attribute) SpinTreatmentWidget (class in schrodinger.application.jaguar.gui.theory_tab_widgets) SpinType (class in schrodinger.application.matsci.espresso.qeinput) SPLAT (schrodinger.application.jaguar.output.JaguarOutput attribute) split() (in module schrodinger.infra.propedit) split_ct() (in module schrodinger.application.desmond.remd) split_file() (in module schrodinger.structutils.sort) split_shadow_bond_tag() (in module schrodinger.application.matsci.coarsegrain) split_structure_files() (in module schrodinger.application.jaguar.input) split_type_name() (in module schrodinger.application.matsci.cgforcefield) SplitColumns (class in schrodinger.application.bioluminate.antibody.search_results_table) splitext() (in module schrodinger.utils.fileutils) splitIntoComponents() (schrodinger.application.matsci.rxn_channel.rxn_channel.Reactants method) splitJobOutputs() (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) splitMaskValue() (schrodinger.infra.phase.PhpSiteMask static method) SplitProxyModel (class in schrodinger.application.bioluminate.antibody.search_results_table) SplitTable (class in schrodinger.application.bioluminate.antibody.search_results_table) splitTriangularGroup() (schrodinger.structutils.assignbondorders.AssignBondOrders method) spmc() (schrodinger.application.macromodel.utils.ComUtil method) SPRING (schrodinger.maestro.markers.Icons attribute) SQUARE (schrodinger.application.matsci.nano.plane.CrystalPlane attribute) SQUARE_PLANAR (in module schrodinger.application.matsci.buildcomplex) SQUARE_PLANAR_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) squared_centroid_distance() (in module schrodinger.structutils.interactions.pi) SquarePlanarSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) sr_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) sr_tot_prop (schrodinger.application.mopac.results71.MopacResults71 attribute) ss_prediction_psipred (schrodinger.protein.residue.Residue attribute) ss_prediction_sspro (schrodinger.protein.residue.Residue attribute) ssa_type (schrodinger.protein.sequence.SecondaryStructure attribute) sse_limits_lambda0 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) sse_limits_lambda1 (schrodinger.application.desmond.fep_edge_data.FEPEdgeData attribute) ssh_check() (in module schrodinger.job.host_check) st (schrodinger.structutils.analyze.Ligand attribute) st_matches_criteria() (in module schrodinger.utils.ligfilter) st_to_graph() (schrodinger.application.jaguar.structure_isomorphism.BaseAtomMapper method) STACK_DIRECTION (schrodinger.application.matsci.nano.sheet.HoneycombBilayers attribute) stackBilayers() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) STACKTYPES (schrodinger.application.matsci.nano.constants.Constants attribute) Stage (class in schrodinger.pipeline.stage) StageControlButton (class in schrodinger.application.matsci.mswidgets) StageData (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) StageFrame (class in schrodinger.application.matsci.mswidgets) StageJob (class in schrodinger.pipeline.pipeline) StageKeywords (class in schrodinger.application.matsci.jaguar_multistage_workflow_utils) STANDARD_AAS (schrodinger.structutils.interactions.salt_bridge.SaltBridgeFinder attribute) STANDARD_SEARCH_ALONG (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateMixin attribute) StandardPanel (class in schrodinger.application.jaguar.gui.base_panel) StandardPanelNoInputTab (class in schrodinger.application.jaguar.gui.base_panel) StandardStatusMixin (class in schrodinger.application.jaguar.gui.base_panel) start (schrodinger.protein.annotation.AntibodyCDR attribute) START (schrodinger.tasks.jobtasks.RunMode attribute) start() (in module schrodinger.application.glide.http_server) (schrodinger.application.desmond.fep_gui.PickAtomToggle method) (schrodinger.application.desmond.fep_gui.PickBondToggle method) (schrodinger.application.desmond.feputils.LabelSpinner method) (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) (schrodinger.application.desmond.feputils.ProteinProcessManager method) (schrodinger.application.desmond.xvfbwrapper.Xvfb method) (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.jaguar.gui.base_panel.InputTabJobMixin method) (schrodinger.application.jaguar.gui.base_panel.NoInputTabJobMixin method) (schrodinger.application.jaguar.gui.base_panel.UseConsistentOrbitalsMixin method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.tasks.jobtasks.AbstractJobTask method) (schrodinger.tasks.runners.TaskRunner method) (schrodinger.tasks.tasks.AbstractTask method) (schrodinger.tasks.tasks_.AbstractFunctionTask method) (schrodinger.tasks.tasks_.AbstractTask method) (schrodinger.tasks.tasks_.SubprocessCmdTask method) start_geometry() (in module schrodinger.application.jaguar.textparser) start_of_program() (in module schrodinger.application.jaguar.textparser) start_picking() (in module schrodinger.maestro.maestro) start_str() (schrodinger.application.licensing.flexlm.Feature method) START_VAL (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) startCommand() (schrodinger.application.desmond.gui.GuiApp method) Starter (class in schrodinger.application.desmond.starter.starter) startErrorQueuing() (schrodinger.structure.FormatReader method) startFailed (schrodinger.tasks.runners.TaskRunner attribute) STARTING (schrodinger.tasks.tasks_.Status attribute) startLoading() (schrodinger.application.bioluminate.bwidgets.LoadingIcon method) startReadyStages() (schrodinger.pipeline.pipeline.Pipeline method) startRequested (schrodinger.tasks.runners.TaskRunner attribute) startTask() (schrodinger.tasks.runners.TaskRunner method) stat_info (class in schrodinger.application.licensing.licadmin) state (schrodinger.job.queue.BaseJob attribute) stateChanged (schrodinger.tasks.runners.TaskRunner attribute) static() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) StatisticalSummary (class in schrodinger.analysis.enrichment) Status (class in schrodinger.application.licensing.licadmin) (class in schrodinger.tasks.tasks) (class in schrodinger.tasks.tasks_) (schrodinger.job.jobcontrol.Job attribute) status (schrodinger.tasks.tasks_.AbstractTask attribute) (schrodinger.tasks.tasks_.TaskManager attribute) status() (schrodinger.tasks.tasks.AbstractTask method) status_param (schrodinger.tasks.tasks.AbstractTask attribute) status_paramChanged (schrodinger.tasks.tasks.AbstractTask attribute) StatusBarDialog (class in schrodinger.application.livedesign.panel_components) statusChanged (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel attribute) (schrodinger.tasks.tasks.AbstractTask attribute) (schrodinger.tasks.tasks_.AbstractTask attribute) (schrodinger.tasks.tasks_.TaskManager attribute) statusOk() (schrodinger.application.mopac.mopac_results.MopacResults method) (schrodinger.application.mopac.results2012.MopacResults2012 method) (schrodinger.application.mopac.results71.MopacResults71 method) staying_atom (schrodinger.structutils.rgroup_enumerate.RGroup attribute) std (schrodinger.analysis.enrichment.StatisticalSummary attribute) std_neighbor_count() (in module schrodinger.application.matsci.mlearn.features) std_neighbor_ion() (in module schrodinger.application.matsci.mlearn.features) std_struct (schrodinger.application.matsci.espresso.qeoutput.OutStruct attribute) Step (class in schrodinger.application.matsci.jaguarworkflows) step_size (schrodinger.application.jaguar.scan.Scan attribute) stepBy() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) STEPDENSEPOINTS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) stepEnabled() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) STEPS (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanCoordinateColumns attribute) steps (schrodinger.application.jaguar.scan.Scan attribute) steps() (schrodinger.analysis.reaction.RouteNode method) stereo() (schrodinger.infra.fast3d.Engine method) (schrodinger.infra.fast3d.SingleConformerEngine method) stereo_change (schrodinger.infra.phase.PhpAlignCoreOptions attribute) stereo_change_action (schrodinger.infra.phase.PhpAlignCoreOptions attribute) stereoFailure() (schrodinger.infra.phase.PhpAlignCore method) stereomethods (schrodinger.utils.pymol.Mapping attribute) STERIC_GROUP (class in schrodinger.protein.residue) steric_group (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) StkFile (class in schrodinger.application.desmond.packages.msys.molfile) StkFile.Reader (class in schrodinger.application.desmond.packages.msys.molfile) stoichiometry() (in module schrodinger.application.jaguar.textparser) stop() (in module schrodinger.application.glide.http_server) (schrodinger.application.desmond.fep_gui.PickAtomToggle method) (schrodinger.application.desmond.fep_gui.PickBondToggle method) (schrodinger.application.desmond.feputils.LabelSpinner method) (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) (schrodinger.application.desmond.xvfbwrapper.Xvfb method) (schrodinger.application.glide.http_client.GlideServerManager method) (schrodinger.application.licensing.licadmin.LocalServerProcess method) stop_picking() (in module schrodinger.maestro.maestro) stopErrorQueuing() (schrodinger.structure.FormatReader method) stopLoading() (schrodinger.application.bioluminate.bwidgets.LoadingIcon method) stopPicking() (schrodinger.application.jaguar.gui.base_panel.CoordinateMarkerMixin method) (schrodinger.application.jaguar.gui.base_panel.OptimizationAndScanMixin method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateTab method) stopping_optimization() (in module schrodinger.application.jaguar.textparser) store_chorus_box_props() (in module schrodinger.application.matsci.desmondutils) (in module schrodinger.application.matsci.nano.xtal) str() (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker method) (schrodinger.application.desmond.fep_reporter.FEPReportMaker method) STRAND (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute) STRAND_BREAKING (schrodinger.protein.residue.BETA_STRAND_PROPENSITY attribute) STRAND_COLOR (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) STRAND_FORMING (schrodinger.protein.residue.BETA_STRAND_PROPENSITY attribute) StrEnum (class in schrodinger.surface) StrictProteinSequence (class in schrodinger.protein.sequence) String (class in schrodinger.application.desmond.enhsamp) string (schrodinger.application.desmond.packages.cui.LazyParser attribute) (schrodinger.application.desmond.packages.msys.InChI attribute) STRING (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.desmond.systype.TyperBase attribute) (schrodinger.application.desmond.systype.WatermapTyper attribute) string() (schrodinger.application.licensing.flexlm.LicenseLine method) (schrodinger.application.licensing.flexlm.Vendor method) string2measurement() (in module schrodinger.application.desmond.measurement) string_to_value() (in module schrodinger.application.matsci.jobutils) StringCleaner (class in schrodinger.application.matsci.jobutils) StringDatabaseCriterion (class in schrodinger.application.bioluminate.propfilter) StringParam (class in schrodinger.models.parameters) StringSearchFilterProxyModel (class in schrodinger.application.livedesign.panel_components) StringStream (in module schrodinger.application.desmond.antlr3.streams) StringStringMap (class in schrodinger.utils.mmutil) stringvector (class in schrodinger.infra.fast3d) strip_extension() (in module schrodinger.utils.fileutils) strip_lines() (in module schrodinger.application.jaguar.check_headers) strip_r() (in module schrodinger.application.canvas.utils) stripSideStructs() (schrodinger.application.matsci.amorphous.Monomer method) strongly_conserved (schrodinger.protein.annotation.Consensus attribute) Struc (class in schrodinger.application.desmond.fep_struc) struc (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntryTuple attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryTuplePka attribute) STRUC_DIFF_WARNING (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) StrucListModel (class in schrodinger.application.desmond.fep_gui) strucSourceChanged (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) Struct (class in schrodinger.application.desmond.packages.viparr1.viparr.viparr) struct (schrodinger.application.matsci.espresso.qeoutput.OutStruct attribute) StructAlign (class in schrodinger.structutils.structalign) StructInfo (class in schrodinger.application.report2d) structToOriginByFrag() (schrodinger.application.matsci.amorphous.PolymerToFragments method) StructuralInteractionFingerprintGenerator (class in schrodinger.structutils.interactionfp) Structure (class in schrodinger.structure) structure (schrodinger.application.mopac.mopac_results.MopacResults attribute) (schrodinger.application.mopac.results2012.MopacResults2012 attribute) (schrodinger.application.mopac.results71.MopacResults71 attribute) (schrodinger.project.ProjectRow attribute) (schrodinger.structure._AtomCollection attribute) (schrodinger.structure._StructureAtom attribute) structure_evaluator() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) structure_file_reader() (in module schrodinger.application.hitexpander) STRUCTURE_FILTERS (schrodinger.application.bioluminate.bwidgets.SequenceFileDialog attribute) structure_fpreader() (in module schrodinger.application.hitexpander) structure_is_open_shell() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) structure_sequences (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) structure_to_rdkit_smiles() (in module schrodinger.analysis.transformations) StructureAlchemist (class in schrodinger.application.matsci.enumeration) structureCbToggled() (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) structureChanged (schrodinger.application.jaguar.gui.tabs.base_tab.ProvidesStructuresMixin attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ParticipantView attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionParticipant attribute) (schrodinger.protein.sequence.Sequence attribute) structureChanged() (schrodinger.application.jaguar.gui.basis_selector.BasisSelector method) StructureFileSorter (class in schrodinger.structutils.sort) StructureFrame (class in schrodinger.application.matsci.reordergui) StructureGenome (class in schrodinger.application.matsci.genetic_optimization.genetic_optimization) StructureLabel (class in schrodinger.application.matsci.builderwidgets) StructureLauncher (class in schrodinger.application.mopac.structure_launchers) StructureLauncherError StructureListWidget (class in schrodinger.application.matsci.reordergui) StructurePic (class in schrodinger.application.matsci.reordergui) StructureReader (class in schrodinger.structure) Structures (class in schrodinger.pipeline.pipeio) structures (schrodinger.application.livedesign.data_classes.ReceptorLigandMap attribute) StructureSequence (class in schrodinger.protein.sequence) StructureType (class in schrodinger.application.matsci.espresso.qeinput) structureUpdated() (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabNoInputSelector method) StructureView (class in schrodinger.application.matsci.reordergui) StructureWriter (class in schrodinger.structure) STU (schrodinger.tasks.jobtasks.RunMode attribute) stub_license() (schrodinger.application.licensing.licadmin.LicenseResource method) Style (class in schrodinger.surface) style (schrodinger.structure._StructureAtom attribute) (schrodinger.structure._StructureBond attribute) (schrodinger.surface.Surface attribute) STYLE_NAMEMAP (schrodinger.application.desmond.gui.EnsembleTab attribute) sub_formula() (in module schrodinger.application.matsci.mswidgets) sub_matrix (schrodinger.protein.align.AbstractAligner attribute) SUB_OPTIONS (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Property attribute) SUB_TAB_NAME (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) SubprocessCmdTask (class in schrodinger.tasks.tasks_) SubprocessJob (class in schrodinger.job.queue) SubSetStage (class in schrodinger.pipeline.stages.filtering) SubstCoreDatabase (class in schrodinger.application.combiglide.corehop) substring() (schrodinger.application.desmond.antlr3.streams.ANTLRStringStream method) (schrodinger.application.desmond.antlr3.streams.CharStream method) Substructure (class in schrodinger.protein.pdbname) subTabChanged (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) SubTabMixin (class in schrodinger.application.jaguar.gui.base_panel) SubTabModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets) SubTabProxyModel (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets) SubTabRow (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets) subTabsVisible() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) SubTabTableView (class in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets) subtract_host_lists() (in module schrodinger.pipeline.pipeline) succeeded() (schrodinger.job.jobcontrol.Job method) suggestReagentClasses() (schrodinger.analysis.reaction.Reaction method) summarize() (schrodinger.structutils.smilesfilter.FilterReporter method) summarize_pkas() (schrodinger.protein.assignment.ProtAssign method) summary (schrodinger.protein.analysis.Report.data_set attribute) summary() (schrodinger.application.licensing.licadmin.LicenseResource method) (schrodinger.job.jobcontrol.Job method) summaryText() (schrodinger.tasks.jobtasks.JobConfig method) SUPER (schrodinger.application.mopac.results71.MopacResults71 attribute) superimpose() (in module schrodinger.application.desmond.packages.topo) (in module schrodinger.structutils.rmsd) superimpose_bond() (in module schrodinger.structutils.rmsd) superimpose_cms() (in module schrodinger.application.desmond.packages.topo) superimpose_independent_molecules() (in module schrodinger.application.jaguar.autots_rmsd) SUPERIMPOSED_PROPERTY (schrodinger.structutils.sitealign.SiteMatchLookup attribute) superpose() (schrodinger.trajectory.prody.ensemble.Ensemble method) SuperpositionAligner (class in schrodinger.protein.align) supersedes() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.Package method) supported_basis_sets() (in module schrodinger.application.jaguar.jaguar_keyword_utils) SUPPORTED_BUILD_RESIDUES (schrodinger.application.bioluminate.protein.Mutator attribute) SUPPORTED_GEOMETRIES (in module schrodinger.application.matsci.buildcomplex) SUPPORTED_IN_EXTS (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) SUPPORTEDINEXTS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) Surface (class in schrodinger.application.matsci.nano.slab) (class in schrodinger.surface) surface (schrodinger.project.ProjectRow attribute) SURFACE (schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY attribute) surface (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) Surface.Color (class in schrodinger.surface) Surface.ColorBy (class in schrodinger.surface) Surface.ColorFrom (class in schrodinger.surface) Surface.Style (class in schrodinger.surface) surface_area (schrodinger.surface.Surface attribute) surface_cmd (schrodinger.utils.pymol.Mapping attribute) surface_type (schrodinger.surface.Surface attribute) SURFACE_TYPE_NAME (schrodinger.surface.Surface attribute) SurfaceDict (class in schrodinger.project_surface) Surfaces (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) surfaces (schrodinger.project.ProjectRow attribute) SURFACES_ORBITAL_HOMOMINUS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) SURFACES_ORBITAL_LUMOPLUS (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab attribute) SurfacesInterfaces (class in schrodinger.application.matsci.nano.surfaces_interfaces_mod) SurfacesSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) surfnet_gaps_supplier() (in module schrodinger.application.bindingsite.cavutils) suspend_auto_update_target() (schrodinger.models.mappers.AbstractParamMapper method) suspend_signals() (schrodinger.models.parameters.Param method) suspend_view_updates() (in module schrodinger.maestro.maestro) sval (schrodinger.utils.sea.Atom attribute) (schrodinger.utils.sea.Sea attribute) SwallowEnterFilter (class in schrodinger.application.livedesign.ld_base_classes) swap() (schrodinger.infra.fast3d.intvector method) (schrodinger.infra.fast3d.stringvector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector method) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 method) (schrodinger.infra.mmgpgpu.SwigIntVector method) (schrodinger.infra.mmgpgpu.SwigStringVector method) (schrodinger.infra.mmgpgpu.SwigUInt64Vector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector method) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 method) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair method) (schrodinger.infra.mmjob.SwigDoubleVector method) (schrodinger.infra.mmjob.SwigDoubleVector3 method) (schrodinger.infra.mmjob.SwigIntVector method) (schrodinger.infra.mmjob.SwigStringVector method) (schrodinger.infra.mmjob.SwigUInt64Vector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector method) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 method) (schrodinger.infra.mmjob.SwigVectorIntIntPair method) (schrodinger.infra.mmsurf.SwigDoubleVector method) (schrodinger.infra.mmsurf.SwigDoubleVector3 method) (schrodinger.infra.mmsurf.SwigIntVector method) (schrodinger.infra.mmsurf.SwigStringVector method) (schrodinger.infra.mmsurf.SwigUInt64Vector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector method) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 method) (schrodinger.infra.mmsurf.SwigVectorIntIntPair method) (schrodinger.utils.colorscheme.SwigDoubleVector method) (schrodinger.utils.colorscheme.SwigDoubleVector3 method) (schrodinger.utils.colorscheme.SwigIntVector method) (schrodinger.utils.colorscheme.SwigStringVector method) (schrodinger.utils.colorscheme.SwigUInt64Vector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector method) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 method) (schrodinger.utils.colorscheme.SwigVectorIntIntPair method) (schrodinger.utils.mmutil.StringStringMap method) swap_atoms() (schrodinger.protein.assignment.ProtAssign.changeable method) swap_ld_library_path (class in schrodinger.utils.env) swapPics() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) SwigDoubleVector (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) SwigDoubleVector3 (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) SwigIntIntPair (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) SwigIntVector (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) SwigPyIterator (class in schrodinger.infra.fast3d) (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.infra.phase) (class in schrodinger.utils.colorscheme) (class in schrodinger.utils.mmutil) SwigStringVector (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) SwigUInt64Vector (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) SwigUnsignedIntVector (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) SwigUnsignedIntVector2 (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) SwigVectorIntIntPair (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) swissprot (schrodinger.utils.fileutils.SeqFormat attribute) switchPair() (schrodinger.application.combiglide.connection_storage.ConnectionStorage method) SYMATOMS (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) SYMBOL_START (in module schrodinger.application.matsci.atomicsymbols) symlink() (in module schrodinger.application.desmond.util) SYMM_ITEMS (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) symmetrized_geometry() (in module schrodinger.application.jaguar.textparser) SYMMETRY (schrodinger.application.matsci.nano.xtal.SpaceGroups attribute) SYMMETRY_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) SYMMETRY_LABEL_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) SYMMETRY_OPERS (schrodinger.application.matsci.nano.xtal.SpaceGroup attribute) SYMMETRY_TITLE (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) SymmetryEquiv (class in schrodinger.application.matsci.nano.sheet) SymmetryType (class in schrodinger.application.matsci.espresso.qeinput) sync() (schrodinger.utils.preferences.Preferences method) sync_pbc() (in module schrodinger.application.matsci.espresso.utils) (in module schrodinger.application.matsci.nano.xtal) syncFeatureDef() (schrodinger.infra.phase.PhpProject method) Syntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) (class in schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) synthesizeCombinations() (schrodinger.analysis.reaction.Synthesizer method) Synthesizer (class in schrodinger.analysis.reaction) synthesizeRandomSample() (schrodinger.analysis.reaction.Synthesizer method) SYSBUILD (schrodinger.application.matsci.desmondutils.MSJStringer attribute) SysbuildMSJStringer (class in schrodinger.application.matsci.desmondutils) System (class in schrodinger.application.desmond.packages.msys) system (schrodinger.application.desmond.packages.msys.atomsel.Atomsel attribute) (schrodinger.application.desmond.packages.msys.Handle attribute) (schrodinger.application.desmond.packages.msys.Param attribute) (schrodinger.application.desmond.packages.msys.Term attribute) (schrodinger.application.desmond.packages.msys.TermTable attribute) system_file (schrodinger.analysis.transformations.TransformsRepository attribute) system_has_charged_particles() (in module schrodinger.application.matsci.coarsegrain) system_hosts_file() (in module schrodinger.application.licensing.licadmin) SystemBuilderInput (class in schrodinger.application.desmond.system_builder_inp) SystemDipoleDirector (class in schrodinger.application.desmond.packages.analysis) SysType (class in schrodinger.application.desmond.systype)

T

T_0 (class in schrodinger.application.desmond.simulation_block_test) tabChange() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) tabChanged() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) tabify_docking_window() (in module schrodinger.maestro.maestro) Table (class in schrodinger.infra.table) table (schrodinger.application.desmond.packages.msys.Param attribute) (schrodinger.application.desmond.packages.msys.Term attribute) table() (schrodinger.application.desmond.packages.msys.System method) table_file_ext (schrodinger.analysis.enrichment.Calculator attribute) TABLE_MODEL_CLASS (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab attribute) (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) table_names (schrodinger.application.desmond.packages.msys.System attribute) table_sep (schrodinger.analysis.enrichment.Calculator attribute) TABLE_VIEW_CLASS (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) TableModel (class in schrodinger.application.desmond.gui) TableRow (class in schrodinger.infra.table) tables (schrodinger.application.desmond.packages.msys.System attribute) TableSchemas() (in module schrodinger.application.desmond.packages.msys) TableView (class in schrodinger.application.bioluminate.antibody.search_results_table) tableViewClicked() (schrodinger.ui.chooseligand.ChooseLigandDialog method) TABS (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) tag (schrodinger.application.licensing.licerror.LicenseError attribute) TAG (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) tag() (schrodinger.utils.sea.Sea method) tag_gcmc_ligand() (in module schrodinger.application.desmond.gcmc_utils) tag_gcmc_ligand_file() (in module schrodinger.application.desmond.gcmc_utils) tag_gcmc_near_ligand() (in module schrodinger.application.desmond.gcmc_utils) tag_gcmc_near_ligand_file() (in module schrodinger.application.desmond.gcmc_utils) tag_protein() (in module schrodinger.application.desmond.fep_edge_data) tag_sim_map() (in module schrodinger.application.desmond.config) TAG_SPECS (class in schrodinger.application.desmond.config) tags (schrodinger.analysis.transformations.TransformsRepository attribute) TagSpec (class in schrodinger.application.desmond.config) taperingModified() (schrodinger.application.desmond.gui.InteractionTab method) tar_files() (in module schrodinger.utils.fileutils) tar_multisim_stage() (in module schrodinger.application.desmond.starter.generator.fep_plus) Target (class in schrodinger.models.mappers) target_namespace (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) target_pattern (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter attribute) TARGET_PLURAL_STRING (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) (schrodinger.application.livedesign.maestro_data_types.DockedPoses attribute) target_prefix (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) TARGET_SINGULAR_STRING (schrodinger.application.livedesign.maestro_data_types.BaseMaestroData attribute) (schrodinger.application.livedesign.maestro_data_types.Complexes attribute) (schrodinger.application.livedesign.maestro_data_types.DockedPoses attribute) TARGET_VAL (schrodinger.application.jaguar.gui.tabs.optimization_tab.ConstraintCoordinateColumns attribute) targetChanged (schrodinger.models.mappers.Target attribute) targetGetValue() (schrodinger.models.mappers.DefaultTargetMixin method) (schrodinger.models.mappers.MapperMixin method) TargetlessBase (class in schrodinger.application.livedesign.maestro_data_types) TargetParamMapper (class in schrodinger.models.mappers) targetSetValue() (schrodinger.models.mappers.DefaultTargetMixin method) (schrodinger.models.mappers.MapperMixin method) targetValueChanged (schrodinger.models.mappers.DefaultTargetMixin attribute) TASK_NAME (schrodinger.application.jaguar.gui.base_panel.BaseJaguarPanel attribute) taskEnded (schrodinger.tasks.runners.TaskRunner attribute) (schrodinger.tasks.tasks_.TaskManager attribute) TaskManager (class in schrodinger.tasks.tasks_) TaskRunner (class in schrodinger.tasks.runners) tasks() (schrodinger.tasks.runners.TaskRunner method) TaskSpecification (class in schrodinger.job.launchapi) TaskSpecificationBuilder (class in schrodinger.job.launchapi) TaskSpecificationError TaskSpecificationKeyError taskStarted (schrodinger.tasks.runners.TaskRunner attribute) (schrodinger.tasks.tasks_.TaskManager attribute) taskStatusChanged (schrodinger.tasks.tasks_.TaskManager attribute) TaskStatusMixin (class in schrodinger.application.jaguar.gui.base_panel) taskValueChanged (schrodinger.tasks.runners.TaskRunner attribute) TD_spctInConverter (class in schrodinger.application.matsci.qexsd.qespresso.converters) TD_TEMPLATE_MAP (schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter attribute) tddft_excitation_energies() (in module schrodinger.application.jaguar.textparser) tddft_excitation_energies_old() (in module schrodinger.application.jaguar.textparser) tddft_geopt_energy() (in module schrodinger.application.jaguar.textparser) TdDocument (class in schrodinger.application.matsci.qexsd.qespresso.documents) TdInputConverter (class in schrodinger.application.matsci.qexsd.qespresso.converters) tearDown() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) tearDownMaeWriter() (schrodinger.application.matsci.mecp_mod.EnergyAndGradients method) (schrodinger.application.matsci.mecp_mod.MECP method) temp (schrodinger.application.jaguar.utils.FreeEnergy attribute) TEMP (schrodinger.application.matsci.desmondutils.MSJStringer attribute) temp_dir() (in module schrodinger.application.desmond.packages.energygroup) TempAtom (class in schrodinger.application.canvas.r_group) Temperature (class in schrodinger.application.desmond.simulation_block_test) temperature_factor (schrodinger.structure._AtomCollection attribute) (schrodinger.structure._StructureAtom attribute) tempfilename (class in schrodinger.utils.fileutils) TempItemDelegate (class in schrodinger.application.desmond.gui) TemplateAtomMapFailure TemplateCombo (class in schrodinger.application.matsci.builderwidgets) TemplateGuessFailure TemplateManager (class in schrodinger.application.matsci.builderwidgets) templates_convert() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) templates_reorder_atoms() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_residue) templatesUpdated (schrodinger.application.matsci.builderwidgets.SketcherBox attribute) temporary_directory() (in module schrodinger.application.licensing.licadmin) temporary_preference() (in module schrodinger.maestro.commands) TemporaryOFStream (class in schrodinger.infra.mmgpgpu) (class in schrodinger.infra.mmjob) (class in schrodinger.infra.mmsurf) (class in schrodinger.utils.colorscheme) TempStructureFile (class in schrodinger.utils.fileutils) Term (class in schrodinger.application.desmond.packages.msys) term() (schrodinger.application.desmond.packages.msys.TermTable method) term_props (schrodinger.application.desmond.packages.msys.TermTable attribute) TERMDICT (schrodinger.application.matsci.nano.constants.Constants attribute) TERMFRAG (schrodinger.application.matsci.nano.constants.Constants attribute) TERMFRAGS (schrodinger.application.matsci.nano.constants.Constants attribute) terminate() (in module schrodinger.structutils.minimize) (schrodinger.application.desmond.antlr3.debug.DebugEventListener method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.feputils.ProteinProcessManager method) (schrodinger.application.jaguar.mmjag.MmJag static method) (schrodinger.application.matsci.mecp_mod.MECPStep method) (schrodinger.infra.mmbitset.Bitset static method) (schrodinger.infra.mminit.Initializer method) (schrodinger.infra.mmlist.mmlist static method) (schrodinger.infra.table.Table static method) (schrodinger.project.Project static method) (schrodinger.structutils.minimize.Minimizer static method) TerminateException terminateLattice() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) Terminator (class in schrodinger.application.matsci.amorphous) TERMINDICIES (schrodinger.application.matsci.nano.sheet.Grow attribute) TermKeywords (class in schrodinger.application.glide.xpdes) termMaestroWriter() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) TERMMAP (schrodinger.application.matsci.nano.constants.Constants attribute) termPropType() (schrodinger.application.desmond.packages.msys.TermTable method) terms (schrodinger.application.desmond.packages.msys.TermTable attribute) TermTable (class in schrodinger.application.desmond.packages.msys) Test (class in schrodinger.application.desmond.simulation_block_test) test() (in module schrodinger.ui.chooseligand) (in module schrodinger.utils.sea) test_pyqt() (in module schrodinger.utils.installation_check) TestApp (class in schrodinger.ui.chooseligand) TestJob (class in schrodinger.utils.installation_check) TestJobDJ (class in schrodinger.utils.installation_check) testModel() (schrodinger.infra.phase.PhpQSAR method) testQsarModel() (schrodinger.infra.phase.PhpProject method) testString() (schrodinger.application.jaguar.input.GenOptions static method) TestSuite (class in schrodinger.application.desmond.util) tet() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) TETRAGONAL_NAME (schrodinger.application.matsci.nano.xtal.CrystalSystems attribute) TETRAHEDRAL (in module schrodinger.application.matsci.buildcomplex) TETRAHEDRAL_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) TetrahedralSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) Tetrahedron (class in schrodinger.application.matsci.shapes) (class in schrodinger.graphics3d.polyhedron) Text (class in schrodinger.pipeline.pipeio) text (schrodinger.application.desmond.antlr3.recognizers.Lexer attribute) (schrodinger.application.desmond.antlr3.tokens.CommonToken attribute) (schrodinger.application.desmond.antlr3.tree.CommonTree attribute) text() (schrodinger.application.desmond.cwidget.EntryField method) (schrodinger.application.desmond.cwidget.FileEntry method) (schrodinger.application.desmond.fep_gui.CustomGPUComboBox method) textFromValue() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) TextParser (class in schrodinger.application.jaguar.textparser) textparser_trace() (in module schrodinger.application.jaguar.textparser) TextualStructure (class in schrodinger.structure) textUpdated() (schrodinger.application.jaguar.gui.basis_selector.BasisSelectorLineEdit method) TG_KEY (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) TG_PARAMETERS (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) TG_PROP (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) TG_UNITS (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) theory (schrodinger.application.qsite.input.Cut attribute) (schrodinger.application.qsite.input.HydrogenCap attribute) THEORY_COMBO_DFT (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_COMBO_HF (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_COMBO_LMP2 (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_INDICES (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) THEORY_TO_INDEX (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) theoryChanged() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) theoryOrBasisUpdated() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) TheoryTab (class in schrodinger.application.jaguar.gui.tabs.theory_tab) TheoryTabNoSoZora (class in schrodinger.application.jaguar.gui.tabs.theory_tab) TheoryTabOptimization (class in schrodinger.application.jaguar.gui.tabs.theory_tab) TheoryTabWithSoZora (class in schrodinger.application.jaguar.gui.tabs.theory_tab) theoryToInput() (schrodinger.application.jaguar.gui.base_panel.SubTabMixin method) theoryUpdated() (schrodinger.application.jaguar.gui.tabs.properties_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.MultipoleSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.SurfacesSubTab method) (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab method) THERMAL_SMEARING_OPTS (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) thermalSmearingChanged() (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab method) thermo_helper() (in module schrodinger.application.jaguar.textparser) ThermoCollection (class in schrodinger.application.jaguar.results) thermoMethodChanged() (schrodinger.application.desmond.gui.EnsembleTab method) ThermoProp (class in schrodinger.application.jaguar.results) third_quartile (schrodinger.analysis.enrichment.StatisticalSummary attribute) thisown (schrodinger.infra.fast3d.Engine attribute) (schrodinger.infra.fast3d.Generalizer attribute) (schrodinger.infra.fast3d.LigPrep3Volumizer attribute) (schrodinger.infra.fast3d.SingleConformerEngine attribute) (schrodinger.infra.fast3d.SwigPyIterator attribute) (schrodinger.infra.fast3d.Volumizer attribute) (schrodinger.infra.fast3d.intvector attribute) (schrodinger.infra.fast3d.stringvector attribute) (schrodinger.infra.licensing.License attribute) (schrodinger.infra.licensing.MMlic3AutoExitOverride attribute) (schrodinger.infra.licensing.MMlic3_Init attribute) (schrodinger.infra.mmgpgpu.SwigDoubleVector attribute) (schrodinger.infra.mmgpgpu.SwigDoubleVector3 attribute) (schrodinger.infra.mmgpgpu.SwigIntIntPair attribute) (schrodinger.infra.mmgpgpu.SwigIntVector attribute) (schrodinger.infra.mmgpgpu.SwigPyIterator attribute) (schrodinger.infra.mmgpgpu.SwigStringVector attribute) (schrodinger.infra.mmgpgpu.SwigUInt64Vector attribute) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector attribute) (schrodinger.infra.mmgpgpu.SwigUnsignedIntVector2 attribute) (schrodinger.infra.mmgpgpu.SwigVectorIntIntPair attribute) (schrodinger.infra.mmgpgpu.ifstream attribute) (schrodinger.infra.mmgpgpu.istream attribute) (schrodinger.infra.mmgpgpu.ofstream attribute) (schrodinger.infra.mmgpgpu.ostream attribute) (schrodinger.infra.mmjob.JobLaunchOptions attribute) (schrodinger.infra.mmjob.SwigDoubleVector attribute) (schrodinger.infra.mmjob.SwigDoubleVector3 attribute) (schrodinger.infra.mmjob.SwigIntIntPair attribute) (schrodinger.infra.mmjob.SwigIntVector attribute) (schrodinger.infra.mmjob.SwigPyIterator attribute) (schrodinger.infra.mmjob.SwigStringVector attribute) (schrodinger.infra.mmjob.SwigUInt64Vector attribute) (schrodinger.infra.mmjob.SwigUnsignedIntVector attribute) (schrodinger.infra.mmjob.SwigUnsignedIntVector2 attribute) (schrodinger.infra.mmjob.SwigVectorIntIntPair attribute) (schrodinger.infra.mmjob.ifstream attribute) (schrodinger.infra.mmjob.istream attribute) (schrodinger.infra.mmjob.ofstream attribute) (schrodinger.infra.mmjob.ostream attribute) (schrodinger.infra.mmsurf.SwigDoubleVector attribute) (schrodinger.infra.mmsurf.SwigDoubleVector3 attribute) (schrodinger.infra.mmsurf.SwigIntIntPair attribute) (schrodinger.infra.mmsurf.SwigIntVector attribute) (schrodinger.infra.mmsurf.SwigPyIterator attribute) (schrodinger.infra.mmsurf.SwigStringVector attribute) (schrodinger.infra.mmsurf.SwigUInt64Vector attribute) (schrodinger.infra.mmsurf.SwigUnsignedIntVector attribute) (schrodinger.infra.mmsurf.SwigUnsignedIntVector2 attribute) (schrodinger.infra.mmsurf.SwigVectorIntIntPair attribute) (schrodinger.infra.mmsurf.ifstream attribute) (schrodinger.infra.mmsurf.istream attribute) (schrodinger.infra.mmsurf.ofstream attribute) (schrodinger.infra.mmsurf.ostream attribute) (schrodinger.infra.phase.PhpAlignCore attribute) (schrodinger.infra.phase.PhpAlignCoreOptions attribute) (schrodinger.infra.phase.PhpAtomClassDescriptions attribute) (schrodinger.infra.phase.PhpComplex attribute) (schrodinger.infra.phase.PhpConfOptions attribute) (schrodinger.infra.phase.PhpDatabaseFp attribute) (schrodinger.infra.phase.PhpDeNovoPharm attribute) (schrodinger.infra.phase.PhpDeltaHypo attribute) (schrodinger.infra.phase.PhpDeltaHypoSite attribute) (schrodinger.infra.phase.PhpExclVol attribute) (schrodinger.infra.phase.PhpExclVolSphere attribute) (schrodinger.infra.phase.PhpFastShape attribute) (schrodinger.infra.phase.PhpFastShapePair attribute) (schrodinger.infra.phase.PhpFeatureClassDescriptions attribute) (schrodinger.infra.phase.PhpFeatureData attribute) (schrodinger.infra.phase.PhpFeatureDefinition attribute) (schrodinger.infra.phase.PhpFeatureFinder attribute) (schrodinger.infra.phase.PhpFeaturePattern attribute) (schrodinger.infra.phase.PhpFeatureRules attribute) (schrodinger.infra.phase.PhpFragPair attribute) (schrodinger.infra.phase.PhpHiCluster attribute) (schrodinger.infra.phase.PhpHiClusterPair attribute) (schrodinger.infra.phase.PhpHypoAdaptor attribute) (schrodinger.infra.phase.PhpHypoOptimizer attribute) (schrodinger.infra.phase.PhpHypoOptimizerSettings attribute) (schrodinger.infra.phase.PhpIntCoord attribute) (schrodinger.infra.phase.PhpLicenseCoreHopping attribute) (schrodinger.infra.phase.PhpLicenseDBCreate attribute) (schrodinger.infra.phase.PhpLicenseDBSearch attribute) (schrodinger.infra.phase.PhpLicenseElements attribute) (schrodinger.infra.phase.PhpLicenseFeature attribute) (schrodinger.infra.phase.PhpLicenseGeneric attribute) (schrodinger.infra.phase.PhpLicensePartition attribute) (schrodinger.infra.phase.PhpLicenseQSAR attribute) (schrodinger.infra.phase.PhpLicenseScoring attribute) (schrodinger.infra.phase.PhpLicenseSelectivity attribute) (schrodinger.infra.phase.PhpLicenseShapeScreen attribute) (schrodinger.infra.phase.PhpMMconfAdaptor attribute) (schrodinger.infra.phase.PhpMatchOptions attribute) (schrodinger.infra.phase.PhpOpenRingFinder attribute) (schrodinger.infra.phase.PhpOptionsParser attribute) (schrodinger.infra.phase.PhpPackedFp attribute) (schrodinger.infra.phase.PhpProject attribute) (schrodinger.infra.phase.PhpQSAR attribute) (schrodinger.infra.phase.PhpQSARModel attribute) (schrodinger.infra.phase.PhpScreener attribute) (schrodinger.infra.phase.PhpSite attribute) (schrodinger.infra.phase.PhpSiteConstrainer attribute) (schrodinger.infra.phase.PhpSiteConstraint attribute) (schrodinger.infra.phase.PhpSiteMask attribute) (schrodinger.infra.phase.PhpSiteMaskData attribute) (schrodinger.infra.phase.PhpSiteMaskGroup attribute) (schrodinger.infra.phase.PhpSiteWithAtoms attribute) (schrodinger.infra.phase.PhpSortCapperDoubleDecreasing attribute) (schrodinger.infra.phase.PhpSortCapperDoubleIncreasing attribute) (schrodinger.infra.phase.PhpStructureBus attribute) (schrodinger.infra.phase.PhpStructureReader attribute) (schrodinger.infra.phase.PhpStructureSplitter attribute) (schrodinger.infra.phase.PhpSubsetSplitter attribute) (schrodinger.infra.phase.PhpTextFileIterator attribute) (schrodinger.infra.phase.PhpTextFileReader attribute) (schrodinger.infra.phase.PhpVolCoords attribute) (schrodinger.infra.phase.SwigPyIterator attribute) (schrodinger.utils.colorscheme.ColorSchemeManager attribute) (schrodinger.utils.colorscheme.MM_CScheme attribute) (schrodinger.utils.colorscheme.MM_CSchemeRule attribute) (schrodinger.utils.colorscheme.MM_Color attribute) (schrodinger.utils.colorscheme.MM_ColorRamp attribute) (schrodinger.utils.colorscheme.MM_ColorRampHolder attribute) (schrodinger.utils.colorscheme.MM_Colormap attribute) (schrodinger.utils.colorscheme.MM_ColormapGL attribute) (schrodinger.utils.colorscheme.MMrange attribute) (schrodinger.utils.colorscheme.SwigDoubleVector attribute) (schrodinger.utils.colorscheme.SwigDoubleVector3 attribute) (schrodinger.utils.colorscheme.SwigIntIntPair attribute) (schrodinger.utils.colorscheme.SwigIntVector attribute) (schrodinger.utils.colorscheme.SwigPyIterator attribute) (schrodinger.utils.colorscheme.SwigStringVector attribute) (schrodinger.utils.colorscheme.SwigUInt64Vector attribute) (schrodinger.utils.colorscheme.SwigUnsignedIntVector attribute) (schrodinger.utils.colorscheme.SwigUnsignedIntVector2 attribute) (schrodinger.utils.colorscheme.SwigVectorIntIntPair attribute) (schrodinger.utils.colorscheme.ifstream attribute) (schrodinger.utils.colorscheme.istream attribute) (schrodinger.utils.colorscheme.ofstream attribute) (schrodinger.utils.colorscheme.ostream attribute) (schrodinger.utils.mmutil.StringStringMap attribute) (schrodinger.utils.mmutil.SwigPyIterator attribute)

THREAD_RUNNER_CLASS (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) thread_safe_evaluator() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) ThreadFunctionTask (class in schrodinger.tasks.tasks) (class in schrodinger.tasks.tasks_) ThreadSyntax (class in schrodinger.application.desmond.enhanced_sampling.FcnTypes) (class in schrodinger.application.desmond.packages.enhanced_sampling.FcnTypes) threshold (schrodinger.application.desmond.packages.timer.Timer.Args attribute) tileParticipants() (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) time (schrodinger.application.desmond.packages.traj.Frame attribute) (schrodinger.application.licensing.lmgrd_log_parser.event attribute) TIME (schrodinger.application.matsci.desmondutils.MSJStringer attribute) time_duration() (in module schrodinger.application.desmond.util) time_weighted_usage() (in module schrodinger.application.licensing.lmgrd_log_parser) timeout (schrodinger.infra.mmjob.JobLaunchOptions attribute) Timer (class in schrodinger.application.desmond.packages.timer) Timer.Args (class in schrodinger.application.desmond.packages.timer) TimeSanityException timestamp() (in module schrodinger.job.jobcontrol) TIMESTEP (schrodinger.application.matsci.desmondutils.MSJStringer attribute) timing() (in module schrodinger.utils.profiling) TITLE (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesColumns attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_hb.InputEntriesColumnsHB attribute) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.InputEntriesColumnsPka attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetColumns attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsColumns attribute) title (schrodinger.application.phase.hypothesis.PhaseHypothesis attribute) (schrodinger.project.EntryGroup attribute) (schrodinger.project.ProjectRow attribute) (schrodinger.protein.analysis.Report.data_set attribute) (schrodinger.structure.SmilesStructure attribute) (schrodinger.structure.Structure attribute) title() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) TITLE_BASE (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel attribute) (schrodinger.application.livedesign.ld_export.AbstractExportPanel attribute) (schrodinger.application.livedesign.ld_export.AbstractExportSetupPanel attribute) TITLE_KEY (schrodinger.application.matsci.nano.xtal.CheckInput attribute) (schrodinger.application.matsci.rxn_channel.rxn_channel.CheckInput attribute) title_rank_re (schrodinger.analysis.enrichment.Calculator attribute) titleChanged (schrodinger.protein.annotation.SequenceAnnotations attribute) titleCopiesAdded() (schrodinger.application.livedesign.export_controller.ExportController method) TitleEnrichmentCalculator (class in schrodinger.analysis.enrichment) TITLEKEY (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) (schrodinger.application.matsci.rxn_path.CheckInput attribute) TITLENAME (schrodinger.application.matsci.nano.sheet.HoneycombLattice attribute) (schrodinger.application.matsci.nano.tube.NanoTube attribute) tk_toplevel_add() (in module schrodinger.maestro.maestro) tk_toplevel_remove() (in module schrodinger.maestro.maestro) TM_METAL_LIST (in module schrodinger.application.matsci.atomicsymbols) TM_METAL_SET (in module schrodinger.application.matsci.atomicsymbols) TMLigandRowMixin (class in schrodinger.application.matsci.builderwidgets) to_dict() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) to_fortran() (in module schrodinger.application.matsci.qexsd.qespresso.converters) to_hostentry() (schrodinger.job.jobcontrol.Host method) to_hostfile() (in module schrodinger.job.jobcontrol) to_json() (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) to_rdkit() (in module schrodinger.thirdparty.rdkit_adapter) to_string() (schrodinger.application.desmond.measurement.Measurement method) to_style (schrodinger.structure._StructureBond attribute) ToArrayCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) ToArrayCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) toClustalFile() (schrodinger.protein.alignment.ProteinAlignment method) toDebugString() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) toDict() (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERDistanceConstraintPair method) (schrodinger.models.parameters.CompoundParam method) toDOT() (in module schrodinger.application.desmond.antlr3.extras) toFastaFile() (schrodinger.protein.alignment.ProteinAlignment method) toFastaString() (schrodinger.protein.alignment.ProteinAlignment method) toFastaStringList() (schrodinger.protein.alignment.ProteinAlignment method) toggleCounterions() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) toggleLigands() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) toggleRelaxModel() (schrodinger.application.desmond.gui.RelaxFrame method) toggleSelection() (schrodinger.application.phase.featureselector.FeatureModel method) toggleVisibility() (schrodinger.application.matsci.mswidgets.StageFrame method) toggleWaters() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) toJson() (schrodinger.application.desmond.packages.restrain.Restraints method) (schrodinger.models.json.JsonableClassMixin method) Token (class in schrodinger.application.desmond.antlr3.tokens) tokenizeDelimitedString() (in module schrodinger.infra.phase) tokenNames (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer attribute) (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser attribute) TokenRewriteStream (class in schrodinger.application.desmond.antlr3.streams) tokens (schrodinger.application.licensing.lmgrd_log_parser.event attribute) tokens() (in module schrodinger.application.licensing.licadmin) (schrodinger.application.licensing.licadmin.LicenseResource method) tokens_str() (schrodinger.application.licensing.flexlm.Feature method) TokenSource (class in schrodinger.application.desmond.antlr3.recognizers) tokenStartIndex (schrodinger.application.desmond.antlr3.tree.CommonTree attribute) tokenStopIndex (schrodinger.application.desmond.antlr3.tree.CommonTree attribute) TokenStream (class in schrodinger.application.desmond.antlr3.streams) tol (schrodinger.infra.phase.PhpSiteConstraint attribute) TolerableError TOLERANCE (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) TOOL_TIP_INSTRUCTIONS (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) TOOL_TIP_WRONG_EID (schrodinger.application.jaguar.gui.input_tab_widgets_pka.AtomSelectionDelegate attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.AtomSelectionDelegate attribute) TOOLTIP_TEXT (schrodinger.application.desmond.gui.EnsembleClassFrame attribute) TOOLTIPS (schrodinger.application.bioluminate.antibody.search_results_table.FullColumns attribute) TooManyGroupsError toOriginalString() (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) TopoError TopologicalDescriptors (class in schrodinger.application.canvas.topo_descriptors) topology (schrodinger.application.desmond.packages.msys.System attribute) tors_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer attribute) Torsion (class in schrodinger.application.desmond.packages.analysis) torsion_energy() (in module schrodinger.application.qsite.output) torsion_iterator() (in module schrodinger.structutils.analyze) TorsionAngler (class in schrodinger.application.matsci.amorphous) torsionEnergySurf() (schrodinger.application.matsci.amorphous.PolymerToFragments method) TorsionPotential (class in schrodinger.application.desmond.torsion_related) TORSIONROTATE (schrodinger.maestro.markers.Icons attribute) TORUS_RADII (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) TORUS_TUBE_RADII (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) TorusCore (class in schrodinger.graphics3d.torus) toString() (schrodinger.application.desmond.antlr3.debug.DebugTokenStream method) (schrodinger.application.desmond.antlr3.streams.CommonTokenStream method) (schrodinger.application.desmond.antlr3.streams.DeleteOp method) (schrodinger.application.desmond.antlr3.streams.ReplaceOp method) (schrodinger.application.desmond.antlr3.streams.RewriteOperation method) (schrodinger.application.desmond.antlr3.streams.TokenRewriteStream method) (schrodinger.application.desmond.antlr3.streams.TokenStream method) (schrodinger.application.desmond.antlr3.tokens.ClassicToken method) (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonErrorNode method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.CommonTreeNodeStream method) (schrodinger.application.desmond.antlr3.tree.Tree method) (schrodinger.application.desmond.antlr3.tree.TreeNodeStream method) (schrodinger.application.desmond.antlr3.treewizard.TreePattern method) (schrodinger.application.jaguar.input.GenOptions method) (schrodinger.application.jaguar.results.ScfIteration method) toStrings() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) toStringTree() (schrodinger.application.desmond.antlr3.tree.BaseTree method) (schrodinger.application.desmond.antlr3.tree.CommonTree method) (schrodinger.application.desmond.antlr3.tree.Tree method) TOT_CHARGE_KEY (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) TOT_MAG_KEY (schrodinger.application.matsci.espresso.qeinput.BandsType attribute) total (schrodinger.application.licensing.licadmin.stat_info attribute) total_active (schrodinger.job.queue.JobDJ attribute) total_added (schrodinger.job.queue.JobDJ attribute) total_atoms() (in module schrodinger.application.qsite.output) total_charge() (in module schrodinger.application.desmond.fep_net_charge) Total_charge() (in module schrodinger.utils.ligfilter) total_charge() (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) total_energy() (in module schrodinger.application.qsite.output) total_failed (schrodinger.job.queue.JobDJ attribute) total_finished (schrodinger.job.queue.JobDJ attribute) total_kinetic_energy() (in module schrodinger.application.qsite.output) total_lo_correction() (in module schrodinger.application.jaguar.textparser) total_mutations (schrodinger.application.bioluminate.protein.Mutator attribute) total_potential_energy() (in module schrodinger.application.qsite.output) total_tokens() (schrodinger.application.licensing.licadmin.LicenseResource method) total_weight (schrodinger.structure.Structure attribute) toTree() (schrodinger.application.desmond.antlr3.tree.RewriteRuleElementStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleNodeStream method) (schrodinger.application.desmond.antlr3.tree.RewriteRuleTokenStream method) ToWorldCoordinate() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) ToWorldCoordinateL() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) traceback (schrodinger.tasks.tasks_.ExceptionInfo attribute) TraceDebugEventListener (class in schrodinger.application.desmond.antlr3.debug) traceIn() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) traceOut() (schrodinger.application.desmond.antlr3.recognizers.BaseRecognizer method) (schrodinger.application.desmond.antlr3.recognizers.Lexer method) (schrodinger.application.desmond.antlr3.recognizers.Parser method) (schrodinger.application.desmond.antlr3.tree.TreeParser method) trackTask() (schrodinger.tasks.runners.TaskRunner method) TrajectoryUnreadableError trajFrames() (schrodinger.application.matsci.equilibrium_md.TrjBase method) TRANS (in module schrodinger.application.matsci.buildcomplex) trans_atoms_cart_to_fract() (in module schrodinger.application.matsci.nano.xtal) trans_atoms_fract_to_cart() (in module schrodinger.application.matsci.nano.xtal) trans_cart_to_frac_from_vecs() (in module schrodinger.application.matsci.nano.xtal) trans_cart_to_fract() (in module schrodinger.application.matsci.nano.xtal) trans_frac_to_cart_from_vecs() (in module schrodinger.application.matsci.nano.xtal) trans_fract_to_cart() (in module schrodinger.application.matsci.nano.xtal) transfer_subjob_files() (in module schrodinger.application.jaguar.file_logger) transform() (schrodinger.application.matsci.mlearn.base.BaseFeaturizer method) (schrodinger.application.matsci.mlearn.features.LatticeFeatures method) (schrodinger.infra.phase.PhpHypoAdaptor method) transform_atom_coordinates() (in module schrodinger.structutils.transform) transform_pbc() (in module schrodinger.application.matsci.nano.xtal) transform_structure() (in module schrodinger.application.ska) (in module schrodinger.structutils.transform) TransformsRepository (class in schrodinger.analysis.transformations) transformVectors() (schrodinger.application.matsci.nano.plane.CrystalPlane method) TRANSITION_STATE (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab attribute) TransitionStateMixin (class in schrodinger.application.jaguar.gui.tabs.transition_state_tab) TransitionStateTab (class in schrodinger.application.jaguar.gui.tabs.transition_state_tab) TRANSLATE (schrodinger.application.matsci.montecarlo.Metropolizer attribute) translate() (schrodinger.application.desmond.packages.msys.System method) translate_atoms() (in module schrodinger.application.matsci.nano.xtal) translate_center_to_origin() (in module schrodinger.structutils.transform) translate_centroid_to_origin() (in module schrodinger.structutils.transform) TRANSLATE_CHOICES (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) TRANSLATE_DEFAULT (schrodinger.application.matsci.nano.xtal.ParserWrapper attribute) translate_output_file_names() (in module schrodinger.application.desmond.config) translate_output_file_names_helper() (in module schrodinger.application.desmond.config) translate_rdkit_props_dict() (in module schrodinger.thirdparty.rdkit_adapter) translate_structure() (in module schrodinger.structutils.transform) translate_to_cell() (in module schrodinger.application.matsci.nano.xtal) translate_to_origin() (in module schrodinger.structutils.transform) translateCentroidToOrigin() (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) translateLayers() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) translateToPlane() (schrodinger.application.matsci.nano.particle.Nanoparticle method) translateTopLayer() (schrodinger.application.matsci.nano.interface_mod.Interface method) translateTube() (schrodinger.application.matsci.nano.tube.NanoTube method) translateVertices() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) translation_points_add() (in module schrodinger.maestro.maestro) translation_points_remove() (in module schrodinger.maestro.maestro) transmit() (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) transmute_atom() (in module schrodinger.application.matsci.buildcomplex) TRANSROT (schrodinger.maestro.markers.Icons attribute) treatSolventFromSolute() (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) Tree (class in schrodinger.application.desmond.antlr3.tree) tree_index() (schrodinger.application.desmond.reorder_atom.Node method) TreeAdaptor (class in schrodinger.application.desmond.antlr3.tree) treeAsString() (schrodinger.analysis.reaction.Node method) treeContextCallback() (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer method) treeify_indices() (in module schrodinger.application.desmond.reorder_atom) TreeNodeStream (class in schrodinger.application.desmond.antlr3.tree) TreeParser (class in schrodinger.application.desmond.antlr3.tree) TreePattern (class in schrodinger.application.desmond.antlr3.treewizard) TreePatternLexer (class in schrodinger.application.desmond.antlr3.treewizard) TreePatternParser (class in schrodinger.application.desmond.antlr3.treewizard) TreePatternTreeAdaptor (class in schrodinger.application.desmond.antlr3.treewizard) TreeRuleReturnScope (class in schrodinger.application.desmond.antlr3.tree) TreeVisitor (class in schrodinger.application.desmond.antlr3.tree) TreeWizard (class in schrodinger.application.desmond.antlr3.treewizard) tria() (schrodinger.application.matsci.espresso.utils.HighSymmetryKPath method) triangle_area() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) TRICLINIC_NAME (schrodinger.application.matsci.nano.xtal.CrystalSystems attribute) TRIGONAL_BIPYRAMIDAL (in module schrodinger.application.matsci.buildcomplex) TRIGONAL_BIPYRAMIDAL_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) TRIGONAL_NAME (schrodinger.application.matsci.nano.xtal.CrystalSystems attribute) TRIGONAL_PLANAR (in module schrodinger.application.matsci.buildcomplex) TRIGONAL_PLANAR_LOCATIONS (in module schrodinger.application.matsci.buildcomplex) TrigonalBipyramidalSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) TrigonalPlanarSiteSelector (class in schrodinger.application.matsci.siteselector.siteselector) trim_parser_skip_md() (in module schrodinger.application.matsci.equilibrium_md) trim_redundant_combinations() (schrodinger.protein.assignment.ProtAssign.hbond_cluster method) Triple (schrodinger.structure.BondType attribute) TripleMarker (class in schrodinger.maestro.markers) TrjBase (class in schrodinger.application.matsci.equilibrium_md) truncate_label() (in module schrodinger.application.desmond.feputils) truncate_solvate_protein() (in module schrodinger.application.desmond.system_builder_util) truncateProtein() (in module schrodinger.application.desmond.system_builder_util) try_import() (in module schrodinger.utils.moduleproxy) TS (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) ts_component_precision (schrodinger.application.jaguar.results.JaguarResults attribute) TSEnergyError TSFailure TSFrequencyError TUBE_OUT_MAE_NAME (schrodinger.application.matsci.nano.constants.Constants attribute) tube_radius (schrodinger.graphics3d.torus.MaestroTorus attribute) tubularizeNanoTubeSheet() (schrodinger.application.matsci.nano.tube.NanoTube method) TURN (schrodinger.application.desmond.packages.analysis.SecondaryStructure attribute) TURN_BREAKING (schrodinger.protein.residue.TURN_PROPENSITY attribute) TURN_FORMING (schrodinger.protein.residue.TURN_PROPENSITY attribute) turn_off_unwanted_wheel_events() (in module schrodinger.application.matsci.mswidgets) TURN_PROPENSITY (class in schrodinger.protein.residue) turn_propensity (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) (schrodinger.protein.residue.Residue attribute) two_e_terms() (in module schrodinger.application.jaguar.textparser) TwoGroupFingerprintAnalyzer (class in schrodinger.analysis.enrichment) TWOPI (schrodinger.application.matsci.nano.tube.NanoTube attribute) type (schrodinger.application.desmond.antlr3.tree.CommonTree attribute) TYPE (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Cylinder attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Parallelepiped attribute) (schrodinger.application.matsci.shapes.Sphere attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) type (schrodinger.structure._StructureBond attribute) type() (schrodinger.application.glide.glide.Constraint method) TYPE1NEIGHBOR (schrodinger.application.matsci.nano.sheet.Grow attribute) TYPE2NEIGHBOR (schrodinger.application.matsci.nano.sheet.Grow attribute) type_cast_jaguar_keywords() (in module schrodinger.application.matsci.reaction_workflow_utils) type_cast_reaction_wf_input() (in module schrodinger.application.matsci.reaction_workflow_utils) type_cast_seed() (in module schrodinger.application.matsci.reaction_workflow_utils) type_cms_file() (in module schrodinger.application.matsci.parserutils) type_cms_with_trj() (in module schrodinger.application.matsci.parserutils) type_element() (in module schrodinger.application.matsci.parserutils) type_file() (in module schrodinger.application.matsci.parserutils) type_forcefield() (in module schrodinger.application.matsci.parserutils) type_forcefield_and_get_number() (in module schrodinger.application.matsci.parserutils) type_json_file() (in module schrodinger.application.matsci.parserutils) TYPE_MAP (schrodinger.application.desmond.packages.energygroup.Energy attribute) type_nonnegative_float() (in module schrodinger.application.matsci.parserutils) type_nonnegative_int() (in module schrodinger.application.matsci.parserutils) type_positive_float() (in module schrodinger.application.matsci.parserutils) type_positive_int() (in module schrodinger.application.matsci.parserutils) type_ranged_int() (in module schrodinger.application.matsci.parserutils) type_ranged_num() (in module schrodinger.application.matsci.parserutils) type_structure_file() (in module schrodinger.application.matsci.parserutils) TYPEAANEIGHBOR (schrodinger.application.matsci.nano.sheet.Grow attribute) typer_cls (schrodinger.application.desmond.systype.TyperBase attribute) TyperBase (class in schrodinger.application.desmond.systype) types (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) TYPES_TO_CLASSES (schrodinger.application.matsci.order_parameter_mod.Descriptor attribute) TYPEZZNEIGHBOR (schrodinger.application.matsci.nano.sheet.Grow attribute)

U

UFFFailure UHF (schrodinger.application.mopac.results71.MopacResults71 attribute) UI (class in schrodinger.application.desmond.starter.ui.fep_plus) ui() (in module schrodinger.application.desmond.starter.ui.fep_plus) Ui_Dialog (class in schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_collection_viewer_ui) (class in schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_constraints_ui) (class in schrodinger.application.desmond.desmond_advanced_tab_ui) (class in schrodinger.application.jaguar.gui.ui.coordinate_dialog_ui) (class in schrodinger.application.livedesign.login_ui) (class in schrodinger.infra.exception_handler_dir.exception_dialog_ui) (class in schrodinger.ui.ligfilter_definition_dialog_ui) (class in schrodinger.ui.picking_dir.pick_constraint_res_no_maestro_dialog_ui) (class in schrodinger.ui.picking_dir.pick_lig_no_maestro_dialog_ui) (class in schrodinger.ui.picking_dir.pick_res_no_maestro_dialog_ui) Ui_Form (class in schrodinger.application.bioluminate.propfilter_ui) (class in schrodinger.application.bioluminate.protein_structure_quality_ui) (class in schrodinger.application.desmond.input_group_ui) (class in schrodinger.application.desmond.rest_tab_ui) (class in schrodinger.application.jaguar.gui.ui.input_hb_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.input_pka_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.input_std_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.input_sub_tabs.basis_set_ui) (class in schrodinger.application.jaguar.gui.ui.input_sub_tabs.charge_constraints_ui) (class in schrodinger.application.jaguar.gui.ui.input_top_ui) (class in schrodinger.application.jaguar.gui.ui.irc_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.irc_top_ui) (class in schrodinger.application.jaguar.gui.ui.molecule_pka_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.molecule_std_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.molecule_top_ui) (class in schrodinger.application.jaguar.gui.ui.multi_structures_ui) (class in schrodinger.application.jaguar.gui.ui.optimization_tab_ui) (class in schrodinger.application.jaguar.gui.ui.output_tab_ui) (class in schrodinger.application.jaguar.gui.ui.properties_tab_ui) (class in schrodinger.application.jaguar.gui.ui.reaction_molecules_tab_ui) (class in schrodinger.application.jaguar.gui.ui.reaction_properties_tab_ui) (class in schrodinger.application.jaguar.gui.ui.reaction_tab_ui) (class in schrodinger.application.jaguar.gui.ui.scan_tab_nextgeom_ui) (class in schrodinger.application.jaguar.gui.ui.scan_tab_ui) (class in schrodinger.application.jaguar.gui.ui.scf_tab_ui) (class in schrodinger.application.jaguar.gui.ui.solvation_gas_phase_ui) (class in schrodinger.application.jaguar.gui.ui.solvation_pka_ui) (class in schrodinger.application.jaguar.gui.ui.solvation_solvent_model_ui) (class in schrodinger.application.jaguar.gui.ui.solvent_tab_ui) (class in schrodinger.application.jaguar.gui.ui.theory_tab_ui) (class in schrodinger.application.jaguar.gui.ui.transition_state_bottom_ui) (class in schrodinger.application.jaguar.gui.ui.transition_state_top_ui) (class in schrodinger.application.livedesign.export_setup_ui) (class in schrodinger.application.livedesign.export_ui) (class in schrodinger.application.prime.gui.ui.analyze_energy_ui) (class in schrodinger.application.prime.gui.ui.environment_options_ui) (class in schrodinger.ui.ligfilter_ui) Ui_MainWindow (class in schrodinger.application.jaguar.gui.ui.edit_dialog_ui) UI_MODULE (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab attribute) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.charge_constraints.ChargeConstraintsSubTab attribute) UI_MODULES (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs attribute) (schrodinger.application.jaguar.gui.tabs.irc_tab.IrcTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab attribute) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka attribute) (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab attribute) (schrodinger.application.jaguar.gui.tabs.output_tab.OutputTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabIGO attribute) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_properties_tab.ReactionPropertiesTab attribute) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab attribute) (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTabNextGeom attribute) (schrodinger.application.jaguar.gui.tabs.scf_tab.ScfTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolvationTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventPkaTab attribute) (schrodinger.application.jaguar.gui.tabs.solvation_tab.SolventTab attribute) (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) (schrodinger.application.jaguar.gui.tabs.transition_state_tab.TransitionStateTab attribute) Ui_Widget (class in schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_cfc_ui) (class in schrodinger.application.combiglide.combenumdock_dir.cg_interactive_enum_dock_ui) (class in schrodinger.application.jaguar.gui.ui.excited_state_widget_ui) (class in schrodinger.application.jaguar.gui.ui.spin_treatment_widget_ui) UNAVAIL_VALUE_TYPES (schrodinger.application.livedesign.panel_components.ColumnCheckboxItem attribute) Unavailable (schrodinger.application.livedesign.maestro_data_types.Export3D attribute) UnavailableFingerprintType uncheckAll() (schrodinger.application.livedesign.panel_components.LDDataSelectionModel method) (schrodinger.application.livedesign.panel_components.LDDataSelectionTreeWidget method) UndefinedBondOperation UndefinedStereochemistry under_job_control() (in module schrodinger.job.jobcontrol) UNDO_REDO_TOOLBAR (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) UNEDITABLE (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets.BasisSetModel attribute) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintsModel attribute) unexpectedType (schrodinger.application.desmond.antlr3.exceptions.RecognitionException attribute) UNFOLDED_PROPERTY (schrodinger.application.bioluminate.protein.Mutator attribute) UNFOLDED_PROPERTY_PRIME (schrodinger.application.bioluminate.protein.Mutator attribute) ungroup() (schrodinger.project.ProjectRow method) UNIQUE (schrodinger.application.matsci.rxn_channel.rxn_channel.Constants attribute) unique() (in module schrodinger.application.desmond.util) unique_list() (in module schrodinger.application.desmond.fep_mapping) unique_smiles (schrodinger.structutils.analyze.Ligand attribute) UniqueSmartsDirector (class in schrodinger.application.matsci.order_parameter_mod) uniquesmiler() (in module schrodinger.utils.cgxutils) uniquify_titles() (in module schrodinger.application.combiglide.combenumdock) uniquify_titles_callback() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) UniquifyResults() (schrodinger.analysis.visanalysis.volumedatautils.DataPointLocator method) uniquifyTitles() (schrodinger.application.combiglide.combenumdock.collectionViewerModel method) UNIT_CELL_DENSITY_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) UNIT_CELL_FORMULA_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) UNIT_CELL_VOLUME_KEY (schrodinger.application.matsci.nano.xtal.Crystal attribute) unit_vector() (in module schrodinger.structutils.interactions.pi) unit_vector_points() (in module schrodinger.structutils.interactions.pi) UNITCELLINDEX (schrodinger.application.matsci.nano.sheet.HoneycombUnitCell attribute) UNKNOWN (schrodinger.application.desmond.systype.DesmondTyper attribute) (schrodinger.application.desmond.systype.McproTyper attribute) (schrodinger.application.jaguar.output.JaguarOutput attribute) UNKNOWN_UNITS (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) UnknownAppError UnknownChiralityError UnknownNameError UnknownPropertySuboptionError UnknownRuleError unmapAtom() (schrodinger.application.matsci.reordergui.StructureFrame method) unmapPair() (schrodinger.application.matsci.reordergui.ReorderAtomFrame method) unmatched_tors (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer attribute) unmatched_total (schrodinger.application.desmond.fep_edge_data.FEPTorsionsContainer attribute) unpack() (schrodinger.application.desmond.antlr3.dfa.DFA class method) unpackFp() (schrodinger.infra.phase.PhpDatabaseFp static method) unproductive() (in module schrodinger.application.matsci.genetic_optimization.genetic_optimization) UnreadableHostsFileException Unrestricted (schrodinger.application.jaguar.gui.utils.SpinTreatment attribute) unrestrictedAvailable() (schrodinger.application.jaguar.gui.theory_tab_widgets.SpinTreatmentWidget method) unselectRows() (schrodinger.infra.table.Table method) unset() (schrodinger.application.matsci.builderwidgets.StructureLabel method) (schrodinger.infra.mmbitset.Bitset method) unsign() (schrodinger.application.licensing.flexlm.Feature method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.licensing.flexlm.LicenseLine method) (schrodinger.application.licensing.flexlm.Package method) UnsupportedFormat UnsupportedOption UnsupportedOptionValue UnsupportedReaction UnwantedTokenException unwrap_lines() (in module schrodinger.application.jaguar.check_headers) unzip_project() (in module schrodinger.project) unzipArchive() (schrodinger.infra.phase.PhpProject method) unzipProject() (schrodinger.infra.phase.PhpProject method) UP_TO_MINDEX (schrodinger.application.matsci.nano.constants.Constants attribute) UP_TO_NINDEX (schrodinger.application.matsci.nano.constants.Constants attribute) update() (schrodinger.application.canvas.similaritygui.CanvasFingerprintSimilarityGUI method) (schrodinger.application.desmond.feputils.ProteinCheckLabelSpinner method) (schrodinger.application.desmond.gui.TableModel method) (schrodinger.application.desmond.rest_inp.RestInput method) (schrodinger.application.desmond.system_builder_util.DesmondBoxSize method) (schrodinger.application.jaguar.gui.input_tab_widgets.ProjEntry method) (schrodinger.application.jaguar.gui.input_tab_widgets_pka.ProjEntryPka method) (schrodinger.application.watermap.watermap_inp.WaterMapInput method) (schrodinger.graphics3d.polyhedron.Polyhedron method) (schrodinger.job.queue.BaseJob method) (schrodinger.job.queue.JobControlJob method) (schrodinger.job.queue.SubprocessJob method) (schrodinger.maestro.markers.LineMarker method) (schrodinger.project.Project method) (schrodinger.structure.Structure method) (schrodinger.utils.scollections.IdentityDict method) (schrodinger.utils.sea.Atom method) (schrodinger.utils.sea.List method) (schrodinger.utils.sea.Map method) update_atom_indices() (schrodinger.protein.assignment.ProtAssign.amide_changeable method) (schrodinger.protein.assignment.ProtAssign.amine_changeable method) (schrodinger.protein.assignment.ProtAssign.carboxyl_changeable method) (schrodinger.protein.assignment.ProtAssign.changeable method) (schrodinger.protein.assignment.ProtAssign.histidine_changeable method) (schrodinger.protein.assignment.ProtAssign.rotatable_changeable method) (schrodinger.protein.assignment.ProtAssign.water_changeable method)

update_cms() (in module schrodinger.application.desmond.packages.topo) update_cms_physical() (in module schrodinger.application.desmond.packages.topo) update_ct() (in module schrodinger.application.desmond.packages.topo) update_ct_box() (in module schrodinger.application.desmond.packages.topo) update_hypothesis_entry() (in module schrodinger.application.phase.phase_markers) (in module schrodinger.application.phase.pt_hypothesis) update_input_file_paths() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) update_internal_coords_to_vector_atoms() (schrodinger.protein.membrane.Membrane_Model method) update_msys() (in module schrodinger.application.desmond.packages.topo) update_pass_fail() (schrodinger.application.desmond.simulation_block_test.Test method) update_pdb_pbc() (in module schrodinger.application.matsci.desmondutils) update_props() (in module schrodinger.application.mopac.results2012) update_pseudo_residue_list() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr) update_surface_display() (in module schrodinger.maestro.maestro) update_templates() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge) update_templates_strict() (in module schrodinger.application.desmond.packages.viparr1.viparr.viparr_merge) updateAllAtomIndexMaps() (schrodinger.application.matsci.amorphous.PolymerToFragments method) updateAllConstraintsPB() (schrodinger.application.jaguar.gui.tabs.optimization_tab.OptimizationTab method) updateAndCheckMmJag() (schrodinger.application.jaguar.gui.base_panel.NoInputTabJobMixin method) updateAnimation() (schrodinger.application.desmond.feputils.LabelSpinner method) updateAnimationSize() (schrodinger.application.desmond.feputils.LabelSpinner method) updateAtomGroupButtons() (schrodinger.application.desmond.gui.AtomGroupFrame method) updateAtomNames() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow method) updateChannelDefReprs() (schrodinger.application.matsci.rxn_channel.rxn_channel.Channels method) updateCheckState() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) updateCoordinates() (schrodinger.application.matsci.montecarlo.MonteCarloMolecule method) (schrodinger.structutils.minimize.Minimizer method) updateDefinitionState() (schrodinger.ui.ligfilter.AddDefinitionDialog method) updateDefParts() (schrodinger.application.matsci.rxn_channel.rxn_channel.Reactants method) updateDialogKeys() (schrodinger.application.desmond.gui.AdvOptionsFrame method) updatedJobs() (schrodinger.job.queue.JobDJ method) updateEditorGeometry() (schrodinger.application.desmond.gui.AtomGroupDelegate method) (schrodinger.application.desmond.gui.PosResDelegate method) (schrodinger.application.desmond.gui.TempItemDelegate method) updateEnabled() (schrodinger.application.livedesign.panel_components.CascadingCheckboxItem method) updateEnsClassFromKey() (schrodinger.application.desmond.gui.EnsembleClassFrame method) updateEntryTitles() (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets.SubTabModel method) updateFeatureNames() (schrodinger.application.phase.featureselector.FeatureModel method) updateFractionals() (schrodinger.application.matsci.nano.xtal.Crystal method) updateFragids() (schrodinger.application.desmond.packages.msys.System method) updateFromDump() (schrodinger.pipeline.pipeline.StageJob method) updateFromKey() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.EnsembleClassFrame method) (schrodinger.application.desmond.gui.EnsembleTab method) (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.application.desmond.gui.IntegrationTab method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.MinOutputFrame method) (schrodinger.application.desmond.gui.MinimizerFrame method) (schrodinger.application.desmond.gui.OutputTab method) (schrodinger.application.desmond.gui.RandVelFrame method) (schrodinger.application.desmond.gui.RelaxFrame method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.gui.SimOptionsFrame method) updateFromVector() (schrodinger.protein.membrane.Membrane_Model method) updateFusedRingIdxsForNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) updateHypothesisFromEntry() (schrodinger.application.phase.phase_widgets.HypothesesListWidget method) updateInclExclState() (schrodinger.ui.ligfilter.AddDefinitionDialog method) updateInternalsForNewBonds() (schrodinger.application.matsci.coarsegrain.Internals method) updateJobdj() (schrodinger.pipeline.stage.Stage method) updateKey() (schrodinger.application.desmond.gui.AdvOptionsFrame method) (schrodinger.application.desmond.gui.AtomGroupFrame method) (schrodinger.application.desmond.gui.EnsembleClassFrame method) (schrodinger.application.desmond.gui.EnsembleTab method) (schrodinger.application.desmond.gui.IntegrationTab method) (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.MinOutputFrame method) (schrodinger.application.desmond.gui.MinimizerFrame method) (schrodinger.application.desmond.gui.OutputTab method) (schrodinger.application.desmond.gui.RandVelFrame method) (schrodinger.application.desmond.gui.RelaxFrame method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.application.desmond.gui.SimOptionsFrame method) updateKeywordEdit() (schrodinger.application.matsci.qualityslider.QualitySlider method) updateLabel() (schrodinger.application.matsci.mswidgets.StageFrame method) (schrodinger.application.matsci.siteselector.siteselector.SiteRadioButton method) updateLatticeBonding() (schrodinger.application.matsci.nano.sheet.HoneycombLattice method) updateLatticeProperties() (schrodinger.application.matsci.nano.xtal.Crystal method) updateLibraryCounts() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) updateLightColVisibility() (schrodinger.application.bioluminate.antibody.search_results_table.FullTable method) updateMapperWidgets() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) updateMaxjobsDefault() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) updateModel() (schrodinger.application.desmond.gui.InteractionTab method) (schrodinger.application.desmond.gui.MdcMiscTab method) (schrodinger.application.desmond.gui.RestraintsTab method) (schrodinger.models.mappers.AbstractParamMapper method) (schrodinger.models.parameters.ParamModel method) updateNow() (schrodinger.tasks.jobtasks.JobStatusLoop method) updateNumCPUsLabel() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) updateNumPickedResiduesLabel() (schrodinger.ui.picking.MaestrolessPickResidueDialog method) updateOrigAtomIdx() (schrodinger.application.matsci.amorphous.PolymerToFragments method) updateParams() (schrodinger.tasks.runners.TaskRunner method) updatePBC() (schrodinger.application.matsci.nano.sheet.HoneycombBilayers method) updatePBCBondOrders() (schrodinger.application.matsci.nano.xtal.PBCBonds method) updatePermanentPic() (schrodinger.application.desmond.feputils.LabelSpinner method) updatePosresButtons() (schrodinger.application.desmond.gui.RestraintsTab method) updateProperties() (schrodinger.application.matsci.chargegui.ChargePropertySelector method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.application.matsci.rxn_channel.rxn_channel.Products method) updatePropertiesTab() (schrodinger.application.jaguar.gui.base_panel.PropertiesMixin method) updatePropertiesTable() (schrodinger.application.jaguar.gui.tabs.properties_tab.PropertiesTabBase method) updatePropNames() (schrodinger.application.livedesign.ld_export.ExportThreadRunner method) updateRecentTemplateFile() (schrodinger.application.matsci.builderwidgets.SketcherBox method) updateResults() (schrodinger.application.canvas.clustergui.CanvasFingerprintClusterGUI method) updateSelection() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) updateSelections() (schrodinger.ui.residueselector.MutationSelectorFrame method) updateShape() (schrodinger.application.matsci.shapes.ConvexPolyhedron method) updateSite() (schrodinger.infra.phase.PhpHypoAdaptor method) updateSlider() (schrodinger.application.matsci.mswidgets.SliderchartVLClass method) updateStageCpus() (schrodinger.pipeline.pipeline.StageJob method) updateStageLabels() (schrodinger.application.matsci.mswidgets.MultiStageArea method) updateStagesCpus() (schrodinger.pipeline.pipeline.Pipeline method) updateStatusText() (schrodinger.tasks.jobtasks.AbstractJobTask method) updateStructureProperties() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.StructureGenome method) updateTables() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) updateTarget() (schrodinger.models.mappers.AbstractParamMapper method) (schrodinger.models.parameters.ParamModel method) (schrodinger.tasks.runners.TaskRunner method) updateTempFromKey() (schrodinger.application.desmond.gui.EnsembleClassFrame method) updateTemplatePolymerResidue() (schrodinger.application.matsci.amorphous.Monomer method) updateTemplates() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) updateText() (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.jaguar.gui.input_tab_widgets.UseFromCombo method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) updateTitle() (schrodinger.application.matsci.genetic_optimization.genetic_optimization.Skip method) updateTotalStructures() (schrodinger.application.jaguar.gui.tabs.scan_tab.ScanTab method) updateToWorkspace() (schrodinger.application.desmond.maestro.NewEntry method) updateVertices() (schrodinger.graphics3d.polyhedron.MaestroPolyhedronCore method) updateWithData() (schrodinger.application.matsci.espresso.qeinput.GenericType method) updateXvolMarker() (schrodinger.application.phase.phase_markers.PhaseMarkers method) UPFParser (class in schrodinger.application.matsci.espresso.utils) upload_ld_attachment() (in module schrodinger.application.livedesign.upload_utils) upload_ld_model() (in module schrodinger.application.livedesign.upload_utils) upper_bound() (schrodinger.utils.mmutil.StringStringMap method) UpperCaseValidator (class in schrodinger.application.jaguar.gui.basis_selector) URL (schrodinger.application.livedesign.ld_base_classes.LDInputType attribute) urlencode() (in module schrodinger.application.desmond.gchart) UsageError, [1] use_detached_jobs() (in module schrodinger.tasks.jobtasks) use_event_loop (schrodinger.application.livedesign.ld_base_classes.ImportExportThreadRunner attribute) use_gfactors (in module schrodinger.protein.analysis) USE_IN_SCREEN (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) use_jc_message() (in module schrodinger.job.queue) USE_PRIM_KEY (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) use_scanning_alignment (schrodinger.structutils.structalign.StructAlign attribute) USE_SYMM_KEY (schrodinger.application.matsci.espresso.qeinput.SymmetryType attribute) useADProjectedPointsChecked() (schrodinger.application.phase.phase_widgets.FeatureOptionsCombo method) UseConsistentOrbitalsMixin (class in schrodinger.application.jaguar.gui.base_panel) useConstraint() (schrodinger.application.glide.glide.Dock method) useCustomTemplate() (schrodinger.application.matsci.builderwidgets.ItemRowWithTemplates method) used (schrodinger.application.licensing.licadmin.stat_info attribute) used_space() (schrodinger.application.desmond.packages.traj.Source method) useDefaultTemplateDirectory() (schrodinger.application.matsci.builderwidgets.TemplateManager method) UseFrom (class in schrodinger.application.jaguar.gui.input_tab_widgets) UseFromCombo (class in schrodinger.application.jaguar.gui.input_tab_widgets) useFromComboChanged() (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) useLocalDriver() (schrodinger.job.app.App method) useParallelArg() (schrodinger.application.jaguar.gui.base_panel.MultiStructureMixin method) user (schrodinger.application.licensing.lmgrd_log_parser.event attribute) user_name (schrodinger.application.livedesign.data_classes.LDData attribute) userName() (schrodinger.structure.PropertyName method) userOutput() (schrodinger.pipeline.input.Writer method) users_default_template_filename() (in module schrodinger.application.jaguar.reactiq_input) useSchrodingerProduct() (schrodinger.job.launchapi.TaskSpecification method) useSchrodingerRun() (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) UseServer (class in schrodinger.application.licensing.flexlm) usesJobServer() (schrodinger.job.queue.JobControlJob method) useStructure() (schrodinger.application.matsci.builderwidgets.SketchDialog method) usingSelected() (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method)

V

V (class in schrodinger.application.desmond.simulation_block_test) va_ (schrodinger.application.desmond.util.Counter attribute) VacancyAlchemist (class in schrodinger.application.matsci.enumeration) VacuumMsjGenerator (class in schrodinger.application.desmond.mapper_msj_generator) val (schrodinger.application.desmond.util.Counter attribute) (schrodinger.utils.sea.Atom attribute) (schrodinger.utils.sea.List attribute) (schrodinger.utils.sea.Map attribute) valence (schrodinger.application.desmond.packages.msys.Atom attribute) valence() (schrodinger.application.desmond.packages.msys.AnnotatedSystem method) VALENCE_LOCALIZATION_METHODS (schrodinger.application.jaguar.gui.tabs.theory_tab.TheoryTab attribute) valid_asl() (in module schrodinger.application.bioluminate.protein) valid_current_OPLS_directory() (in module schrodinger.application.ffbuilder.utils) valid_forcefield_info() (in module schrodinger.application.matsci.parserutils) valid_methods (schrodinger.application.mopac.mopac_launchers.MopacLauncher attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher2012 attribute) (schrodinger.application.mopac.mopac_launchers.MopacLauncher71 attribute) valid_type (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword attribute) validate (schrodinger.analysis.transformations.TransformsRepository attribute) validate() (schrodinger.application.bioluminate.bwidgets.NumericLineEdit method) (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) (schrodinger.application.desmond.gui.AtomGroupRow method) (schrodinger.application.desmond.gui.DesmondBasicConfigDialog method) (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) (schrodinger.application.desmond.gui.PosResRow method) (schrodinger.application.jaguar.gui.basis_selector.UpperCaseValidator method) (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.coordinates.CoordinateData method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.basis_set.BasisSetSubTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTab method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabWithSubTabs method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTab method) (schrodinger.application.jaguar.gui.tabs.molecule_tab.MoleculeTabPka method) (schrodinger.application.jaguar.gui.tabs.multi_structure_tab.MultiStructureTab method) (schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab.ReactionMoleculesTab method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.matsci.atomicsymbolsgui.ElementValidator method) (schrodinger.application.matsci.chargegui.BasisSetSelector method) (schrodinger.application.matsci.chargegui.NeighborTreatment method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDSimpleType method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDType method) (schrodinger.application.matsci.smartsutilsgui.SMARTSNameValidator method) (schrodinger.job.launchapi.JobSpecification method) (schrodinger.job.launchapi.TaskSpecification method) validate_asl() (in module schrodinger.application.desmond.packages.cui) (in module schrodinger.structutils.analyze) VALIDATE_CONCAT (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) validate_ff_name_and_get_number() (in module schrodinger.application.matsci.desmondutils) VALIDATE_GCMC (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) validate_host() (in module schrodinger.application.desmond.platforms) validate_jaguar_keywords() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) validate_keywords() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) validate_le_float_input() (in module schrodinger.application.jaguar.gui.utils) VALIDATE_MD (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) VALIDATE_META (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) VALIDATE_MINIMIZE (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) validate_mutated_residues() (schrodinger.application.bioluminate.protein.Mutator static method) validate_mutations() (schrodinger.application.bioluminate.protein.Mutator static method) validate_name() (in module schrodinger.application.matsci.smartsutils) validate_no_cg() (in module schrodinger.application.matsci.coarsegrain) validate_options() (in module schrodinger.application.macromodel.paraUtils) VALIDATE_REMD (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) validate_smarts() (in module schrodinger.structutils.analyze) validate_smarts_canvas() (in module schrodinger.structutils.analyze) validate_stages() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) validate_stoichiometry() (in module schrodinger.application.jaguar.utils) validate_structures() (schrodinger.application.jaguar.reactiq_input.ReactiqInput method) validate_temp_press() (in module schrodinger.application.jaguar.reactiq_validation) validate_value() (in module schrodinger.application.matsci.espresso.qeinput) VALIDATE_VRUN (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) validateInput() (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) validateJobCount() (schrodinger.application.matsci.guibase.MultiJobApp method) validateKeywords() (schrodinger.application.matsci.qualityslider.KeywordEdit method) (schrodinger.application.phase.input.PhaseHypothesisInputConfig method) validateLinkerChange() (schrodinger.application.combiglide.combenumdock.BaseInteractiveEnumeration method) validateModelLoaded() (schrodinger.application.matsci.guibase.MultiDesmondJobApp method) validateNumCpus() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) validateNumGpus() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) validateNumProcs() (schrodinger.application.desmond.gui.DesmondGuiConfigDialog method) validateRAtomIdentity() (schrodinger.application.matsci.builderwidgets.ComplexTemplateSketcher method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) validateRAtomStructure() (schrodinger.application.matsci.builderwidgets.ComplexTemplateSketcher method) (schrodinger.application.matsci.builderwidgets.SketcherBox method) validateStruct() (schrodinger.application.matsci.espresso.qeinput.StructureType method) validateSubHost() (schrodinger.application.desmond.fep_gui.FEPConfigDialog method) validateValues() (schrodinger.application.glide.glide.GlideJob method) (schrodinger.application.inputconfig.InputConfig method) (schrodinger.pipeline.stage.Stage method) validateWorkspace() (schrodinger.application.prime.gui.analyze_energy.AnalyzeEnergyWidget method) validation_specs() (in module schrodinger.application.glide.glide) value (schrodinger.application.jaguar.reactiq_keywords.ReactiqKeyword attribute) (schrodinger.infra.phase.PhpSiteConstraint attribute) (schrodinger.tasks.tasks_.ExceptionInfo attribute) value() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method) (schrodinger.infra.fast3d.SwigPyIterator method) (schrodinger.infra.mmgpgpu.SwigPyIterator method) (schrodinger.infra.mmjob.SwigPyIterator method) (schrodinger.infra.mmsurf.SwigPyIterator method) (schrodinger.infra.phase.SwigPyIterator method) (schrodinger.utils.colorscheme.SwigPyIterator method) (schrodinger.utils.mmutil.SwigPyIterator method) value_is_type() (in module schrodinger.application.jaguar.validation) value_iterator() (schrodinger.utils.mmutil.StringStringMap method) VALUE_PATTERN (schrodinger.application.matsci.genetic_optimization.genetic_optimization.CanvasKPLS attribute) valueChanged (schrodinger.models.parameters.Param attribute) valueChanged() (schrodinger.application.matsci.qualityslider.QualitySlider method) valueFromText() (schrodinger.application.jaguar.gui.input_tab_widgets.BlankableSpinBox method)

valueIsNumeric() (in module schrodinger.infra.phase) values (schrodinger.application.jaguar.reactiq_input.ReactiqInput attribute) (schrodinger.protein.analysis.Report.data_set.data_point attribute) values() (schrodinger.utils.mmutil.StringStringMap method) (schrodinger.utils.sea.Map method) ValueSelectionDialog (class in schrodinger.application.bioluminate.propfilter) Var (class in schrodinger.application.desmond.enhsamp) var() (in module schrodinger.job.launchapi) variant_map (schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter attribute) varWithType() (schrodinger.application.desmond.enhanced_sampling.mexpParser.mexpParser method) vbr2() (schrodinger.application.macromodel.utils.ComUtil method) VDException Vdw (class in schrodinger.application.desmond.cms) vdw (schrodinger.application.desmond.packages.energygroup.EnergyComponent attribute) (schrodinger.application.matsci.espresso.qeinput.DftType attribute) (schrodinger.surface.MolSurfType attribute) vdw_radius (schrodinger.structure._StructureAtom attribute) VDWData (class in schrodinger.application.matsci.cgforcefield) VDWMask() (in module schrodinger.analysis.visanalysis.volumedatastructureutils) VDWSCALE (schrodinger.application.matsci.rxn_path.ParserWrapper attribute) VdwType (class in schrodinger.application.matsci.espresso.qeinput) Vector (class in schrodinger.application.desmond.packages.analysis) (class in schrodinger.trajectory.prody.mode) vector_cross() (in module schrodinger.graphics3d.arrow) (in module schrodinger.graphics3d.torus) vector_normalize() (in module schrodinger.graphics3d.arrow) (in module schrodinger.graphics3d.torus) vector_to_matrix() (in module schrodinger.application.matsci.mecp_mod) vector_weight (schrodinger.infra.phase.PhpHypoOptimizerSettings attribute) VectorBase (class in schrodinger.trajectory.prody.mode) vel (schrodinger.application.desmond.packages.msys.Atom attribute) vel() (schrodinger.application.desmond.packages.topo.DuckFrame method) (schrodinger.application.desmond.packages.traj.Frame method) Vendor (class in schrodinger.application.licensing.flexlm) vendor() (schrodinger.application.licensing.flexlm.Vendor method) VERBOSE (schrodinger.application.desmond.fep_edge_report_maker.FEPEdgeReportMaker attribute) verbose (schrodinger.infra.phase.PhpHypoOptimizerSettings attribute) (schrodinger.structutils.minimize.Minimizer attribute) verify() (schrodinger.job.launchparams.LaunchParameters method) verifySettings() (schrodinger.application.desmond.gui.GuiApp method) VERSION_8_1 (schrodinger.application.livedesign.import_controller.ImportController attribute) version_at_least() (in module schrodinger) version_at_most() (in module schrodinger) version_compatible() (in module schrodinger) version_str_to_tuple() (in module schrodinger.application.desmond.antlr3) version_string() (in module schrodinger.utils.cmdline) version_uptodate() (in module schrodinger.application.licensing.licadmin) Vertex (class in schrodinger.application.matsci.shapes) vertex (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) vertex_colors (schrodinger.surface.Surface attribute) vertex_coords (schrodinger.surface.Surface attribute) vertex_count (schrodinger.surface.Surface attribute) vertex_normals (schrodinger.surface.Surface attribute) VERTICES (schrodinger.application.matsci.shapes.Cube attribute) (schrodinger.application.matsci.shapes.Cubeoctahedron attribute) (schrodinger.application.matsci.shapes.Dodecahedron attribute) (schrodinger.application.matsci.shapes.Icosahedron attribute) (schrodinger.application.matsci.shapes.Octahedron attribute) (schrodinger.application.matsci.shapes.Tetrahedron attribute) vertices (schrodinger.graphics3d.polyhedron.Polyhedron attribute) vibr() (schrodinger.application.macromodel.utils.ComUtil method) VIBRATION_MASS_METHOD (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VIBRATION_SCALING_AUTO (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VIBRATION_SCALING_CUSTOM (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VIBRATION_SCALING_NONE (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VIBRATION_SCALING_PULAY (schrodinger.application.jaguar.gui.tabs.properties_tab.VibrationalSubTab attribute) VibrationalSubTab (class in schrodinger.application.jaguar.gui.tabs.properties_tab) view() (schrodinger.ui.ligfilter.AddDefinitionDialog method) VIEW_CLASS (schrodinger.application.bioluminate.antibody.search_results_table.FullTable attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabHB attribute) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabPka attribute) viewAllProteins() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) viewAtomLabels() (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) ViewerWindow (class in schrodinger.application.bioluminate.ssv.viewer) viewFirstProtein() (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar method) viewname (schrodinger.tasks.jobtasks.JobConfig attribute) viewnameChanged (schrodinger.tasks.jobtasks.JobConfig attribute) viewPattern() (schrodinger.ui.ligfilter.LigfilterFrame method) violate_midpoint() (in module schrodinger.application.desmond.fepana) visibility (schrodinger.protein.sequence.Sequence attribute) visibilityChanged (schrodinger.protein.sequence.Sequence attribute) visible (schrodinger.structure._StructureAtom attribute) (schrodinger.surface.Surface attribute) VISIBLE (schrodinger.utils.pandasutils.WhichColumns attribute) visiblePropLabels() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visibleRefCt() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visibleTol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visibleXvol() (schrodinger.application.phase.hypothesis.PhaseHypothesis method) visit() (schrodinger.application.desmond.antlr3.tree.TreeVisitor method) (schrodinger.application.desmond.antlr3.treewizard.TreeWizard method) VisRecord (class in schrodinger.utils.pymol) VisRecordVol (class in schrodinger.utils.pymol) VMAGGLASS (schrodinger.maestro.markers.Icons attribute) Void (class in schrodinger.application.matsci.freevolume) VoidInfo (class in schrodinger.application.matsci.freevolume) voids() (schrodinger.application.matsci.amorphous.XYZVolumeGraph method) vol_per_anion() (in module schrodinger.application.matsci.mlearn.features) volume (schrodinger.application.desmond.packages.analysis.Pbc attribute) (schrodinger.surface.ColorFrom attribute) (schrodinger.surface.Surface.ColorFrom attribute) volume_name (schrodinger.surface.Surface attribute) VolumeData (class in schrodinger.analysis.visanalysis.volumedata) VolumeMapper (class in schrodinger.application.desmond.packages.analysis) VolumeMemoryError volumeNames (schrodinger.infra.phase.PhpQSARModel attribute) volumeOfGraph() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) Volumizer (class in schrodinger.infra.fast3d) voxelize() (schrodinger.application.desmond.packages.msys.SpatialHash method) VRUN (schrodinger.application.desmond.config.DEFAULT_SETTING attribute) vrun (schrodinger.application.desmond.config.TAG_SPECS attribute) VSWWriter (class in schrodinger.application.vsw.vswinput) vtype (schrodinger.application.matsci.cgforcefield.VDWData attribute) vx (schrodinger.application.desmond.packages.msys.Atom attribute) vy (schrodinger.application.desmond.packages.msys.Atom attribute) vz (schrodinger.application.desmond.packages.msys.Atom attribute)

W

wait() (in module schrodinger.tasks.tasks_) (schrodinger.job.jobcontrol.Job method) (schrodinger.tasks.tasks.ThreadFunctionTask method) (schrodinger.tasks.tasks_.AbstractTask method) (schrodinger.tasks.tasks_.SubprocessCmdTask method) (schrodinger.tasks.tasks_.TaskManager method) (schrodinger.tasks.tasks_.ThreadFunctionTask method) waitForSchrodDaemon() (schrodinger.application.licensing.licadmin.LocalServerProcess method) waiting_jobs (schrodinger.job.queue.JobDJ attribute) WALLSEP (schrodinger.application.matsci.nano.constants.Constants attribute) (schrodinger.application.matsci.nano.tube.MultiWalledNanoTube attribute) warn() (in module schrodinger.application.desmond.packages.cui) warn_about_mmjag_unknowns() (in module schrodinger.application.jaguar.gui.utils) warning (schrodinger.application.desmond.gui.AtomGroupModel attribute) (schrodinger.application.desmond.gui.PosResModel attribute) warning() (in module schrodinger.maestro.maestro) (in module schrodinger.structutils.assignbondorders) (schrodinger.application.bioluminate.propfilter.PropFilterDialog method) (schrodinger.application.jaguar.gui.tabs.base_tab.BaseTab method) (schrodinger.application.jaguar.gui.tabs.input_sub_tabs.base_sub_tab.BaseSubTab method) (schrodinger.application.report2d.Report2D method) (schrodinger.pipeline.stage.Stage method) (schrodinger.tasks.runners.AbstractTaskReporter method) (schrodinger.tasks.runners.CmdlineTaskReporter method) (schrodinger.tasks.runners.PanelTaskReporter method) (schrodinger.tasks.runners.TaskRunner method) (schrodinger.ui.ligfilter.AddDefinitionDialog method) (schrodinger.ui.ligfilter.LigfilterFrame method) warning_dialog() (in module schrodinger.application.desmond.gui) warningRaised (schrodinger.application.livedesign.ld_base_classes.ImportExportBasePanel attribute) warnings (schrodinger.application.desmond.packages.msys.SmartsPattern attribute) water_action (schrodinger.application.bioluminate.ssv.toolbars.ConsensusToolBar attribute) water_mol() (in module schrodinger.application.desmond.fep_edge_data) WaterBridges (in module schrodinger.application.desmond.packages.analysis) WATERMAP_EXEC_DIR (schrodinger.application.desmond.envir.CONST attribute) WATERMAP_VERSION (schrodinger.application.desmond.envir.CONST attribute) WaterMapInput (class in schrodinger.application.watermap.watermap_inp) WatermapTyper (class in schrodinger.application.desmond.systype) WatLigFragDistance (class in schrodinger.application.desmond.packages.analysis) WEAK (schrodinger.protein.residue.HELIX_PROPENSITY attribute) weakly_conserved (schrodinger.protein.annotation.Consensus attribute) weight (schrodinger.application.jaguar.gui.utils.Solvent attribute) weightsByNum() (schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets.ChargeConstraintRow method) WfcType (class in schrodinger.application.matsci.espresso.qeoutput) what() (schrodinger.infra.phase.PhpException method) WheelEventFilterer (class in schrodinger.application.matsci.mswidgets) which() (in module schrodinger.job.remote_command) WhichColumns (class in schrodinger.utils.pandasutils) WhichRows (class in schrodinger.utils.pandasutils) WHOLE_FILE (schrodinger.application.jaguar.gui.edit_dialog.EditDialog attribute) whole_ring_test() (in module schrodinger.application.desmond.r_group_asl) WholePDB (class in schrodinger.protein.getpdb_utility) wholePDB() (schrodinger.protein.getpdb_utility.Code method) WidgetWithClosedSignal (class in schrodinger.application.combiglide.combenumdock) WILDCARD_PATTERN (schrodinger.utils.sea.Atom attribute) WildcardTreePattern (class in schrodinger.application.desmond.antlr3.treewizard) will_create_scratch_entry() (in module schrodinger.maestro.maestro) window_hydrophobicity (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) window_isoelectric_point (schrodinger.protein.annotation.ProteinSequenceAnnotations attribute) (schrodinger.protein.annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES attribute) window_length (schrodinger.structutils.structalign.StructAlign attribute) WINDOW_TITLE (schrodinger.application.bioluminate.ssv.viewer.SequenceDockWidget attribute) (schrodinger.application.bioluminate.ssv.viewer.ViewerWindow attribute) windowClosed (schrodinger.application.combiglide.combenumdock.WidgetWithClosedSignal attribute) within_group1_global_max (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer attribute) within_group1_global_min (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer attribute) within_group2_global_max (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer attribute) within_group2_global_min (schrodinger.analysis.enrichment.TwoGroupFingerprintAnalyzer attribute) within_three_bonds() (schrodinger.protein.analysis.Report.steric_clash_data_set method) WMAGGLASS (schrodinger.maestro.markers.Icons attribute) WorkFlow (class in schrodinger.application.matsci.jaguarworkflows) working_directory() (in module schrodinger.application.licensing.licadmin) (in module schrodinger.application.matsci.jobutils) Workspace (class in schrodinger.application.desmond.maestro) WORKSPACE (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer attribute) (schrodinger.job.launchparams.ProjectDisposition attribute) workspace_bounding_box_function_add() (in module schrodinger.maestro.maestro) workspace_bounding_box_function_remove() (in module schrodinger.maestro.maestro) workspace_changed_function_add() (in module schrodinger.maestro.maestro) workspace_changed_function_remove() (in module schrodinger.maestro.maestro) workspace_draw_function_add() (in module schrodinger.maestro.maestro) workspace_draw_function_remove() (in module schrodinger.maestro.maestro) workspace_get() (in module schrodinger.maestro.maestro) workspace_get_coordinate_center() (in module schrodinger.maestro.maestro) workspace_get_size_and_scale() (in module schrodinger.maestro.maestro) workspace_get_translation() (in module schrodinger.maestro.maestro) workspace_get_view_matrix() (in module schrodinger.maestro.maestro) workspace_get_view_matrix_inverse() (in module schrodinger.maestro.maestro) workspace_get_view_matrix_inverse_no_center() (in module schrodinger.maestro.maestro) workspace_get_viewing_volume() (in module schrodinger.maestro.maestro) workspace_set() (in module schrodinger.maestro.maestro) workspace_transform_local_scope() (in module schrodinger.maestro.maestro) workspaceChanged() (schrodinger.application.bioluminate.protein_report_widget.ReportFrame method) (schrodinger.application.jaguar.gui.base_panel.InputTabMixin method) (schrodinger.application.jaguar.gui.input_tab_widgets.InputEntriesModel method) (schrodinger.application.jaguar.gui.tabs.input_tab.InputTabBase method) (schrodinger.application.jaguar.gui.tabs.reaction_tab.ReactionTab method) WorkspaceIdMapper (class in schrodinger.utils.pymol) WorkspaceInclusionCheckBox (class in schrodinger.application.jaguar.gui.utils) WorkspaceLabeler (class in schrodinger.application.bioluminate.workspacelabeler) WorldCoordinates() (schrodinger.analysis.visanalysis.volumedata.VolumeData method) worst_saved_score() (schrodinger.application.glide.ensemble_selection.Ensemble_Priority_Queue method) wrap() (schrodinger.application.desmond.packages.analysis.Pbc method) wrap_module() (in module schrodinger.infra.mmcheck) wrapper_build_attach_structure() (in module schrodinger.application.matsci.rxn_channel.rxn_channel) writable_server_log() (in module schrodinger.application.licensing.licadmin) WRITE (schrodinger.tasks.jobtasks.RunMode attribute) write() (schrodinger.analysis.reaction.RouteNode method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchAnalysis method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PatchFinder method) (schrodinger.application.bioluminate.patch_utils.patch_finder.PreAnalyzer method) (schrodinger.application.bioluminate.protein_protein_docking_shared.PIPERConstraint static method) (schrodinger.application.canvas.fingerprint.CanvasFingerprintGenerator method) (schrodinger.application.desmond.antlr3.debug.DebugEventSocketProxy method) (schrodinger.application.desmond.cms.Cms method) (schrodinger.application.desmond.cns_io.CNSData method) (schrodinger.application.desmond.fep_struc.SchrodStruc method) (schrodinger.application.desmond.fep_struc.Struc method) (schrodinger.application.desmond.ffiostructure.FFIOStructure method) (schrodinger.application.desmond.gaussian_filter.GaussianFilter method) (schrodinger.application.desmond.maestro.NewEntry method) (schrodinger.application.desmond.maestro.NewEntryGroup method) (schrodinger.application.desmond.packages.traj.Frame method) (schrodinger.application.desmond.rest_inp.RestInput method) (schrodinger.application.desmond.system_builder_inp.SystemBuilderInput method) (schrodinger.application.glide.glideanalysis.PoseLibrary method) (schrodinger.application.jaguar.gui.edit_dialog.EditDialog method) (schrodinger.application.jaguar.output.JaguarOutput method) (schrodinger.application.licensing.flexlm.License method) (schrodinger.application.matsci.amorphous.BaseMoiety class method) (schrodinger.application.matsci.amorphous.Cascader class method) (schrodinger.application.matsci.amorphous.Monomer class method) (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) (schrodinger.application.matsci.jaguarworkflows.WorkFlow method) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument method) (schrodinger.application.mopac.structure_launchers.StructureLauncher method) (schrodinger.application.phase.hypothesis.PhaseHypothesis method) (schrodinger.application.prime.input.Prime method) (schrodinger.application.qsite.input.QSiteInput method) (schrodinger.application.watermap.watermap_inp.WaterMapInput method) (schrodinger.infra.mmgpgpu.ostream method) (schrodinger.infra.mmjob.ostream method) (schrodinger.infra.mmsurf.ostream method) (schrodinger.pipeline.input.Writer method) (schrodinger.protein.getpdb_utility.Chain method) (schrodinger.protein.getpdb_utility.Code method) (schrodinger.protein.getpdb_utility.WholePDB method) (schrodinger.structure.PDBWriter method) (schrodinger.structure.SmilesStructure method) (schrodinger.structure.Structure method) (schrodinger.structure.TextualStructure method) (schrodinger.structutils.sort.StructureFileSorter method) (schrodinger.surface.Surface method) (schrodinger.tasks.jobtasks.AbstractJobTask method) (schrodinger.tasks.runners.JobTaskRunner method) (schrodinger.utils.colorscheme.ostream method)

write_apbs_input_with_ligand() (in module schrodinger.application.desmond.fep_net_charge) write_apbs_input_with_protein() (in module schrodinger.application.desmond.fep_net_charge) write_asl_file() (in module schrodinger.application.bioluminate.patch_utils.patch_finder) write_builder_input() (in module schrodinger.application.matsci.desmondutils) write_cms() (in module schrodinger.application.desmond.ffiostructure) write_cms_to_string() (in module schrodinger.application.desmond.ffiostructure) write_complex_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) write_config() (in module schrodinger.application.glide.http_server) write_core_only() (in module schrodinger.application.canvas.r_group) write_ct() (in module schrodinger.structure) write_ct_as_text() (in module schrodinger.structure) write_ct_mol2() (in module schrodinger.structure) write_ct_pdb() (in module schrodinger.structure) write_ct_sd() (in module schrodinger.structure) write_ct_smiles() (in module schrodinger.structure) write_ct_to_sd_string() (in module schrodinger.structure) write_ct_to_string() (in module schrodinger.structure) write_cts() (in module schrodinger.structure) write_data() (schrodinger.application.desmond.bennett.CalcBAR method) write_elec_block() (in module schrodinger.application.desmond.fep_net_charge) write_entries_from_project() (in module schrodinger.maestro.maestro) write_events_csv() (in module schrodinger.application.licensing.lmgrd_log_parser) write_fepsubst_to_file() (in module schrodinger.application.desmond.fep_mapping) write_ff_solute_tempering() (in module schrodinger.application.desmond.remd) write_file() (in module schrodinger.application.licensing.licadmin) write_glide_input_file() (schrodinger.pipeline.stages.glide.DockingStage method) write_hst_file() (in module schrodinger.application.macromodel.utils) write_hypotheses() (in module schrodinger.application.phase.hypothesis) write_idfile() (in module schrodinger.application.matsci.jobutils) write_input() (in module schrodinger.application.bioluminate.escomp) write_master_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) write_mop_file() (schrodinger.application.mopac.mopac_launchers.MopacLauncher method) (schrodinger.application.mopac.mopac_launchers.MopacLauncher2012 method) (schrodinger.application.mopac.mopac_launchers.MopacLauncher71 method) write_n_ct() (in module schrodinger.application.desmond.util) write_output() (in module schrodinger.application.canvas.r_group) write_overall_usage_csv() (in module schrodinger.application.licensing.lmgrd_log_parser) write_parameter_file() (schrodinger.protein.membrane.Membrane_Model method) write_phase_subset() (in module schrodinger.infra.phase) write_pqr() (in module schrodinger.application.bioluminate.escomp) (in module schrodinger.application.desmond.fep_net_charge) write_pqrs() (in module schrodinger.application.desmond.fep_net_charge) write_qe_input() (schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument method) write_reactions_file() (in module schrodinger.analysis.reaction) write_reagent_classes_file() (in module schrodinger.analysis.reaction) write_reference_structure() (schrodinger.trajectory.prody.ensemble.Ensemble method) write_restart_parameters_file() (in module schrodinger.application.matsci.jobutils) write_results() (schrodinger.application.desmond.bennett.CalcBAR method) write_sba_file() (in module schrodinger.application.desmond.simulation_block_data) write_sequences_to_fasta() (in module schrodinger.application.prepwizard) write_solvent_msj() (schrodinger.application.desmond.fep_scholar_msj_generator.FEPScholarMsjGenerator method) (schrodinger.application.desmond.mapper_msj_generator.MapperMsjGenerator method) write_stages_file() (in module schrodinger.application.matsci.jaguar_multistage_workflow_utils) write_structure() (schrodinger.protein.membrane.Membrane_Model method) write_to_stdout() (schrodinger.protein.analysis.Report method) write_to_string() (schrodinger.application.desmond.cms.Cms method) write_traj() (in module schrodinger.application.desmond.packages.traj) write_usage_csv() (in module schrodinger.application.licensing.lmgrd_log_parser) write_vacuum_msj() (schrodinger.application.desmond.mapper_msj_generator.VacuumMsjGenerator method) write_vis_files() (schrodinger.application.mopac.mopac_results.MopacResults method) (schrodinger.application.mopac.results2012.MopacResults2012 method) (schrodinger.application.mopac.results71.MopacResults71 method) writeAlignData() (schrodinger.structutils.sitealign.BindingSiteAligner method) writeAnalyzeDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AnalyzeStageData static method) writeBestStereos() (schrodinger.pipeline.stages.ligprep.PostLigPrepStage method) writeCluFile() (schrodinger.application.macromodel.utils.CluUtil method) writeCMS() (schrodinger.application.matsci.cgforcefield.CGFFIOStructure method) writeColorSchemeFile() (schrodinger.utils.colorscheme.ColorSchemeManager method) writeComFile() (schrodinger.application.macromodel.utils.ComUtil method) writeCommand() (schrodinger.application.desmond.gui.GuiApp method) (schrodinger.structutils.rmsd.ConformerRmsd method) writeCsv() (schrodinger.analysis.enrichment.ActiveDecoyFingerprintAnalyzer method) writeCSVFile() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) writeData() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint static method) writeDictDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords static method) writeDihedralDis() (schrodinger.application.matsci.amorphous.BuilderGrowInCellMixin method) writeDockingStage() (schrodinger.application.vsw.vswinput.VSWWriter method) writeDstFile() (schrodinger.application.macromodel.utils.CluUtil method) writeFES() (schrodinger.application.desmond.meta.MetaDynamicsAnalysis static method) writeFile() (schrodinger.infra.phase.PhpMMconfAdaptor method) (schrodinger.job.jobcontrol.Job method) (schrodinger.utils.colorscheme.MM_CScheme method) writeFiles() (schrodinger.application.matsci.freevolume.FreeVolumeDriver method) writeFPFile() (schrodinger.structutils.interactionfp.StructuralInteractionFingerprintGenerator method) writeGenConfsStage() (schrodinger.application.vsw.vswinput.VSWWriter method) writeGrd() (schrodinger.application.jaguar.output.JaguarOutput method) writeHypoFiles() (schrodinger.infra.phase.PhpProject method) writeInheritableParentDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParentStageData static method) writeInput() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.JMSStep method) (schrodinger.application.matsci.jaguarworkflows.Step method) writeInputFile() (schrodinger.application.inputconfig.InputConfig method) (schrodinger.application.vsw.vswinput.VSWWriter method) writeInterfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Interfaces method) writeJSON() (schrodinger.application.glide.glide.GlideJob method) writeKeyStringToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.OverrideKeywords static method) writeKeywordsToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.StageKeywords static method) writeLigand() (schrodinger.application.glide.poseviewconvert.Complex method) writeMaefile() (schrodinger.application.jaguar.input.JaguarInput method) writeMapToFile() (schrodinger.application.livedesign.ld_export.ExportMap method) writeMatrixData() (schrodinger.structutils.sitealign.BindingSiteAligner method) writeModelDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ActiveCoord static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.AtomBasis static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ChargeConstraint static method) (schrodinger.application.matsci.jaguar_multistage_workflow_utils.GeomConstraint static method) writeMSJ() (schrodinger.application.watermap.watermap_inp.WaterMapInput method) writeNMD() (in module schrodinger.trajectory.prody.writenmd) writeNMDmae() (in module schrodinger.trajectory.prody.writenmd) writeNonInheritableParentDataToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ParentStageData static method) writePreFilterStage() (schrodinger.application.vsw.vswinput.VSWWriter method) writePrepareStages() (schrodinger.application.vsw.vswinput.VSWWriter method) writePrimeInput() (schrodinger.application.bioluminate.protein.Refiner method) writePv() (schrodinger.application.glide.poseviewconvert.Complex method) Writer (class in schrodinger.pipeline.input) writer_open() (in module schrodinger.utils.csv_unicode) writeReceptor() (schrodinger.application.glide.poseviewconvert.Complex method) writeRoot() (schrodinger.pipeline.stages.filtering.DrugLikeSplitStage method) writeSbcFile() (schrodinger.application.macromodel.utils.ComUtil method) (schrodinger.application.macromodel.utils.SbcUtil method) writeSchemeFile() (schrodinger.structutils.color.ColorScheme method) writeSectionsToFile() (schrodinger.application.matsci.jaguar_multistage_workflow_utils.ExtraSectionData static method) writeSIFFile() (schrodinger.pipeline.stages.macromodel.ConfSearchStage method) (schrodinger.pipeline.stages.macromodel.SampleRingsStage method) writeSimplified() (schrodinger.application.glide.glide.GlideJob method) writeStructures() (schrodinger.structutils.rmsd.ConformerRmsd method) (schrodinger.structutils.sitealign.BindingSiteAligner method) writeSummary() (schrodinger.infra.phase.PhpHypoAdaptor method) (schrodinger.infra.phase.PhpProject method) writeSurfaces() (schrodinger.application.matsci.nano.surfaces_interfaces_mod.Surfaces method) writeTask() (schrodinger.tasks.runners.JobTaskRunner method) writeTopNFromBlock() (schrodinger.structutils.sort.StructureFileSorter method) writeTopPoses() (schrodinger.application.glide.glideanalysis.PoseLibrary method) writeToString() (schrodinger.structure.Structure method) writeValidPoses() (schrodinger.application.glide.glideanalysis.PoseLibrary method) wt_frag_st (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) wt_name (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) wt_residue_sequence_list (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) wt_residue_sequence_tags (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute) wt_st (schrodinger.application.desmond.fep_edge_data.CovalentFEPEdgeData attribute) (schrodinger.application.desmond.fep_edge_data.PRMEdgeData attribute)

X

x (schrodinger.application.desmond.packages.msys.Atom attribute) X (schrodinger.application.matsci.amorphous.Box attribute) (schrodinger.application.matsci.espresso.qeinput.StructureType attribute) x (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.infra.phase.PhpExclVolSphere attribute) (schrodinger.infra.phase.PhpVolCoords attribute) (schrodinger.structure._StructureAtom attribute) x0 (schrodinger.graphics3d.torus.MaestroTorus attribute) x1 (schrodinger.graphics3d.torus.MaestroTorus attribute) X_ALIAS (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) X_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) xhead (schrodinger.graphics3d.arrow.MaestroArrow attribute) xmax (schrodinger.infra.phase.PhpQSARModel attribute) xmin (schrodinger.infra.phase.PhpQSARModel attribute) xml2in() (in module schrodinger.application.matsci.qexsd.utils) XML_SCHEMA_NAMESPACES (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema.XMLSchema attribute) xml_to_dict() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.etree) XMLDecodeError XmlDocument (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument) XMLEncodeError XMLSchema (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmlschema) XMLSchemaValidationError XMLValueError XP_SCORE (schrodinger.application.phase.phase_markers.PhaseFeatureMarker attribute) XpPVParser (class in schrodinger.application.glide.xpdes)

xsd_attribute_type_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) XSD_BUILTIN_TYPES (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) xsd_builtin_types_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) xsd_complex_type_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) xsd_element_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) xsd_get_type() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) xsd_group_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) xsd_simple_type_factory() (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) xsd_type (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDAttribute attribute) (schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes.XSDElement attribute) XSDAttribute (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) XSDComplexType (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) XSDElement (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) XSDGroup (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) XSDSimpleType (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) XSDType (class in schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) XSI_ATTRIBUTES (in module schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xsdtypes) xtail (schrodinger.graphics3d.arrow.MaestroArrow attribute) XTC (schrodinger.application.desmond.packages.traj.Fmt attribute) XtcSource (class in schrodinger.application.desmond.packages.traj) Xvfb (class in schrodinger.application.desmond.xvfbwrapper) XVOL_TEXT (schrodinger.application.phase.featureselector.FeatureModel attribute) xyz (schrodinger.application.desmond.fep_scholar_util.MetaAtom attribute) (schrodinger.structure._StructureAtom attribute) XYZVolumeGraph (class in schrodinger.application.matsci.amorphous)

Y

y (schrodinger.application.desmond.packages.msys.Atom attribute) Y (schrodinger.application.matsci.amorphous.Box attribute) (schrodinger.application.matsci.espresso.qeinput.StructureType attribute) y (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.infra.phase.PhpExclVolSphere attribute) (schrodinger.infra.phase.PhpVolCoords attribute) (schrodinger.structure._StructureAtom attribute)

y0 (schrodinger.graphics3d.torus.MaestroTorus attribute) y1 (schrodinger.graphics3d.torus.MaestroTorus attribute) Y_ALIAS (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) Y_KEY (schrodinger.application.matsci.bandshape_utils.BandshapeSpectrumFile attribute) yhead (schrodinger.graphics3d.arrow.MaestroArrow attribute) ymax (schrodinger.infra.phase.PhpQSARModel attribute) ymin (schrodinger.infra.phase.PhpQSARModel attribute) ytail (schrodinger.graphics3d.arrow.MaestroArrow attribute)

Z

z (schrodinger.application.desmond.packages.msys.Atom attribute) Z (schrodinger.application.matsci.amorphous.Box attribute) (schrodinger.application.matsci.espresso.qeinput.StructureType attribute) z (schrodinger.graphics3d.sphere.MaestroSphere attribute) (schrodinger.infra.phase.PhpExclVolSphere attribute) (schrodinger.infra.phase.PhpVolCoords attribute) (schrodinger.structure._StructureAtom attribute) z0 (schrodinger.graphics3d.torus.MaestroTorus attribute) z1 (schrodinger.graphics3d.torus.MaestroTorus attribute) z_variables() (in module schrodinger.application.jaguar.textparser) ZAtom (class in schrodinger.application.matsci.zmutils) Zero (schrodinger.structure.BondType attribute) zero_order_metal_bonds() (in module schrodinger.application.jaguar.autots_bonding) zero_point_energy() (schrodinger.application.matsci.espresso.qeoutput.PhDOS method) ZERO_VEC (schrodinger.application.matsci.rxn_channel.rxn_channel.ReactantMolecule attribute) ZEROVEC (schrodinger.application.matsci.nano.sheet.HoneycombBilayers attribute) (schrodinger.application.matsci.nano.tube.NanoTubeSheet attribute)

zhead (schrodinger.graphics3d.arrow.MaestroArrow attribute) ZIGZAG (schrodinger.application.matsci.nano.constants.Constants attribute) ZIGZAG_BY_ONE_BASE (schrodinger.application.matsci.nano.sheet.Grow attribute) zip_and_set_incorporation() (in module schrodinger.application.matsci.jobutils) zip_dir() (in module schrodinger.application.livedesign.export_controller) zip_project() (in module schrodinger.project) zipDirectory() (schrodinger.infra.phase.PhpProject method) zipProject() (schrodinger.infra.phase.PhpProject method) ZMATNUMBER (schrodinger.application.matsci.rxn_path.InternalCoords attribute) ZMatrix (class in schrodinger.application.matsci.zmutils) zmax (schrodinger.infra.phase.PhpQSARModel attribute) zmin (schrodinger.infra.phase.PhpQSARModel attribute) zpe() (in module schrodinger.application.jaguar.textparser) zpe_precision (schrodinger.application.jaguar.results.JaguarResults attribute) ztail (schrodinger.graphics3d.arrow.MaestroArrow attribute) ZVariables (class in schrodinger.application.jaguar.results)