[ Identifiers | To Do | Deprecations ]

Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

a (in schrodinger.application.desmond.mdkey)	addTempHydrogens() (in ReactantMolecule)	append() (in SwigRingList)
a (in PhpFastShapePair)	addTempInputFile() (in Launcher)	append() (in SwigSaltBridgeList)
A_IDX (in schrodinger.application.matsci.nano.interface_mod)	addTestIDArg() (in TestRunnerParser)	append() (in MaestroWriter)
A_KEY (in schrodinger.application.matsci.desmondutils)	addTestLimitations() (in TestRunnerParser)	append() (in Mol2Writer)
A_KEY (in Crystal)	addTextToSet() (in AsetFrame)	append() (in MultiFileStructureWriter)
A_PARAM (in ParserWrapper)	addToAuxListbox() (in PropertySelector)	append() (in PDBWriter)
A_VACUUM (in NanoTube)	addToAuxListbox() (in PropertySelector)	append() (in SDWriter)
AA_1_LETTER_MAP (in schrodinger.application.bioluminate.protein)	addTol() (in PhpHypoAdaptor)	append() (in SmilesCsvWriter)
AA_3_LETTER_MAP (in schrodinger.application.bioluminate.protein)	addTolByType() (in PhpHypoAdaptor)	append() (in SmilesStructure)
AACG (in _licensing')	addToolBars() (in ViewerWindow)	append() (in SmilesWriter)
aacg (in schrodinger.application)	addTorsionRestraint() (in Minimizer)	append() (in Structure)
AACG (in schrodinger.infra.licensing)	addToWorkspace() (in ParticipantView)	append() (in StructureWriter)
Aacg_SiteMap_Multijob	addToWorkspace() (in ReactionParticipant)	append() (in TextualStructure)
ABAB (in Constants)	Adduct (in schrodinger.application.combiglide.packages.chutils)	append() (in SwigDoubleVector)
ABC_VALUE (in schrodinger.application.matsci.nano.particle)	AdductAttachment (in schrodinger.application.combiglide.packages.chutils)	append() (in SwigDoubleVector3)
ABCD (in Constants)	adducts (in Adduct)	append() (in SwigIntVector)
ABCMeta	addUndoRedoToolBar() (in ViewerWindow)	append() (in SwigStringVector)
aboutToSort() (in SortProxyModel)	addVar() (in LinearWriter)	append() (in SwigUInt64Vector)
aboutToUpdatePositions() (in DendrogramGraphicTree)	addVar() (in Writer)	append() (in SwigUnsignedIntVector)
absolute (in schrodinger.protein.assignment)	addVdwtype() (in _FFIO)	append() (in SwigUnsignedIntVector2)
AbstractAligner (in schrodinger.application.msv.domain.align)	addVdwtypes() (in _FFIO)	append() (in SwigVectorIntIntPair)
AbstractAlignmentView (in schrodinger.application.msv.gui.view)	addVdwtypescombined() (in _FFIO)	append() (in List)
AbstractMsvContextMenu (in schrodinger.application.msv.gui.view)	addVdwtypescombineds() (in _FFIO)	append_comment() (in schrodinger.application.desmond.util)
AbstractMsvWidget (in schrodinger.application.msv.gui.msv_widget)	addVerbosityArgs() (in TestRunnerParser)	append_path() (in schrodinger.utils.env)
AbstractStructureModel (in schrodinger.application.msv.io.structure_model)	addVirtual() (in _FFIO)	append_project_command() (in schrodinger.maestro.maestro)
ACCEPT (in schrodinger.application.jaguar.gui.basis_selector)	addVirtuals() (in _FFIO)	append_stage() (in schrodinger.application.desmond.cmj)
accept() (in ActiveDatabaseDialog)	addXvol() (in PhaseFeatureMixin)	appendChargeConstraints() (in JaguarInput)
accept() (in PropFilterDialog)	addXvol() (in PhpHypoAdaptor)	appendFile() (in createFragmentDelegate)
accept() (in ValueSelectionDialog)	adf() (in ComUtil)	appendFile() (in simpleEnumDockDelegate)
accept() (in DEE_Backtracking)	adjust() (in Structure)	appendFile() (in StructureReaderDelegate)
accept() (in EditDialog)	adjust_phi() (in Rama)	appendLigand() (in Complex)
accept() (in NewJobDirDialog)	adjust_psi() (in Rama)	appendNewCollection() (in SimpleEnumDockPanel)
accept() (in SolventDialog)	adjust_symbol_size() (in Rama)	appendReceptor() (in Complex)
accept() (in ReorderAtomsDialog)	adjustACellClashVDWScale() (in AmorphousCellBuilder)	appendRepository() (in Engine)
accept() (in EditFeatureDialog)	adjustACellDensity() (in AmorphousCellBuilder)	appendStruct() (in collectionViewerModel)
accept() (in ChooseLigandDialog)	adjustDum() (in schrodinger.application.mcpro.perturbations)	appendSubalignment() (in BaseAlignment)
accept() (in DontShowAgainDialog)	adjustIndices() (in _Region)	appendSubalignment() (in ProteinAlignment)
accept() (in OpenDirAsFileDialog)	ADME_HERG (in _licensing')	appframework (in schrodinger.ui)
accept() (in PropertyGrabPanel)	ADME_HERG (in schrodinger.infra.licensing)	AppFramework (in schrodinger.ui.appframework)
ACCEPT_MULTI (in schrodinger.application.jaguar.gui.basis_selector)	ADME_HERG (in schrodinger.infra.mm)	appframework (in schrodinger.ui.qt)
accept_reject_parse() (in schrodinger.application.desmond.replica_exchange_review)	ADME_P450 (in _licensing')	AppFramework (in schrodinger.ui.qt.appframework)
accepted() (in EditDialog)	ADME_P450 (in schrodinger.infra.licensing)	AppJobInputFrame (in schrodinger.ui.appframework)
ACCEPTED_FRAMEWORK_COLOR (in FullProxyModel)	ADME_P450 (in schrodinger.infra.mm)	application (in schrodinger)
AcceptMode	ADME_PERM (in _licensing')	APPLICATION_NAME (in Startup)
ACCEPTOR_POS (in StructuralInteractionFingerprintGenerator)	ADME_PERM (in schrodinger.infra.licensing)	APPLICATION_NAME (in UI)
AcceptorConstraint (in schrodinger.application.glide.glide)	ADME_PERM (in schrodinger.infra.mm)	apply() (in GaussianFilter)
ACCURACY (in schrodinger.application.matsci.optoelectronics)	ADSORPTION (in schrodinger.application.matsci.nano.interface_mod)	apply() (in schrodinger.application.desmond.periodicfix)
ACCURACY_LEVELS (in ScfTab)	adv_callback() (in _BaseGroup)	apply() (in _Rotamer)
ACCURATE (in QualitySlider)	advance() (in SwigPyIterator)	apply() (in ColorScheme)
ACIDIC_RESIDUES (in schrodinger.application.bioluminate.protein)	advance() (in SwigPyIterator)	apply() (in Superimposer)
ACIDIC_RESIDUES (in schrodinger.structutils)	advance() (in SwigPyIterator)	apply() (in List)
ack() (in DebugEventSocketProxy)	advance() (in SwigPyIterator)	apply() (in Map)
actinide_series (in schrodinger.application.prime.primefix)	advance() (in SwigPyIterator)	apply() (in Sea)
ACTION_NAME (in schrodinger.application.bioluminate.actions.factory)	advance() (in SwigPyIterator)	apply_color_scheme() (in schrodinger.structutils.color)
ActionComboBox (in schrodinger.application.phase.phase_widgets)	advance() (in SwigPyIterator)	apply_dihedral() (in Rama)
ActionEvent	advance() (in SwigPyIterator)	apply_exclusion() (in schrodinger.application.desmond.r_group_asl)
actionEvent() (in DendrogramView)	advance() (in SwigPyIterator)	apply_jaguar_atom_naming() (in schrodinger.application.jaguar.gui.utils)
actionEvent() (in MM_QLineEdit)	advanceSelection() (in ReferenceFrame)	apply_pkas() (in ProtAssign)
actionEvent() (in SHView)	advice (in LicenseError)	apply_state() (in schrodinger.application.prepwizard)
actionEvent() (in sketcher)	AdvLabel (in schrodinger.application.desmond.cwidget)	apply_state_and_calc_score() (in schrodinger.application.prepwizard)
actionEvent() (in sketcherGUIMultiColumnToolBar)	AdvLabel (in schrodinger.application.desmond.fep_gui)	apply_style_sheet() (in schrodinger.ui.qt.style)
actionEvent() (in sketcherView)	AdvOptionsFrame (in schrodinger.application.desmond.gui)	apply_styles() (in schrodinger.ui.qt.style)
ActionMenu (in schrodinger.application.bioluminate.pml_menus)	af2SettingsGetValue() (in FeatureOptionsCombo)	apply_uniform_operator_weights() (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
ActionPopUp (in schrodinger.application.phase.phase_widgets)	af2SettingsSetValue() (in FeatureOptionsCombo)	applyColorScheme() (in AbstractMsvWidget)
actions (in schrodinger.application.bioluminate)	after_upper_edge() (in schrodinger.application.matsci.nano.xtal)	applyContextDependentDefaults() (in Dock)
activate() (in StartDialogBase)	afterStep() (in PhpProject)	applyContextDependentDefaults() (in GlideJob)
activate() (in BaseTab)	AFTERSUPERPOSITION (in ParserWrapper)	applyCurrentCollection() (in SimpleEnumDockPanel)
activate() (in BaseSubTab)	AGGREGATE_CALCULATIONS (in PropertyCalculator)	applyCurrentSelection() (in SimpleEnumDockPanel)
activate() (in BasisSetSubTab)	AHEAD (in PBCBond)	applyEnergyFilter() (in DEE_EnergyMatrix)
activate() (in InputTabWithSubTabs)	AHEAD_BASE_TRIPLES (in schrodinger.application.matsci.nano.xtal)	applyGoldsteinSingles() (in DEE_EnergyMatrix)
activate() (in WriteDialog)	AHEAD_TRIPLES (in schrodinger.application.matsci.nano.xtal)	applyGroupSelections() (in MutationSelectorFrame)
activate() (in ConfigDialog)	ahomo_prop (in MopacResults71)	ApplyJoiningRules (in schrodinger.application.combiglide.packages.chutils)
activate() (in WriteDialog)	ai (in _FEPIOAngleMap)	applyOptions() (in AbstractMsvWidget)
ACTIVE (in schrodinger.job.queue)	ai (in _FEPIOAtomMap)	applyRampToColorSchemeRules() (in ColorSchemeManager)
active_jobs (in JobDJ)	ai (in _FEPIOBondMap)	applyRule() (in MM_CSchemeRule)
ActiveDatabaseDialog (in schrodinger.application.bioluminate.antibody.management)	ai (in _FEPIODihedMap)	applyScheme() (in ColorSchemeManager)
ActiveDatabaseTable (in schrodinger.application.bioluminate.antibody.management)	ai (in _FEPIOExclMap)	applyScheme() (in MM_CScheme)
ActiveDecoyFingerprintAnalyzer (in schrodinger.analysis.enrichment)	ai (in _FEPIOPairMap)	applySchemeDescriptive() (in ColorSchemeManager)
activeSubTab() (in InputTabWithSubTabs)	ai (in _FFIOAngle)	applySettings() (in FEPConfigDialog)
activeSubTabName() (in InputTabWithSubTabs)	ai (in _FFIOAngleFBHW)	applySettings() (in AdvOptionsFrame)
adapt_dummy_types() (in Zmat)	ai (in _FFIOBond)	applySettings() (in DesmondGuiConfigDialog)
adaptor (in mexpParser)	ai (in _FFIOConstraint)	applySettings() (in _BaseMarker)
ADD (in schrodinger.application.bioluminate.actions.icons)	ai (in _FFIODihedral)	applySettings() (in ConfigDialog)
ADD (in schrodinger.project)	ai (in _FFIOExclusion)	applySettings() (in GPGPUConfigDialog)
add (in schrodinger.protein.assignment)	ai (in _FFIOImproperFBHW)	applyStyle() (in Structure)
add() (in RewriteRuleElementStream)	ai (in _FFIOPair)	applyStyle() (in _Chain)
add() (in JobOutput)	ai (in _FFIOPosFBHW)	applyStyle() (in _Molecule)
add() (in EnergyComponent)	ai (in _FFIORestraint)	applyStyle() (in _Residue)
add() (in IndexDict)	ai (in _FFIOVirtual)	applyStyle() (in _Ring)
add() (in TupleDict)	ai (in _FFAngle)	applyToStructure() (in PBC)
add() (in _MdcBase)	ai (in _FFBond)	APPROACH_PROP (in schrodinger.application.matsci.clusterstruct)
add() (in GlideWorkspaceMarkers)	ai (in _FFConstraint)	approximateVolume() (in Scaffold)
add() (in Group)	ai (in _FFDihedral)	apps (in schrodinger.application.macromodel)
add() (in LinkedList)	ai (in _FFExclusion)	aquamarine (in Color)
add() (in RunningJobs)	ai (in _FFPair)	ar_type (in BitArray)
add() (in _Callback)	ai (in _FFRestraint)	arccosh (in schrodinger.protein.assignment)
add() (in ColorScheme)	ai (in _FFVirtual)	ARCHIMEDEAN (in schrodinger.application.matsci.shapes)
add() (in SurfaceDict)	aj (in _FEPIOAngleMap)	archive_job_data() (in schrodinger.application.matsci.jobutils)
add() (in ButtonBox)	aj (in _FEPIOAtomMap)	archive_wm() (in schrodinger.application.watermap.utils)
add() (in NoteBook)	aj (in _FEPIOBondMap)	ArchivedProjectException (in schrodinger.project)
add() (in PanedWidget)	aj (in _FEPIODihedMap)	arcsinh (in schrodinger.protein.assignment)
add() (in RadioSelect)	aj (in _FEPIOExclMap)	arctan (in schrodinger.protein.assignment)
add_and_parse_SMILES() (in schrodinger.application.desmond.report_helper)	aj (in _FEPIOPairMap)	arctan2 (in schrodinger.protein.assignment)
add_atom() (in PertReorder)	aj (in _FFIOAngle)	are_sts_the_same() (in schrodinger.structutils.createfragments)
add_atom_highlight() (in FEPEdgeReportMaker)	aj (in _FFIOAngleFBHW)	are_times_insane() (in schrodinger.application.desmond.fepana)
add_atoms_onto_tree() (in schrodinger.application.desmond.reorder_atom)	aj (in _FFIOBond)	AREA (in schrodinger.application.matsci.shapes)
add_attachment_points() (in Data)	aj (in _FFIOConstraint)	AreaPerLipid (in schrodinger.trajectory.lipid_analysis)
add_attribute_aliases() (in schrodinger.application.jaguar.results)	aj (in _FFIODihedral)	areAtomsOrtho() (in AssignBondOrders)
add_bonds_in_rings() (in Data)	aj (in _FFIOExclusion)	areBound() (in Structure)
add_child() (in Node)	aj (in _FFIOImproperFBHW)	areCOsPara() (in AssignBondOrders)
add_code() (in ReturnCode)	aj (in _FFIOPair)	ARG (in schrodinger.application.desmond.antlr3.treewizard)
add_common_context_items() (in schrodinger.application.bioluminate.pml_menus)	aj (in _FFIOVirtual)	argc (in schrodinger.application.desmond.gchart)
add_core() (in Data)	aj (in _FFAngle)	ARGININE (in schrodinger.application.msv.domain.residue)
add_core_bonds() (in Data)	aj (in _FFBond)	args (in schrodinger.application.msv.gui.color)
add_core_ct() (in Data)	aj (in _FFConstraint)	argv() (in schrodinger.utils.unicodesupport)
add_ct_data() (in schrodinger.application.canvas.r_group)	aj (in _FFDihedral)	ark (in schrodinger.infra)
add_ct_offset() (in Data)	aj (in _FFExclusion)	ark_str() (in FEPReport)
add_cubic_chorus_box_props() (in schrodinger.application.matsci.desmondutils)	aj (in _FFPair)	ARMCHAIR (in Constants)
add_current_to_states() (in changeable)	aj (in _FFVirtual)	ARMCHAIR_BY_ONE_BASE (in Grow)
add_current_to_states() (in rotatable_changeable)	ak (in _FEPIOAngleMap)	AROMATIC_H_DONOR (in _structure')
add_current_to_states() (in water_changeable)	ak (in _FEPIODihedMap)	AROMATIC_H_DONOR (in schrodinger.infra.structure)
add_desmond_ms_logo() (in schrodinger.application.matsci.mswidgets)	ak (in _FFIOAngle)	AROMATIC_POS (in StructuralInteractionFingerprintGenerator)
add_error() (in LicenseResource)	ak (in _FFIOAngleFBHW)	AROMATIC_RESIDUE (in StructuralInteractionFingerprintGenerator)
add_error() (in ServerInfo)	ak (in _FFIOConstraint)	AROMATIC_RESIDUES (in schrodinger.application.bioluminate.protein)
add_functional_rings() (in Data)	ak (in _FFIODihedral)	AROMATIC_RESIDUES (in schrodinger.structutils)
add_histo() (in schrodinger.application.desmond.event_analysis.pl_image_tools)	ak (in _FFIOImproperFBHW)	AROMATIC_RESIDUES (in StructuralInteractionFingerprintGenerator)
add_host_lists() (in schrodinger.pipeline.pipeline)	ak (in _FFIOVirtual)	Around (in schrodinger.application.bioluminate.pml_menus)
add_hydrogens() (in SchrodStruc)	ak (in _FFAngle)	AroundExpandSubMenu (in schrodinger.application.bioluminate.pml_menus)
add_hydrogens() (in schrodinger.structutils.build)	ak (in _FFConstraint)	Array_Prop (in schrodinger.application.desmond.simulation_block_data)
ADD_HYPO_FILE (in HypothesesListWidget)	ak (in _FFDihedral)	ArrayCoordinates() (in _VDAxis)
ADD_HYPO_PT (in HypothesesListWidget)	ak (in _FFVirtual)	ArrayCoordinates() (in _VDCoordinateFrame)
ADD_HYPO_WS (in HypothesesListWidget)	al (in _FEPIODihedMap)	ArrayCoordinates() (in VolumeData)
add_jaguar_files_to_jc_backend() (in schrodinger.application.matsci.jaguarworkflows)	al (in _FFIOConstraint)	ArraySyntax (in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
add_job_launch_log() (in schrodinger.maestro.maestro)	al (in _FFIODihedral)	arrow (in schrodinger.graphics3d)
add_keyword_parser_argument() (in schrodinger.application.matsci.jobutils)	al (in _FFIOImproperFBHW)	Arrow (in schrodinger.graphics3d.arrow)
add_labeled_pbc_bond() (in schrodinger.application.matsci.nano.xtal)	al (in _FFIOVirtual)	ARROW_GROUP (in schrodinger.application.desmond.maestro)
add_lig_solvent_cap() (in Zmat)	al (in _FFConstraint)	ARROW_GROUP_refcount (in schrodinger.application.desmond.maestro)
add_methyl_ring() (in schrodinger.application.canvas.r_group)	al (in _FFDihedral)	ARROW_OPACITY (in schrodinger.trajectory.prody.test_arrow)
add_methyl_standard() (in schrodinger.application.canvas.r_group)	al (in _FFVirtual)	ARROW_RADII (in PhaseFeatureMarker)
add_moldescriptors_options() (in schrodinger.application.moldescriptors)	ALANINE (in schrodinger.application.msv.domain.residue)	ArrowCore (in schrodinger.graphics3d.arrow)
add_multi_job_finalizer() (in schrodinger.job.queue)	Alchemist (in schrodinger.application.matsci.enumeration)	ARROWDOWN (in Icons)
add_neighbor_charges_to_jaginput() (in schrodinger.application.matsci.clusterstruct)	alie_analysis() (in schrodinger.application.jaguar.textparser)	ASCENDING (in schrodinger.structutils.sort)
add_notes() (in ModelCheck)	alie_analysis_precision (in JaguarResults)	asDock() (in SimplifiedSequenceViewer)
add_options() (in CmdlineParser)	alie_precision (in JaguarAtomicResults)	asea_copy() (in schrodinger.utils.sea)
add_output() (in Env)	align (in schrodinger.application.msv.domain)	aset() (in ComUtil)
add_output() (in LicenseError)	align() (in StructAlign)	AsetFrame (in schrodinger.ui.macromodel)
add_overlapEnergyTable() (in FEPReportMaker)	align_structure() (in schrodinger.application.desmond.mdpose.mdpose_average_structure)	asFrame() (in SimplifiedSequenceViewer)
add_package_dir_to_path() (in schrodinger.application.utils)	ALIGN_TOOLBAR (in ViewerWindow)	asGrid() (in ImportWidget)
add_para_job_options() (in schrodinger.application.macromodel.paraUtils)	alignCenterCollect() (in MultiWalledNanoTube)	asJSON() (in JobSpecification)
add_plugin() (in schrodinger.application.desmond.config)	AlignCore	asJSON() (in RuntimeParameters)
add_plugin() (in schrodinger.application.desmond.mdkey)	alignCt() (in PhpFastShape)	asJSON() (in TaskSpecification)
add_point() (in data_set)	alignCtPy() (in PhpFastShape)	askdirectory() (in schrodinger.ui.widget.tkinterwidget)
add_point() (in primex_steric_clash_data_set)	ALIGNED_COLOR (in schrodinger.structutils.sitealign)	askopenfilename() (in schrodinger.ui.widget.tkinterwidget)
add_position() (in Data)	ALIGNED_STYLE (in schrodinger.structutils.sitealign)	askopenfilenames() (in schrodinger.ui.widget.tkinterwidget)
add_property_value() (in Data)	alignLigands() (in PhpProject)	askOverwrite() (in AppFramework)
add_prot_solvent_cap() (in Zmat)	alignment (in schrodinger.application.msv.domain)	askOverwrite() (in AppFramework)
add_r_group() (in Data)	ALIGNMENT_ACTIONS (in schrodinger.application.bioluminate.actions.configs)	askOverwriteIfNecessary() (in AppFramework)
add_r_groups_to_atom() (in Data)	ALIGNMENT_KEYS (in schrodinger.application.matsci.nano.particle)	askOverwriteIfNecessary() (in AppFramework)
add_replicas_dF_table() (in FEPReportMaker)	alignmentChanged() (in AbstractStructureModel)	asksaveasfilename() (in schrodinger.ui.widget.tkinterwidget)
add_rest_region() (in schrodinger.application.desmond.rest_inp)	AlignmentException (in schrodinger.application.msv.domain.align)	askUsernamePassword() (in ProxyPasswordManager)
add_restart_parser_arguments() (in schrodinger.application.matsci.jobutils)	alignmentLengthAboutToChange() (in BaseAlignment)	asl (in schrodinger.application.desmond.fepana)
add_rg_ct() (in Data)	alignmentLengthChanged() (in BaseAlignment)	asl (in amide_changeable)
add_rings() (in Data)	alignmentLocked() (in BaseAlignment)	asl (in amine_changeable)
add_set() (in ModelCheck)	AlignmentMetricOption (in schrodinger.application.msv.gui.viewmodel)	asl (in carboxyl_changeable)
add_signature() (in Feature)	AlignmentMetricsDelegate (in schrodinger.application.msv.gui.delegates)	asl (in changeable)
add_signatures() (in License)	AlignmentMetricsFilterProxy (in schrodinger.application.msv.gui.viewmodel)	asl (in histidine_changeable)
add_smiles() (in schrodinger.structutils.smilesfilter)	AlignmentMetricsProxyModel (in schrodinger.application.msv.gui.viewmodel)	asl (in rotatable_changeable)
add_spacer() (in schrodinger.application.desmond.report_helper)	AlignmentMetricsView (in schrodinger.application.msv.gui.view)	asl (in water_changeable)
add_static() (in Env)	alignmentResiduesChanged() (in AbstractStructureModel)	ASL (in schrodinger.utils.ligfilter)
add_step() (in Guide)	alignmentResiduesChanged() (in MaestroStructureModel)	asl() (in NewEntry)
add_step() (in Guide)	alignmentResiduesRemoved() (in MaestroStructureModel)	asl_expr (in _AtomSelection)
add_table() (in schrodinger.application.desmond.report_helper)	AlignmentSelectionModel (in schrodinger.application.msv.gui.view)	ASL_IONS (in Consensus)
add_tag() (in Sea)	AlignmentVerticalHeader (in schrodinger.application.msv.gui.view)	ASL_IONS (in ConsensusToolBar)
add_temp_hydrogen() (in schrodinger.application.matsci.rxn_path)	alignPolyhedron() (in ConvexPolyhedron)	ASL_LIGAND (in Consensus)
add_to_data() (in schrodinger.application.canvas.r_group)	alignSites() (in BindingSiteAligner)	ASL_LIGAND (in ConsensusToolBar)
add_var() (in binding)	alignStructure() (in StructAlign)	ASL_NAME_SEARCH_SPEEDUP (in _mmutil')
add_vtable() (in schrodinger.application.desmond.report_helper)	ALIPHATIC_RESIDUES (in schrodinger.structutils)	ASL_NAME_SEARCH_SPEEDUP (in schrodinger.utils.mmutil)
add_zmatrix_lines() (in schrodinger.application.matsci.zmutils)	alkali_metals (in schrodinger.application.prime.primefix)	ASL_WATER (in Consensus)
addActionItem() (in RowActionItem)	alkaline_earth_metals (in schrodinger.application.prime.primefix)	ASL_WATER (in ConsensusToolBar)
addActions() (in Factory)	ALL (in schrodinger.application.desmond.starter.ui.cmdline)	AslCriterion (in schrodinger.utils.ligfilter)
addAlignmentAxesToTemplate() (in ConvexPolyhedron)	ALL (in schrodinger.application.glide.glide)	AslLigandSearcher
addAlignToolBar() (in ViewerWindow)	ALL (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	ASLObject (in schrodinger.application.desmond.enhsamp)
addAngle() (in _FFIO)	ALL (in ParserWrapper)	aslselect_atom() (in schrodinger.application.desmond.cms)
addAnglefbhw() (in _FFIO)	ALL (in schrodinger.project)	AslValidator (in schrodinger.application.desmond.cmj)
addAnglefbhws() (in _FFIO)	ALL (in schrodinger.utils.cmdline)	AsMenu (in schrodinger.application.bioluminate.pml_menus)
addAnglemap() (in _FEPIO)	all_annotations (in BaseAlignment)	asNamedTuple() (in PhaseHypothesisInputConfig)
addAnglemaps() (in _FEPIO)	all_basisnames() (in schrodinger.application.jaguar.jaguar_keyword_utils)	asp_prop (in MopacResults71)
addAngleRestraint() (in Minimizer)	all_buttons (in ColorEditor)	asp_tot_prop (in MopacResults71)
addAngles() (in _FFIO)	ALL_CONSTRAINTS_BUTTON (in OptimizationTab)	ASPARAGINE (in schrodinger.application.msv.domain.residue)
addAnnotationAction() (in SimplifiedSequenceViewer)	all_dftnames() (in schrodinger.application.jaguar.jaguar_keyword_utils)	ASPARTIC_ACID (in schrodinger.application.msv.domain.residue)
addAntibodyNumberingToolBar() (in ViewerWindow)	ALL_FILE_SUFFIX (in schrodinger.application.matsci.mecp_mod)	aspectScale() (in schrodinger.application.desmond.report_helper)
addAtom() (in Structure)	all_jobs (in JobDJ)	assemble_bulk_results() (in schrodinger.trajectory.analyze_trajectories)
addAtomGroupRow() (in AtomGroupFrame)	all_keywords() (in schrodinger.application.jaguar.jaguar_keyword_utils)	assemble_energy_results() (in schrodinger.trajectory.analyze_trajectories)
addAtommap() (in _FEPIO)	ALL_LINES (in schrodinger.test.stu.outcomes.compare_csv')	assemble_interaction_energy_results() (in schrodinger.trajectory.analyze_trajectories)
addAtommaps() (in _FEPIO)	all_meaningful_keywords() (in schrodinger.application.jaguar.jaguar_keyword_utils)	assert_build_id_matches() (in schrodinger.test.stu.common)
addAtoms() (in Structure)	all_metals (in schrodinger.application.prime.primefix)	assert_ct_smarts() (in schrodinger.test.stu.outcomes.smarts_check')
addAtomsToSet() (in AsetFrame)	all_multicomb() (in schrodinger.application.desmond.autopartition)	assert_no_major_problems() (in schrodinger.test.structurecheck)
addAttachmentPoint() (in AtomMappingData)	ALL_OLD_MARKER_PROPS (in schrodinger.application.matsci.builderwidgets)	assertAtomMapsEqual() (in schrodinger.test.canvas_utils)
addAttr() (in PhpHypoAdaptor)	ALL_PL_INTERACTIONS (in schrodinger.application.desmond.fep_edge_report_maker)	assertConformersAlmostEqual() (in StructureAssertionsTestCase)
addAutoGpuCbToLayout() (in FEPConfigDialog)	all_properties() (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	assertConformersAlmostEqual() (in schrodinger.test.custom_assertions)
addAutoGpuCbToLayout() (in DesmondGuiConfigDialog)	ALL_PROPERTIES_TERM (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	assertCSVFilesMatch() (in schrodinger.test.canvas_utils)
addBidentateLigand() (in ComplexBuilder)	ALL_PROTEINS (in schrodinger.application.bioluminate.actions.icons)	assertCSVFilesMatchByLine() (in schrodinger.test.canvas_utils)
addBond() (in _FFIO)	ALL_RANDOM_CHANNELS (in Constants)	assertEqual() (in schrodinger.test.canvas_utils)
addBond() (in Structure)	ALL_RESIDUES (in schrodinger.application.bioluminate.protein)	assertFileMatches() (in GlideSystemTest)
addBond() (in _StructureAtom)	ALL_RESIDUES (in PrimeConfig)	AssertionError
addBondmap() (in _FEPIO)	all_rows (in EntryGroup)	assertLogFileNoDiff() (in GlideSystemTest)
addBondmaps() (in _FEPIO)	all_rows (in Project)	assertOutFilesExists() (in GlideSystemTest)
addBonds() (in _FFIO)	ALL_SEARCH_ALONG (in TransitionStateTab)	assertProteinHealth() (in ProteinReportCheck)
addBonds() (in Structure)	ALL_SHAPES (in schrodinger.application.matsci.nano.particle)	assertPWFilesMatch() (in schrodinger.test.canvas_utils)
addButtonToBottomLayout() (in AppFramework)	ALL_SMARTS (in Constants)	assertSame() (in _LicenseInfo)
addc() (in ComUtil)	ALL_SOLVENT_KEYVALUES (in schrodinger.application.jaguar.gui.tabs.solvation_tab)	assertSameNumberOfAtoms() (in StructureAssertionsTestCase)
addCallback() (in JobInputFrame)	ALL_SOLVENTS (in schrodinger.application.jaguar.gui.utils)	assertSameNumberOfAtoms() (in schrodinger.test.custom_assertions)
addcascademenu() (in MainMenuBar)	ALL_STRUCS (in MultiStructureTab)	assertSameStructure() (in StructureAssertionsTestCase)
addCellForEachRow() (in _Column)	all_tors (in FEPTorsionsContainer)	assertSameStructure() (in schrodinger.test.custom_assertions)
addCentralWidget() (in AppFramework)	ALL_TYPES (in Constants)	assign() (in stringvector)
addChain() (in Code)	ALL_TYPES (in schrodinger.utils.preferences)	assign() (in SwigDoubleVector)
addCharges() (in SpeciesData)	allCoordinatesDeleted() (in CoordinateTab)	assign() (in SwigDoubleVector3)
addChild() (in Partition)	allFacesIntersected() (in ConvexPolyhedron)	assign() (in SwigIntVector)
addChild() (in Partitioning)	allGroupIndices() (in RowModel)	assign() (in SwigStringVector)
addChild() (in DebugEventListener)	ALLINDICIES (in Grow)	assign() (in SwigUInt64Vector)
addChild() (in DebugEventSocketProxy)	allLigandNames() (in sketcherLID)	assign() (in SwigUnsignedIntVector)
addChild() (in DebugTreeAdaptor)	allocate() (in Queue)	assign() (in SwigUnsignedIntVector2)
addChild() (in TraceDebugEventListener)	ALLOW_ADSORPTION_ONTO (in Constants)	assign() (in SwigVectorIntIntPair)
addChild() (in BaseTree)	ALLOW_ADSORPTION_ONTO_METAVAR (in Constants)	assign() (in SwigDoubleVector)
addChild() (in BaseTreeAdaptor)	ALLOW_FRAGMENTS (in schrodinger.application.matsci.nano.particle)	assign() (in SwigDoubleVector3)
addChild() (in Tree)	ALLOW_FRAGMENTS (in schrodinger.application.matsci.nano.slab)	assign() (in SwigIntVector)
addChild() (in TreeAdaptor)	ALLOW_THREADS (in schrodinger.protein.assignment)	assign() (in SwigStringVector)
addChild() (in DendrogramNode)	ALLOWED_ANGLES (in schrodinger.test.stu.outcomes.custom.glide)	assign() (in SwigUInt64Vector)
addChildren() (in BaseTree)	ALLOWED_COLOR (in Rama)	assign() (in SwigUnsignedIntVector)
addClearButton() (in MM_QLineEdit)	allowed_function_modules (in schrodinger.infra.propedit)	assign() (in SwigUnsignedIntVector2)
addCnst() (in PhpHypoAdaptor)	allowed_function_names (in schrodinger.infra.propedit)	assign() (in SwigVectorIntIntPair)
addColumn() (in WidgetTable)	allowed_functions (in schrodinger.infra.propedit)	assign() (in SwigDoubleVector)
addCommandLineOptions() (in App)	ALLOWED_ISOMERS (in schrodinger.application.matsci.buildcomplex)	assign() (in SwigDoubleVector3)
addConsButtonPressed() (in OptimizationTab)	allowed_operators (in schrodinger.infra.propedit)	assign() (in SwigIntVector)
addConsensusToolBar() (in ViewerWindow)	ALLOWS_NEGATIVE_SCORES (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	assign() (in SwigStringVector)
addConstraint() (in _FFIO)	allTransmutationsCompleted() (in Alchemist)	assign() (in SwigUInt64Vector)
addConstraint() (in ConstraintGroup)	allTransmutationsCompleted() (in ElementAlchemist)	assign() (in SwigUnsignedIntVector)
addConstraint() (in PhpSiteConstrainer)	allTransmutationsCompleted() (in VacancyAlchemist)	assign() (in SwigUnsignedIntVector2)
addConstraintForLID() (in sketcherScene)	aln (in SequenceAlignmentModel)	assign() (in SwigVectorIntIntPair)
addConstraintGroup() (in Dock)	aln_by_homology (in AlignmentMetricsFilterProxy)	assign() (in SwigDoubleVector)
addConstraints() (in _FFIO)	aln_by_identity (in AlignmentMetricsFilterProxy)	assign() (in SwigDoubleVector3)
addContext() (in Factory)	aln_by_score (in AlignmentMetricsFilterProxy)	assign() (in SwigIntVector)
addCoord() (in ZAtom)	aln_by_similarity (in AlignmentMetricsFilterProxy)	assign() (in SwigStringVector)
addCoordinate() (in ConstraintCoordinatesModel)	alnByHomologyChanged() (in ViewStylePopUp)	assign() (in SwigUInt64Vector)
addCoordinate() (in OptimizationTab)	alnByIdentityChanged() (in ViewStylePopUp)	assign() (in SwigUnsignedIntVector)
addCoordinate() (in ScanCoordinatesModel)	alnByScoreChanged() (in ViewStylePopUp)	assign() (in SwigUnsignedIntVector2)
addCoordinate() (in ScanTab)	alnBySimilarityChanged() (in ViewStylePopUp)	assign() (in SwigVectorIntIntPair)
addCostProperties() (in Ionizer)	alnColumnsChanged() (in ViewStylePopUp)	assign() (in DoubleDoubleList)
addCPUArg() (in TestRunnerParser)	ALOGP_INTERVAL (in schrodinger.application.moldescriptors)	assign() (in DoubleList)
addCriterion() (in PropFilterDialog)	ALPHA (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)	assign() (in StringList)
addCt() (in PhpHypoAdaptor)	ALPHA (in schrodinger.application.desmond.enhanced_sampling.mexpParser)	assign() (in SwigAtomList)
addCV() (in Meta)	ALPHA_IDX (in schrodinger.application.matsci.nano.interface_mod)	assign() (in SwigAtomPairList)
addData() (in Grid)	ALPHA_KEY (in schrodinger.application.matsci.desmondutils)	assign() (in SwigAtomPairWithValueList)
addData() (in PhaseDB)	ALPHA_KEY (in Crystal)	assign() (in SwigAtomQueryParamsList)
addData() (in Structures)	ALPHA_ORBITALS (in SurfacesSubTab)	assign() (in SwigDcNonPbcAtomIdxList)
addData() (in Text)	ALPHA_PARAM (in ParserWrapper)	assign() (in SwigDcPbcAtomList)
addDatabase() (in ActiveDatabaseDialog)	alpha_polar() (in schrodinger.application.jaguar.textparser)	assign() (in SwigPiCationList)
addDefinition() (in ChannelDefinitions)	alpha_polar_precision (in JaguarResults)	assign() (in SwigPiPiInteractionList)
AddDefinitionDialog (in schrodinger.ui.ligfilter)	alphabetizeNames() (in PropertySelector)	assign() (in SwigRingList)
addDefinitionsFromFile() (in ChannelDefinitions)	alphabetizeNames() (in PropertySelector)	assign() (in SwigSaltBridgeList)
addDesmondPBC() (in Scaffold)	alreadyParsedRule() (in BaseRecognizer)	assign() (in AssignBondOrders)
addDihedmap() (in _FEPIO)	ALSO_REG_BOND_KEY (in schrodinger.application.matsci.desmondutils)	assign() (in SwigDoubleVector)
addDihedmaps() (in _FEPIO)	ALSO_REG_BOND_KEY (in PBCBond)	assign() (in SwigDoubleVector3)
addDihedral() (in _FFIO)	alt_matches() (in Feature)	assign() (in SwigIntVector)
addDihedrals() (in _FFIO)	alt_xyz (in _StructureAtom)	assign() (in SwigStringVector)
addDirectories() (in TestRunnerParser)	alternateFurthurBonds() (in _StructureFragmenter)	assign() (in SwigUInt64Vector)
addDistanceRestraint() (in Minimizer)	alumo_prop (in MopacResults71)	assign() (in SwigUnsignedIntVector)
addDisulfideBond() (in ProteinSequenceAnnotations)	always_true() (in schrodinger.test.stu.outcomes.custom.demo_custom_workup)	assign() (in SwigUnsignedIntVector2)
added() (in DictDiffer)	alwaysLocal() (in App)	assign() (in SwigVectorIntIntPair)
addEigenpair() (in NMA)	am (in _FFIOConstraint)	assign_best_combinations() (in ProtAssign)
addEigenpair() (in PCA)	am (in _FFIOVirtual)	assign_bond_orders() (in schrodinger.application.matsci.nano.xtal)
addElement() (in _OtherBlock)	am (in _FFConstraint)	assign_bond_orders_w_mmlewis() (in schrodinger.application.matsci.nano.xtal)
addElements() (in _OtherBlock)	am (in _FFVirtual)	assign_cluster_combination() (in ProtAssign)
addEnv() (in Launcher)	amide_changeable (in ProtAssign)	assign_combination() (in hbond_cluster)
addExclmap() (in _FEPIO)	amine_changeable (in ProtAssign)	assign_forcefield() (in schrodinger.application.desmond.fepdiff)
addExclmaps() (in _FEPIO)	AMINO_ACIDS (in schrodinger.application.msv.domain.constants)	assign_st() (in schrodinger.structutils.assignbondorders)
addExclusion() (in _FFIO)	AMINO_ACIDS (in schrodinger.application.msv.domain.residue)	assign_state() (in amide_changeable)
addExclusions() (in _FFIO)	AMINO_ACIDS_3_TO_1 (in schrodinger.application.msv.domain.constants)	assign_state() (in amine_changeable)
addExecuteOptions() (in TestRunnerParser)	AMINO_ACIDS_ONE_AND_THREE_LETTER (in schrodinger.application.msv.domain.residue)	assign_state() (in carboxyl_changeable)
addExpandArg() (in TestRunnerParser)	AMINO_ACIDS_ONE_LETTER (in schrodinger.application.msv.domain.residue)	assign_state() (in changeable)
addExpectedInput() (in Stage)	AMINO_ACIDS_THREE_LETTER (in schrodinger.application.msv.domain.residue)	assign_state() (in histidine_changeable)
addExpectedKeyword() (in QSiteStage)	amorphous (in schrodinger.application.matsci)	assign_state() (in rotatable_changeable)
addExpectedOutput() (in Stage)	AmorphousCellBuilder (in schrodinger.application.matsci.amorphous)	assign_state() (in water_changeable)
addext() (in schrodinger.trajectory.prody.writenmd)	an (in _FFIOVirtual)	assign_state_of_changeable() (in ProtAssign)
addExtractArgs() (in TestRunnerParser)	an (in _FFVirtual)	assignActives() (in PhpProject)
addFeature() (in PhaseFeatureMixin)	ana (in schrodinger.application.desmond)	assignAromaticBonders() (in AssignBondOrders)
addFeaturesForWorkspaceLigands() (in PhaseFeatureMixin)	analysis (in schrodinger)	assignAromaticRing() (in AssignBondOrders)
addFileWidgets() (in JobInputFrame)	Analysis	assignAromaticRingGroup() (in AssignBondOrders)
addFinalizer() (in BaseJob)	Analysis (in schrodinger.application.desmond.title_to_hex)	assignAromaticRingOrders() (in AssignBondOrders)
addFindToolBar() (in ViewerWindow)	analysis (in schrodinger.protein)	assignbondorders (in schrodinger.structutils)
addForce() (in TestRunnerParser)	analysis (in schrodinger.trajectory)	AssignBondOrders (in schrodinger.structutils.assignbondorders)
addForceInputFile() (in Launcher)	ANALYSIS_DIR_NAME (in Analysis)	assignChainOrders() (in AssignBondOrders)
addFromFile() (in SurfaceDict)	analysis_params (in schrodinger.protein)	assignColorsWithThreshold() (in DendrogramGraphicTree)
addGaps() (in BaseAlignment)	AnalysisJob	assignDefaultGroups() (in PhpProject)
addGaps() (in Sequence)	analysistool (in schrodinger.trajectory)	ASSIGNED_AROMATIC (in schrodinger.structutils.assignbondorders)
addGaps() (in ProteinAlignment)	AnalysisTool (in schrodinger.trajectory.analysistool)	AssignForcefield
addGaps() (in ProteinSequence)	analyze (in schrodinger.structure)	assignGroupDoubleBonds() (in AssignBondOrders)
addGPGPUGroupToLayout() (in DesmondGuiConfigDialog)	analyze (in schrodinger.structutils)	assignGroups() (in PhpProject)
addGPGPUGroupToLayout() (in DesmondRestGuiConfigDialog)	analyze() (in Bfactor_data_set)	assignGroupTripleBonds() (in AssignBondOrders)
addGPGPUTableToLayout() (in FEPConfigDialog)	analyze() (in Gfactor_summary_data_set)	assignInactives() (in PhpProject)
addGPGPUTableToLayout() (in DesmondGuiConfigDialog)	analyze() (in backbone_dihedral_data_set)	assignment (in schrodinger.protein)
addGPGPUTableToLayout() (in GPGPUConfigDialog)	analyze() (in bond_angle_data_set)	assignQsarSet() (in PhpProject)
addGroupActionSlot() (in sketcher)	analyze() (in bond_length_data_set)	assignTemplatedSubstructures() (in AssignBondOrders)
addGroupPrereq() (in BaseJob)	analyze() (in chirality_data_set)	assignTripleBonds() (in AssignBondOrders)
addHost() (in JobSpecificationBuilder)	analyze() (in data_set)	ASSOCIATION_TYPE (in Constants)
addHost() (in RuntimeParametersBuilder)	analyze() (in gamma_Bfactor_data_set)	ASU_LABEL_KEY (in Crystal)
addHydrogenCap() (in QSiteInput)	analyze() (in improper_torsion_data_set)	ASU_TAG (in SpaceGroup)
AddHydrogens (in schrodinger.application.bioluminate.pml_menus)	analyze() (in missing_atoms_data_set)	AT_LEAST_ONE_MOL (in schrodinger.application.matsci.clusterstruct)
addHypothesisFromEntry() (in HypothesesListWidget)	analyze() (in peptide_planarity_data_set)	at_values (in Scan)
addIcon() (in JobStatusToolButton)	analyze() (in primex_steric_clash_data_set)	atid2atomsel() (in CmsModel)
addImportToolBar() (in ViewerWindow)	analyze() (in sidechain_dihedral_data_set)	atidToResname() (in ContactCmd)
addImproperfbhw() (in _FFIO)	analyze() (in sidechain_planarity_data_set)	ATOM (in BasisSetColumns)
addImproperfbhws() (in _FFIO)	analyze() (in steric_clash_data_set)	atom (in TextualStructure)
addInputFile() (in App)	analyze() (in DesmondSimulation)	atom (in _AtomCollection)
addInputFile() (in Launcher)	analyze_data() (in CalcBAR)	Atom (in schrodinger.utils.sea)
addInteraction() (in sketcherLID)	analyze_energy (in schrodinger.application.prime.gui)	atom() (in mexpParser)
addIonProperties() (in Ionizer)	analyze_energy_ui (in schrodinger.application.prime.gui.ui)	atom() (in AcceptorConstraint)
addIons() (in SystemBuilderInput)	analyze_it() (in Analysis)	atom() (in DonorConstraint)
ADDITIONAL_ROLE (in schrodinger.application.phase.constants)	analyze_pair() (in steric_clash_data_set)	atom() (in MetalConstraint)
ADDITIONAL_ROLE (in HypothesesListWidget)	analyze_paths() (in Perturbations)	atom() (in Structure)
addIvol() (in PhpHypoAdaptor)	analyze_pr_set() (in ModelCheck)	ATOM_ACHIRAL (in StructureAtom)
addJaguarMarker() (in BaseSubTab)	analyze_trajectories (in schrodinger.trajectory)	ATOM_ATTRIBUTES (in schrodinger.application.desmond.fepdiff)
addJaguarMarker() (in InputTabWithSubTabs)	analyzeBetweenGroups() (in TwoGroupFingerprintAnalyzer)	atom_b_factor() (in schrodinger.application.bioluminate.pml_menus)
addJaguarMarker() (in SubTabModel)	AnalyzeEnergyOptions (in schrodinger.application.prime.gui.analyze_energy)	ATOM_BALLNSTICK (in schrodinger.application.bioluminate.pml_menus)
addJaguarMarker() (in AtomSelectionDelegate)	AnalyzeEnergyWidget (in schrodinger.application.prime.gui.analyze_energy)	ATOM_BALLNSTICK (in schrodinger.structure)
addJaguarMarker() (in ChargeConstraintsTableView)	analyzeFingerprints() (in ActiveDecoyFingerprintAnalyzer)	ATOM_CHIRAL_ANR (in StructureAtom)
addJaguarMarkerForRow() (in SubTabModel)	analyzeGroups() (in TwoGroupFingerprintAnalyzer)	ATOM_CHIRAL_ANS (in StructureAtom)
addJaguarMarkerForRow() (in ChargeConstraintsModel)	analyzeStericClashes() (in ModelCheck)	ATOM_CHIRAL_R (in StructureAtom)
addJob() (in JobDJ)	analyzeWithinGroups() (in TwoGroupFingerprintAnalyzer)	ATOM_CHIRAL_S (in StructureAtom)
addJob() (in TestQueue)	AND (in schrodinger.application.bioluminate.propfilter)	ATOM_CIRCLE (in schrodinger.structure)
addJobControlOptions() (in TestRunnerParser)	ANG_TOL (in schrodinger.application.mcpro.modelsystemwizard)	atom_clicked() (in StructureListWidget)
addKey() (in Key)	angle (in schrodinger.application.desmond.fepana)	atom_color (in ColorBy)
addKey() (in Definition)	ANGLE (in Coord)	ATOM_CPK (in schrodinger.structure)
addLicense() (in JobSpecificationBuilder)	angle (in CationPiInteraction)	atom_exch (in schrodinger.protein.remediate)
addLicense() (in TaskSpecificationBuilder)	angle (in PiPiInteraction)	atom_highlighted() (in StructureView)
addLicense() (in Launcher)	Angle (in schrodinger.trajectory.analysis)	atom_index() (in Node)
addLigand() (in sketcher)	angle() (in _FFIO)	atom_indexes (in Ligand)
addLigands() (in PhpProject)	angle_bend_energy() (in schrodinger.application.qsite.output)	atom_indices (in Consensus)
addLine() (in CriteriaListModel)	angle_builtin_prop (in schrodinger.trajectory.ffstructure)	atom_indices (in _Group)
addLogFile() (in App)	anglefbhw() (in _FFIO)	atom_is_nonpolar() (in schrodinger.application.bioluminate.protein)
addLogFile() (in _Backend)	ANGLELARGE (in HoneycombUnitCell)	ATOM_LABELS (in MultiStructureTab)
addLogFile() (in Launcher)	anglemap() (in _FEPIO)	ATOM_MARKER_PROP_BASE (in schrodinger.application.matsci.builderwidgets)
addMask() (in PhpHypoAdaptor)	ANGLEMEDIUM (in HoneycombUnitCell)	atom_name (in _StructureAtom)
addMember() (in SpeciesData)	ANGLEMEDIUM (in NanoSheet)	atom_name_regex (in schrodinger.application.jaguar.gui.utils)
addmenu() (in MainMenuBar)	ANGLES_ONE_UNIQUE (in CrystalSystems)	atom_name_sort_key() (in schrodinger.application.jaguar.gui.utils)
addmenuitem() (in MainMenuBar)	ANGLES_ONE_UNIQUE_NOT_RIGHT (in CrystalSystems)	ATOM_NONE (in schrodinger.application.bioluminate.pml_menus)
addMessageName() (in _Backend)	ANGLES_THREE_UNIQUE (in CrystalSystems)	ATOM_NOSTYLE (in schrodinger.structure)
addMolecule() (in sketcherScene)	ANGLES_TWO_UNIQUE (in CrystalSystems)	ATOM_NUMS_ROLE (in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets)
addMolsToSet() (in AsetFrame)	ANGLES_TWO_UNIQUE_HEXAGONAL (in CrystalSystems)	atom_prop_link (in schrodinger.structure)
addMonitorFile() (in _Backend)	ANGLESMALL (in HoneycombUnitCell)	ATOM_RADII_DICT (in schrodinger.structutils.assignbondorders)
addMonodentateLigand() (in ComplexBuilder)	ANGLEWEIGHT (in ParserWrapper)	ATOM_RAINBOW_COLORS (in schrodinger.application.bioluminate.pml_menus)
addNavigationNode() (in CommonTreeNodeStream)	ANGSTROM_DEFAULT (in schrodinger.application.matsci.nano.slab)	atom_return (in mexpParser)
addNewConstraint() (in ChargeConstraintsSubTab)	angstrom_per_bohr (in schrodinger.application.jaguar.constants)	atom_selection_dialog() (in schrodinger.maestro.maestro)
addNormalsToTemplate() (in ConvexPolyhedron)	ANNIHILATION (in schrodinger.application.desmond.fep_gui)	atom_style (in _StructureAtom)
addNumericLineEdit() (in FEPConfigDialog)	annotate() (in CgHydrogenFragmentAnnotator)	atom_to_resID() (in schrodinger.protein._reliability)
addOneRow() (in AtomGroupModel)	annotate() (in MappingAnnotator)	atom_total (in JaguarResults)
addOneRow() (in PosResModel)	ANNOTATE_ACTIONS (in schrodinger.application.bioluminate.actions.configs)	atom_total (in Structure)
ADDOP (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)	annotation (in schrodinger.application.msv.domain)	atom_total (in _DesmondFrame)
ADDOP (in schrodinger.application.desmond.enhanced_sampling.mexpParser)	ANNOTATION_TYPE (in BaseRowDelegate)	atom_total (in FFStructure)
addOptions() (in SequenceFileDialog)	ANNOTATION_TYPE (in BetaStrandDelegate)	atom_type (in MetaAtom)
addOptions() (in CanvasFingerprintClusterCLI)	ANNOTATION_TYPE (in ConsensusFreqDelegate)	atom_type (in _StructureAtom)
addOptions() (in CanvasFingerprintGeneratorCLI)	ANNOTATION_TYPE (in ConsensusSeqDelegate)	atom_type (in ColorBy)
addOptions() (in CanvasFingerprintSimilarityCLI)	ANNOTATION_TYPE (in ConsensusSymbolsDelegate)	atom_type_name (in _StructureAtom)
addOrderedPartitiones() (in Partition)	ANNOTATION_TYPE (in DisulfideBondDelegate)	atom_typeMM (in ColorBy)
addOrReplaceSeqs() (in BaseAlignment)	ANNOTATION_TYPE (in ExposureTendencyDelegate)	ATOM_TYPING_SCHEMES (in CanvasFingerprintGenerator)
addOrReplaceSeqs() (in ProteinAlignment)	ANNOTATION_TYPE (in HelixPropensityDelegate)	ATOM_WIRE (in schrodinger.application.bioluminate.pml_menus)
addOtherBlock() (in _FEPIO)	ANNOTATION_TYPE (in HelixTermTendencyDelegate)	AtomBasisSetDelegate (in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets)
addOtherBlock() (in _FFIO)	ANNOTATION_TYPE (in HydrophobicityDelegate)	atomClasses (in PhpQSARModel)
addOutputFile() (in _Backend)	ANNOTATION_TYPE (in IsoelectricPointDelegate)	AtomContextMenu (in schrodinger.application.bioluminate.pml_menus)
addOutputFile() (in Launcher)	ANNOTATION_TYPE (in MeanHydrophobicityDelegate)	AtomGroup (in schrodinger.application.desmond.cms)
addOutputFile() (in Stage)	ANNOTATION_TYPE (in MeanIsoelectricPointDelegate)	AtomGroup (in schrodinger.application.desmond.mdkey)
addOutputFileBE() (in App)	ANNOTATION_TYPE (in RescodeDelegate)	ATOMGROUP_PREFIX (in Cms)
addOutputFileFE() (in App)	ANNOTATION_TYPE (in ResidueDelegate)	ATOMGROUP_PREFIX_LEN (in schrodinger.application.desmond.mdkey)
addPair() (in ConnectionStorage)	ANNOTATION_TYPE (in ResnumDelegate)	ATOMGROUP_PREFIX_NAME (in schrodinger.application.desmond.mdkey)
addPair() (in _FFIO)	ANNOTATION_TYPE (in RulerDelegate)	AtomGroupDelegate (in schrodinger.application.desmond.gui)
addPairmap() (in _FEPIO)	ANNOTATION_TYPE (in SequenceLogoDelegate)	AtomGroupFrame (in schrodinger.application.desmond.gui)
addPairmaps() (in _FEPIO)	ANNOTATION_TYPE (in SideChainChemDelegate)	AtomGroupModel (in schrodinger.application.desmond.gui)
addPairs() (in _FFIO)	ANNOTATION_TYPE (in SpaceRowDelegate)	AtomGroupRow (in schrodinger.application.desmond.gui)
addPairwiseStructuralAnnotationActionSlot() (in sketcher)	ANNOTATION_TYPE (in StericGroupDelegate)	atomic_charge_prop (in MopacResults71)
addParent() (in Partition)	ANNOTATION_TYPE (in TurnPropensityDelegate)	atomic_number (in _StructureAtom)
addParent() (in Partitioning)	ANNOTATION_TYPES (in ProteinAlignmentAnnotations)	ATOMIC_SYMBOL (in Constants)
addPattern() (in LigfilterFrame)	ANNOTATION_TYPES (in ProteinSequenceAnnotations)	ATOMIC_SYMBOLS (in schrodinger.application.matsci.atomicsymbols)
addPatternCriterion() (in LigfilterFrame)	annotation_types (in Sequence)	ATOMIC_SYMBOLS_LIST (in schrodinger.application.matsci.atomicsymbols)
addPBCProperties() (in Scaffold)	AnnotationClass (in Sequence)	atomic_weight (in _StructureAtom)
addPiPiInteraction() (in sketcher)	AnnotationFilterProxyModel (in schrodinger.application.msv.gui.viewmodel)	atomicsymbols (in schrodinger.application.matsci)
addPkaMarkers() (in InputEntriesModelPka)	AnnotationProxyModel (in schrodinger.application.msv.gui.viewmodel)	atomicsymbolsgui (in schrodinger.application.matsci)
addPoints() (in _RamachandranCallback)	AnnotationType (in schrodinger.application.msv.gui.viewconstants)	atommap() (in _FEPIO)
addPointsToTemplate() (in ConvexPolyhedron)	annotationTypes() (in SequenceAlignmentModel)	AtomMappingData (in schrodinger.application.desmond.fep_mapping)
addPosfbhw() (in _FFIO)	answer (in schrodinger.application.desmond.ana)	AtomMarker (in schrodinger.maestro.markers)
addPosfbhws() (in _FFIO)	antibody (in schrodinger.application.bioluminate)	AtomPairWithValue (in schrodinger.infra.structure)
addPosFrozen() (in Minimizer)	ANTIBODY (in PIPERConstraint)	atomPicked() (in BasisSetSubTab)
addPosResRow() (in RestraintsTab)	ANTIBODY_NUM_TOOLBAR (in ViewerWindow)	AtomQueryParams (in schrodinger.infra.structure)
addPosRestraint() (in Minimizer)	antibody_utils (in schrodinger.application.bioluminate)	atoms (in Consensus)
addPredefinedCriterion() (in LigfilterFrame)	AntibodyNumberingToolBar (in schrodinger.application.bioluminate.ssv.toolbars)	ATOMS (in MultiStructureTab)
addPrereq() (in BaseJob)	AntibodyPreset (in schrodinger.application.bioluminate.pml_menus)	ATOMS (in ChargeConstraintsColumns)
addPreviousFreezerFile() (in StructureGenome)	ANTIGEN (in PIPERConstraint)	ATOMS (in ParserWrapper)
addProduct() (in ReactionTab)	ANTIGEN_TYPE (in FullColumns)	atoms (in PhpIntCoord)
addProp() (in PhpHypoAdaptor)	ANTIGEN_TYPE (in SplitColumns)	ATOMS (in schrodinger.structutils.rmsd)
addPropCriterion() (in LigfilterFrame)	antlr3 (in schrodinger.application.desmond)	atoms() (in AcceptorConstraint)
addProperty() (in schrodinger.infra.propedit)	antlr_version (in BaseRecognizer)	atoms() (in DonorConstraint)
addpropop1Modified() (in LigfilterFrame)	antlr_version (in mexpLexer)	atoms() (in MetalConstraint)
addPseudo() (in _FFIO)	antlr_version (in mexpParser)	ATOMS_ROLE (in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.base_widgets)
addPseudos() (in _FFIO)	antlr_version_str (in BaseRecognizer)	atoms_within_3_bonds() (in schrodinger.application.desmond.reorder_atom)
addQMCut() (in QSiteInput)	antlr_version_str (in mexpLexer)	atomsasl() (in schrodinger.application.prepwizard)
addQMMolecule() (in QSiteInput)	antlr_version_str (in mexpParser)	atomsChanged() (in WorkspaceHub)
addQsar() (in PhpHypoAdaptor)	ANTLRFileStream (in schrodinger.application.desmond.antlr3.streams)	atomsel() (in ASLObject)
addRad() (in PhpHypoAdaptor)	ANTLRInputStream (in schrodinger.application.desmond.antlr3.streams)	atomselection (in schrodinger.trajectory)
addRandomChannels() (in ChannelDefinitions)	ANTLRStringStream (in schrodinger.application.desmond.antlr3.streams)	atomSelectionChanged() (in WorkspaceHub)
addRandomChannelsFromAll() (in ChannelDefinitions)	ANY_CONTACT (in StructuralInteractionFingerprintGenerator)	AtomSelectionDelegate (in schrodinger.application.jaguar.gui.input_tab_widgets_pka)
addRandomChannelsOnTheFly() (in ChannelDefinitions)	APBS_INPUT (in schrodinger.application.desmond.fep_net_charge)	AtomSelectionDelegate (in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.charge_constraints_widgets)
addRangeWidgets() (in JobInputFrame)	api (in schrodinger.test.performance)	AtomType (in Packing)
addReactant() (in ReactionTab)	api_url() (in schrodinger.test.performance.reporter)	atomTypingCB() (in CanvasFingerprintGeneratorGUI)
addReferenceSeries() (in _BasePlotter)	ApiKeyAuth	attach_fragment() (in schrodinger.structutils.build)
addRequiredOutputFile() (in _Backend)	aposteri_e() (in schrodinger.application.jaguar.textparser)	attach_structure() (in schrodinger.structutils.build)
addRequiredOutputFile() (in Launcher)	app (in schrodinger.application.bioluminate.sliderchart)	attachAdjacentResidue() (in MmpdbxReader)
addResidue() (in RegionInfo)	app (in schrodinger.job)	attachCap() (in CapTermini)
addResidue() (in sketcher)	App (in schrodinger.job.app)	Attachment (in schrodinger.application.combiglide.packages.chutils)
addResidueAtom() (in sketcher)	APP_DIR (in schrodinger.application.matsci.jobutils)	ATTACHMENT_PAIRS_TO_SKIP (in schrodinger.application.canvas.r_group)
addResidueInteraction() (in sketcher)	APPDATA (in schrodinger.utils.fileutils)	ATTACHMENT_PROPERTY (in schrodinger.application.matsci.buildcomplex)
addResidues() (in PrimeConfig)	APPDATA_DIR (in schrodinger.application.combiglide.combenumdock)	attachments (in AdductAttachment)
addResidues() (in BaseAlignment)	APPDATA_DIR (in schrodinger.application.desmond.mdkey)	attachments (in SubstrateAttachment)
addResidues() (in ProteinAlignment)	appdata_dir (in schrodinger.utils.ligfilter)	ATTACHPROP (in schrodinger.structutils.createfragments)
addResource() (in LocalServerProcess)	appdata_file (in schrodinger.utils.ligfilter)	attachStructConnInteraction() (in MmpdbxReader)
addRestraint() (in _FFIO)	AppDockWidget (in schrodinger.ui.qt.appframework)	ATTRACTION (in PIPERConstraint)
addRestraints() (in _FFIO)	append() (in FFIOStructure)	ATYP_MW_TARGET (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addResult() (in PerformanceTestCase)	append() (in XpDesWriter)	ATYP_MW_WEIGHT (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addResult() (in Test)	append() (in ProteinSequence)	ATYP_NAT_TARGET (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addRow() (in ActiveDatabaseTable)	append() (in Sequence)	ATYP_NAT_WEIGHT (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addRow() (in PathModel)	append() (in QMRegion)	ATYP_NEL_TARGET (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addRow() (in ResiduesModel)	append() (in stringvector)	ATYP_NEL_WEIGHT (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addRow() (in StrucListModel)	append() (in SwigDoubleVector)	ATYPICAL (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addRow() (in SubTabModel)	append() (in SwigDoubleVector3)	ATYPICAL_PATTERNS (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addRow() (in WidgetTable)	append() (in SwigIntVector)	ATYPICAL_PROPS (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
addRule() (in PhpFeatureRules)	append() (in SwigStringVector)	AU_TO_KG_CONST (in MSEnergyGroup)
addRule() (in MM_CScheme)	append() (in SwigUInt64Vector)	auth (in _BaseClient)
addRules() (in PhpHypoAdaptor)	append() (in SwigUnsignedIntVector)	AUTO (in schrodinger.application.matsci.reordergui)
addSalt() (in SystemBuilderInput)	append() (in SwigUnsignedIntVector2)	AUTO (in schrodinger.protein.getpdb)
addScript() (in Runner)	append() (in SwigVectorIntIntPair)	auto_partition() (in schrodinger.application.desmond.autopartition)
addScriptArgs() (in Launcher)	append() (in SwigDoubleVector)	auto_write_lines (in schrodinger.protein.getpdb_utility)
addSearchIcon() (in MM_QLineEdit)	append() (in SwigDoubleVector3)	AutoColorCarbons (in schrodinger.application.bioluminate.pml_menus)
addSegmentPlaneIntersectionsToTemplate() (in ConvexPolyhedron)	append() (in SwigIntVector)	AutoColorObjects (in schrodinger.application.bioluminate.pml_menus)
addSeq() (in BaseAlignment)	append() (in SwigStringVector)	AutoColorSubMenu (in schrodinger.application.bioluminate.pml_menus)
addSeq() (in AbstractMsvWidget)	append() (in SwigUInt64Vector)	AutoCycleCarbonColor (in schrodinger.application.bioluminate.pml_menus)
addSeqs() (in BaseAlignment)	append() (in SwigUnsignedIntVector)	AutoCycleColor (in schrodinger.application.bioluminate.pml_menus)
addSeqs() (in ProteinAlignment)	append() (in SwigUnsignedIntVector2)	autoGpuToggled() (in DesmondGuiConfigDialog)
addSeqs() (in AbstractMsvWidget)	append() (in SwigVectorIntIntPair)	AUTOHOST (in schrodinger.application.matsci.jaguarworkflows)
addSeries() (in _BasePlotter)	append() (in MMKVArgList)	autoMap() (in ReorderAtomFrame)
addServerArg() (in TestRunnerParser)	append() (in SwigDoubleVector)	Automatic (in SpinTreatment)
addSettings() (in WriteInputs)	append() (in SwigDoubleVector3)	automatic_analysis_generator (in schrodinger.trajectory)
addSite() (in _FFIO)	append() (in SwigIntVector)	AUTOMATIC_CACHE_FREEING (in schrodinger.project)
addSiteData() (in PhpDeltaHypo)	append() (in SwigStringVector)	AutomaticJobnameMixin (in schrodinger.application.jaguar.gui.base_panel)
addSiteMaskData() (in PhpSiteMask)	append() (in SwigUInt64Vector)	autopartition (in schrodinger.application.desmond)
addSiteMaskGroup() (in PhpSiteMask)	append() (in SwigUnsignedIntVector)	autoPlace() (in Membrane_Model)
addSites() (in _FFIO)	append() (in SwigUnsignedIntVector2)	autoPlaceByMolecule() (in Membrane_Model)
addSites() (in PhaseFeatureMixin)	append() (in SwigVectorIntIntPair)	autoprojectsync_call() (in schrodinger.application.desmond.maestro)
addSkipArg() (in TestRunnerParser)	append() (in SwigDoubleVector)	AUTOQSAR_MAIN (in _licensing')
addSpaceGroupPBC() (in Scaffold)	append() (in SwigDoubleVector3)	AUTOQSAR_MAIN (in schrodinger.infra.licensing)
addSphere() (in PhaseXvolMarkers)	append() (in SwigIntVector)	AUTOQSAR_MAIN (in schrodinger.infra.mm)
addSphere() (in PhpExclVol)	append() (in SwigStringVector)	autoResize() (in ViewerTable)
addStage() (in MultiStageArea)	append() (in SwigUInt64Vector)	autoResizeCells() (in _GenericViewerDelegate)
addStage() (in LinearWriter)	append() (in SwigUnsignedIntVector)	autoSetGpuList() (in Host)
addStage() (in Writer)	append() (in SwigUnsignedIntVector2)	autosetToggled() (in _Pert)
addStretchfbhw() (in _FFIO)	append() (in SwigVectorIntIntPair)	AUX_DATA_NAME (in schrodinger.infra.mmproj)
addStretchfbhws() (in _FFIO)	append() (in DoubleDoubleList)	available_color_schemes() (in schrodinger.structutils.color)
addString() (in sketcher)	append() (in DoubleList)	AVAILABLE_FF (in _Flex)
addStructToCollection() (in _zoomViewItem)	append() (in StringList)	available_tokens() (in LicenseResource)
addStructure() (in sketcher)	append() (in Structure)	average_cavity() (in WaterMapAnaJob)
addStructureFeatures() (in PhaseFeatureMixin)	append() (in SwigAtomList)	average_cavity_cns() (in WaterMapAnaJob)
addSubMenu() (in Factory)	append() (in SwigAtomPairList)	average_energy() (in WaterMapAnaJob)
addSubprocessStackedWidget() (in FEPConfigDialog)	append() (in SwigAtomPairWithValueList)	average_hbond() (in WaterMapAnaJob)
addSubTabMarker() (in SubTabMixin)	append() (in SwigAtomQueryParamsList)	AverageStructure (in schrodinger.trajectory.analysis)
addSubTabs() (in InputTabWithSubTabs)	append() (in SwigDcNonPbcAtomIdxList)	AXES (in Box)
addSurfaceToProject() (in ProjectSurface)	append() (in SwigDcPbcAtomList)	AXES (in schrodinger.application.matsci.buildcomplex)
addTab() (in MSVPanel)	append() (in SwigPiCationList)	Axis() (in _VDCoordinateFrame)
addTab() (in MSVTabWidget)	append() (in SwigPiPiInteractionList)	AXIS_KEY (in schrodinger.application.matsci.nano.particle)