[ Identifiers | To Do | Deprecations ]

Identifier Index

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R

r (in MaestroArrow)	removeMarker (in InputTabWithSubTabs)	resKey() (in InteractionReader)
r (in MaestroSphere)	removeMarker (in SubTabModel)	resnum (in _Residue)
r_clone (in schrodinger.application.desmond.fepana)	removeMarker (in AtomSelectionDelegate)	resnum (in _StructureAtom)
R_GAS_CONSTANT (in MSEnergyGroupAnalysis)	removeMarker (in ChargeConstraintsTableView)	resnum() (in Cut)
r_group (in schrodinger.application.canvas)	removeMarkerForRow() (in SubTabModel)	resolution() (in _VDAxis)
r_group_asl (in schrodinger.application.desmond)	removeMarkerForRow() (in ChargeConstraintsModel)	resolution() (in _VDCoordinateFrame)
r_group_dee (in schrodinger.application.canvas)	removeMissingPoints() (in SliderPlot)	RESOLUTION_DEFAULT (in schrodinger.graphics3d.arrow)
RADICALS_FORCE_OFF (in _mmutil')	removeOneRow() (in AtomGroupModel)	RESOLUTION_DEFAULT (in schrodinger.graphics3d.sphere)
RADICALS_FORCE_OFF (in schrodinger.utils.mmutil)	removeOneRow() (in PosResModel)	RESOLUTION_MAX (in schrodinger.graphics3d.arrow)
RADICALS_FORCE_ON (in _mmutil')	removeOrientDummyAtoms() (in schrodinger.application.mcpro.zmat)	RESOLUTION_MAX (in schrodinger.graphics3d.sphere)
RADICALS_FORCE_ON (in schrodinger.utils.mmutil)	removeParticipant() (in ReactionMoleculesTab)	RESOLUTION_MIN (in schrodinger.graphics3d.arrow)
Radiobutton (in schrodinger.ui.widget.tkinterwidget)	removeParticipant() (in ReactionTab)	RESOLUTION_MIN (in schrodinger.graphics3d.sphere)
RadiobuttonCell (in schrodinger.ui.widgettable)	RemovePC (in schrodinger.application.bioluminate.pml_menus)	resolve_atomsel() (in FcnCall)
RadiobuttonColumn (in schrodinger.ui.widgettable)	removePkaMarkers() (in InputEntriesModelPka)	resolve_atomsel() (in Node)
RadioSelect (in schrodinger.ui.widget.pmwwidget)	removeProperties() (in StructureGenome)	resolve_atomsel() (in schrodinger.application.desmond.enhsamp)
RADIUS (in NanoTube)	removeRow() (in CoordinatesModel)	resolve_links() (in schrodinger.application.combiglide.combenumdock)
radius (in MaestroArrow)	removeRow() (in CriteriaListModel)	resolveCoordsConflict() (in OptimizationAndScanMixin)
radius (in MaestroSphere)	removeRowNumbers() (in ResiduesModel)	RESONANCE (in TheoryTab)
RadiusOfGyration (in schrodinger.trajectory.analysis)	removeRows() (in SubTabModel)	resource_id() (in schrodinger.test.performance.reporter)
raise_for_status() (in schrodinger.test.stu.client)	removeRows() (in BasisSetModel)	RESOURCE_OK (in schrodinger.application.licensing.licadmin)
raise_main_window() (in schrodinger.maestro.maestro)	removeRows() (in WidgetTable)	RESOURCE_PROBLEMS (in schrodinger.application.licensing.licadmin)
rama (in schrodinger.ui)	removeSelectedRow() (in WidgetTable)	resource_summary() (in schrodinger.application.licensing.licadmin)
Rama (in schrodinger.ui.rama)	removeSelectedRows() (in SubTabTableView)	RESOURCE_UNAVAILABLE (in schrodinger.application.licensing.licadmin)
Ramachandran (in schrodinger.trajectory.analysis)	removeSelectedRows() (in WidgetTable)	resources() (in schrodinger.application.licensing.licadmin)
raman_intensity_precision (in NormalMode)	removeStruct() (in collectionViewerModel)	resources_from_list() (in schrodinger.application.licensing.licadmin)
RamanSubTab (in schrodinger.application.jaguar.gui.tabs.properties_tab)	removeSubTabMarker() (in SubTabMixin)	resources_from_path() (in schrodinger.application.licensing.licadmin)
ramp_colors (in Mapping)	removeTerminalAtoms() (in _StructureFragmenter)	respaBondChanged() (in IntegrationTab)
RANDOM_ALL_TO_ON_THE_FLY_THRESH (in ChannelDefinitions)	removeToolBar() (in ViewerWindow)	ResStats (in Packing)
RANDOM_INT_BOUND (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	RemoveWaters (in schrodinger.application.bioluminate.pml_menus)	REST_DEFAULT_NUM_CPUS (in schrodinger.application.desmond.fep_gui)
random_rotation() (in schrodinger.application.matsci.amorphous)	Rename (in schrodinger.application.bioluminate.pml_menus)	REST_DEFAULT_NUM_GPUS (in schrodinger.application.desmond.fep_gui)
RANDOM_SEED (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	rename() (in NewEntry)	rest_inp (in schrodinger.application.desmond)
RANDOM_SEED (in Constants)	rename() (in ProjectSurface)	REST_MARKER (in schrodinger.application.desmond.rest_inp)
random_shuffle() (in schrodinger.application.desmond.fep_mapping)	rename() (in Surface)	rest_tab_ui (in schrodinger.application.desmond)
random_string() (in schrodinger.application.desmond.util)	rename_atom_property() (in schrodinger.application.desmond.struc)	RESTART (in schrodinger.application.desmond.starter.ui.cmdline)
RANDOM_TYPES_CHOICES (in Constants)	rename_cms_title() (in Analysis)	restart (in JaguarInput)
randomize_st() (in schrodinger.application.desmond.fepdiff)	renameCollection() (in SimpleEnumDockPanel)	restart (in JaguarOutput)
RandVelFrame (in schrodinger.application.desmond.gui)	renameColorScheme() (in ColorSchemeManager)	RESTART (in schrodinger.utils.cmdline)
range() (in Bitset)	renameProperty() (in schrodinger.infra.propedit)	restart() (in RetryTimer)
ranges (in schrodinger.infra.propedit)	rend (in SwigDoubleVector)	Restart() (in schrodinger.pipeline.pipeline)
RANK_SELECTION (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	rend (in SwigDoubleVector3)	restart() (in StageJob)
RAW_AFEP (in DesmondTyper)	rend (in SwigIntVector)	Restart() (in schrodinger.pipeline.stage)
RAW_FEP (in DesmondTyper)	rend (in SwigStringVector)	restart_for_backend_error() (in JobErrorHandler)
RAW_FEP (in McproTyper)	rend (in SwigUInt64Vector)	restart_for_backend_error() (in FepJob)
RAW_REGULAR (in DesmondTyper)	rend (in SwigUnsignedIntVector)	restart_name() (in schrodinger.application.jaguar.output)
RAW_REGULAR (in McproTyper)	rend (in SwigUnsignedIntVector2)	restart_re (in schrodinger.application.jaguar.output)
RAW_REGULAR (in WatermapTyper)	rend (in SwigVectorIntIntPair)	restart_subjobs() (in StageBase)
RAW_SCORE_KEY (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	rend (in SwigDoubleVector)	restart_subjobs() (in FepLauncher)
raw_val (in Atom)	rend (in SwigDoubleVector3)	restart_subjobs() (in LambdaHopping)
raw_val (in List)	rend (in SwigIntVector)	restart_subjobs() (in Multisim)
raw_val (in Map)	rend (in SwigStringVector)	restart_subjobs() (in Simulate)
Ray (in schrodinger.application.bioluminate.pml_menus)	rend (in SwigUInt64Vector)	RESTARTING (in schrodinger.pipeline.pipeline)
rbegin (in SwigDoubleVector)	rend (in SwigUnsignedIntVector)	RESTFEPConfigDialog (in schrodinger.application.desmond.fep_gui)
rbegin (in SwigDoubleVector3)	rend (in SwigUnsignedIntVector2)	RestInput (in schrodinger.application.desmond.rest_inp)
rbegin (in SwigIntVector)	rend (in SwigVectorIntIntPair)	restore() (in Rotamers)
rbegin (in SwigStringVector)	rend() (in SwigDoubleVector)	restore_cursor() (in schrodinger.application.bioluminate.pml_menus)
rbegin (in SwigUInt64Vector)	rend() (in SwigDoubleVector3)	restore_stages() (in Engine)
rbegin (in SwigUnsignedIntVector)	rend() (in SwigIntVector)	restore_workspace (in EditDialog)
rbegin (in SwigUnsignedIntVector2)	rend() (in SwigStringVector)	restoreCurrentColorScheme() (in ColorSchemeManager)
rbegin (in SwigVectorIntIntPair)	rend() (in SwigUInt64Vector)	restoreCursor() (in ItemRow)
rbegin (in SwigDoubleVector)	rend() (in SwigUnsignedIntVector)	restoreIonCenterProps() (in Ionizer)
rbegin (in SwigDoubleVector3)	rend() (in SwigUnsignedIntVector2)	restoreLabelOptions() (in WorkspaceLabeler)
rbegin (in SwigIntVector)	rend() (in SwigVectorIntIntPair)	restoreMasterData() (in PhpProject)
rbegin (in SwigStringVector)	rend() (in DoubleDoubleList)	restorePreviouslyIncludedEntry() (in ReadEditMixin)
rbegin (in SwigUInt64Vector)	rend() (in DoubleList)	RestoreTitlesStage (in schrodinger.pipeline.stages.gencodes)
rbegin (in SwigUnsignedIntVector)	rend() (in StringList)	restr_grp_selector() (in schrodinger.application.desmond.mdkey)
rbegin (in SwigUnsignedIntVector2)	rend() (in SwigAtomList)	Restrain (in schrodinger.application.desmond.cms)
rbegin (in SwigVectorIntIntPair)	rend() (in SwigAtomPairList)	restraint (in _FFIO)
rbegin() (in SwigDoubleVector)	rend() (in SwigAtomPairWithValueList)	restraint_builtin_prop (in schrodinger.trajectory.ffstructure)
rbegin() (in SwigDoubleVector3)	rend() (in SwigAtomQueryParamsList)	RestraintsTab (in schrodinger.application.desmond.gui)
rbegin() (in SwigIntVector)	rend() (in SwigDcNonPbcAtomIdxList)	restrictByChains() (in DataModelWithChart)
rbegin() (in SwigStringVector)	rend() (in SwigDcPbcAtomList)	Restricted (in SpinTreatment)
rbegin() (in SwigUInt64Vector)	rend() (in SwigPiCationList)	RestrictSelection (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in SwigUnsignedIntVector)	rend() (in SwigPiPiInteractionList)	RestrictSubMenu (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in SwigUnsignedIntVector2)	rend() (in SwigRingList)	RestrictToInorganic (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in SwigVectorIntIntPair)	rend() (in SwigSaltBridgeList)	RestrictToOrganic (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in DoubleDoubleList)	rend() (in SwigDoubleVector)	RestrictToPolymer (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in DoubleList)	rend() (in SwigDoubleVector3)	RestrictToSolvent (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in StringList)	rend() (in SwigIntVector)	RestrictToVisible (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in SwigAtomList)	rend() (in SwigStringVector)	restToggled() (in DesmondApp)
rbegin() (in SwigAtomPairList)	rend() (in SwigUInt64Vector)	ResultReporter (in schrodinger.test.stu.client)
rbegin() (in SwigAtomPairWithValueList)	rend() (in SwigUnsignedIntVector)	Results (in schrodinger.application.matsci.jaguarworkflows)
rbegin() (in SwigAtomQueryParamsList)	rend() (in SwigUnsignedIntVector2)	Results (in schrodinger.protein.reliability)
rbegin() (in SwigDcNonPbcAtomIdxList)	rend() (in SwigVectorIntIntPair)	Results() (in DataPointLocator)
rbegin() (in SwigDcPbcAtomList)	RenderFlag	results() (in MopacLauncher)
rbegin() (in SwigPiCationList)	RenderFlags	results() (in MopacLauncher2012)
rbegin() (in SwigPiPiInteractionList)	renderSurface() (in SurfaceRender)	results() (in MopacLauncher71)
rbegin() (in SwigRingList)	renumber_structures (in ConformerRmsd)	results2012 (in schrodinger.application.mopac)
rbegin() (in SwigSaltBridgeList)	renumberAtomLists() (in NanoTubeSheet)	results71 (in schrodinger.application.mopac)
rbegin() (in SwigDoubleVector)	renumberByMolecule() (in FixForPrime)	results_window (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in SwigDoubleVector3)	reorder (in schrodinger.application.matsci)	ResultsWindow (in schrodinger.application.bioluminate.pml_menus)
rbegin() (in SwigIntVector)	REORDER (in ParserWrapper)	RETAIN_ONLY_SELECTED_MENU_ITEM (in schrodinger.application.combiglide.combenumdock)
rbegin() (in SwigStringVector)	reorder_atom (in schrodinger.application.desmond)	RETAIN_ONLY_STRUCTURE_MENU_ITEM (in schrodinger.application.combiglide.combenumdock)
rbegin() (in SwigUInt64Vector)	reorder_atom() (in schrodinger.application.desmond.reorder_atom)	retranslateUi() (in Ui_Form)
rbegin() (in SwigUnsignedIntVector)	reorder_atoms() (in schrodinger.application.desmond.fep_mapping)	retranslateUi() (in Ui_Form)
rbegin() (in SwigUnsignedIntVector2)	reorder_atoms() (in schrodinger.structutils.build)	retranslateUi() (in glidePrecisionDialog)
rbegin() (in SwigVectorIntIntPair)	reorder_improper() (in schrodinger.application.desmond.fepdiff)	retranslateUi() (in Ui_Widget)
rc (in schrodinger.application.desmond.replica_dE)	reorder_protein_atoms_by_sequence() (in schrodinger.structutils.build)	retranslateUi() (in Ui_Dialog)
RCE (in schrodinger.application.macromodel.input)	reorder_solute() (in WaterMapInput)	retranslateUi() (in Ui_Dialog)
RCE_SPECS (in schrodinger.application.macromodel.input)	reorder_st() (in schrodinger.application.desmond.fep_mapping)	retranslateUi() (in Ui_Widget)
rdf (in schrodinger.trajectory)	reorder_tuple() (in schrodinger.application.desmond.fepdiff)	retranslateUi() (in Ui_Dialog)
rdf_backend (in schrodinger.trajectory)	ReorderAtomFrame (in schrodinger.application.matsci.reordergui)	retranslateUi() (in Ui_Form)
RDFException (in schrodinger.trajectory.rdf)	ReorderAtomPanel (in schrodinger.application.matsci.reordergui)	retranslateUi() (in Ui_Form)
re_comment (in _ParseRulesFile)	ReorderAtomsDialog (in schrodinger.application.matsci.reordergui)	retranslateUi() (in Ui_Dialog)
re_d (in _ParseRulesFile)	reorderColorSchemes() (in ColorSchemeManager)	retranslateUi() (in Ui_MainWindow)
re_def (in _ParseRulesFile)	reordergui (in schrodinger.application.matsci)	retranslateUi() (in Ui_Widget)
re_def_name (in _ParseRulesFile)	reorderResidues() (in proteinHandler)	retranslateUi() (in Ui_Form)
re_obl (in _ParseRulesFile)	repair_box_vector() (in schrodinger.application.desmond.repair_cms)	retranslateUi() (in Ui_Form)
re_ok (in _ParseRulesFile)	repair_cms (in schrodinger.application.desmond)	retranslateUi() (in Ui_Form)
re_okm (in _ParseRulesFile)	replace() (in TokenRewriteStream)	retranslateUi() (in Ui_Form)
REACTANT (in ParserWrapper)	replace_coords_with_zmat() (in schrodinger.application.matsci.zmutils)	retranslateUi() (in Ui_Form)
REACTANT_LIKE (in ParserWrapper)	replace_output_logger_stream() (in schrodinger.test.ioredirect)	retranslateUi() (in Ui_Form)
REACTANT_NAME_BASE (in CheckInput)	replace_slot() (in schrodinger.application.bioluminate.actions.factory)	retranslateUi() (in Ui_Form)
REACTANT_PREFIX (in schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab)	replaceChildren() (in DebugTreeAdaptor)	retranslateUi() (in Ui_Form)
ReactantMolecule (in schrodinger.application.matsci.rxn_channel.rxn_channel)	replaceChildren() (in BaseTree)	retranslateUi() (in Ui_Form)
REACTANTPREFIX (in ReactionCoords)	replaceChildren() (in CommonTreeAdaptor)	retranslateUi() (in Ui_Form)
Reactants (in schrodinger.application.matsci.rxn_channel.rxn_channel)	replaceChildren() (in CommonTreeNodeStream)	retranslateUi() (in Ui_Form)
reaction_molecules_tab (in schrodinger.application.jaguar.gui.tabs)	replaceChildren() (in Tree)	retranslateUi() (in Ui_Form)
reaction_molecules_tab_ui (in schrodinger.application.jaguar.gui.ui)	replaceChildren() (in TreeAdaptor)	retranslateUi() (in Ui_Form)
reaction_properties_tab (in schrodinger.application.jaguar.gui.tabs)	replaceChildren() (in TreeNodeStream)	retranslateUi() (in Ui_Form)
reaction_properties_tab_ui (in schrodinger.application.jaguar.gui.ui)	ReplaceOp (in schrodinger.application.desmond.antlr3.streams)	retranslateUi() (in Ui_Form)
reaction_tab (in schrodinger.application.jaguar.gui.tabs)	replica_container (in schrodinger.application.desmond.replica_dE)	retranslateUi() (in Ui_Form)
reaction_tab_ui (in schrodinger.application.jaguar.gui.ui)	replica_dE (in schrodinger.application.desmond)	retranslateUi() (in Ui_Form)
REACTIONANGLETHRESH (in ReactionCoords)	replica_energy (in schrodinger.application.desmond.replica_dE)	retranslateUi() (in Ui_Form)
REACTIONBONDTHRESH (in ReactionCoords)	replica_exchange_review (in schrodinger.application.desmond)	retranslateUi() (in Ui_Form)
ReactionCoords (in schrodinger.application.matsci.rxn_path)	replica_name (in schrodinger.application.desmond.report_helper)	retranslateUi() (in Ui_Form)
REACTIONDIHEDRALTHRESH (in ReactionCoords)	replica_sid_generator (in schrodinger.application.desmond)	retranslateUi() (in Ui_Form)
ReactionMoleculesTab (in schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab)	ReplicaExchange (in schrodinger.application.desmond.stage)	retranslateUi() (in Ui_Form)
ReactionParticipant (in schrodinger.application.jaguar.gui.tabs.reaction_tab)	replicas_monitor (in schrodinger.application.desmond.replica_dE)	retranslateUi() (in Ui_Form)
reactionParticipantAdded (in ReactionTab)	replot() (in SliderPlot)	retranslateUi() (in Ui_Form)
reactionParticipantRemoved (in ReactionTab)	replotChart() (in MultiReportWithChart)	retranslateUi() (in Ui_Widget)
reactionParticipantStructChanged (in ReactionTab)	repopulateSearchAlongCombo() (in TransitionStateTab)	retranslateUi() (in Ui_Form)
ReactionPath (in schrodinger.application.matsci.rxn_path)	Report (in schrodinger.protein.analysis)	retranslateUi() (in Ui_Form)
ReactionPropertiesTab (in schrodinger.application.jaguar.gui.tabs.reaction_properties_tab)	report (in PerformanceTestCase)	retranslateUi() (in Ui_Form)
ReactionTab (in schrodinger.application.jaguar.gui.tabs.reaction_tab)	report() (in Calculator)	retranslateUi() (in Ui_Form)
REACTIVEATOM (in ReactionPath)	report() (in FEPEdgeReportMaker)	retranslateUi() (in Ui_Form)
reactWith() (in ReactantMolecule)	report() (in FEPReportMaker)	retranslateUi() (in Ui_Dialog)
read (in istream)	report() (in data_set)	retranslateUi() (in Ui_Dialog)
read (in istream)	report() (in Test)	retranslateUi() (in Ui_Form)
read() (in _ParseRulesFile)	report() (in ResultReporter)	RETRIABLE_FAILURE (in JobStatus)
read() (in SystemBuilderInput)	report2d (in schrodinger.application)	RETRIES (in schrodinger.application.desmond.starter.ui.cmdline)
read() (in ReadEditMixin)	Report2D (in schrodinger.application.report2d)	RETRIES (in schrodinger.utils.cmdline)
read() (in schrodinger.application.jaguar.input)	report_add_logo() (in schrodinger.application.desmond.report_helper)	retrieve() (in TestClient)
read() (in istream)	report_add_ms_logo() (in schrodinger.application.desmond.report_helper)	retrieve() (in schrodinger.test.stu.client)
read() (in schrodinger.job.jobcontrol)	report_data_points() (in data_set)	retrieve_ent() (in schrodinger.protein.getpdb)
read() (in MaestroReader)	report_helper (in schrodinger.application.desmond)	retrieve_pdb() (in schrodinger.protein.getpdb)
read() (in Structure)	REPORT_LEVELS (in FEPEdgeReportMaker)	retry_http_basic_auth() (in ProxyBasicAuthHandler)
read() (in ProjectSurface)	report_results() (in schrodinger.test.performance.reporter)	retry_http_digest_auth() (in ProxyDigestAuthHandler)
read() (in Surface)	report_t() (in SimulatedAnnealing)	retry_interval() (in RetryTimer)
read() (in istream)	Reporter (in schrodinger.application.desmond.stage)	RETRY_INTERVAL_BASE (in RetryTimer)
read_all_ct() (in schrodinger.application.desmond.struc)	reporter (in schrodinger.test.performance)	retryFailure() (in RobustSubmissionJob)
read_anni_fep_cms() (in schrodinger.application.desmond.struc)	reportError() (in DebugParser)	retryFailure() (in JobControlJob)
read_atomtype() (in Packing)	reportError() (in BaseRecognizer)	RetryTimer (in schrodinger.application.desmond.cmj)
read_cfg() (in FEPSimulationReport)	reportError() (in Lexer)	return_codes (in schrodinger.infra.mm)
read_cluster_file() (in WaterMapAnaJob)	reportError() (in mexpLexer)	return_codes (in schrodinger.infra.mmgpgpu)
read_cms() (in FEPSimulationReport)	reportError() (in mexpParser)	return_codes (in schrodinger.infra.mmproj)
read_cms() (in schrodinger.trajectory.cmsstructure)	reportFinalResults() (in FEPReportMaker)	return_codes (in schrodinger.infra.mmreflect)
read_constraints() (in schrodinger.application.glide.glide)	ReportFrame (in schrodinger.application.bioluminate.protein_report_widget)	return_codes (in schrodinger.infra.mmsurf)
read_csv() (in EnsembleSelection)	reportLigandsDetails() (in FEPReportMaker)	ReturnCode (in schrodinger.infra.mmcheck)
read_csv() (in schrodinger.test.canvas_utils)	reportParameters() (in Pipeline)	retype() (in Structure)
read_ct() (in schrodinger.structure)	reportParameters() (in Stage)	retype() (in _StructureAtom)
read_data_from_CT() (in ModelCheck)	reportProteinDetails() (in FEPReportMaker)	REVERSE_INTERPOLATION (in ParserWrapper)
read_data_from_log_file() (in schrodinger.application.desmond.replica_exchange_review)	reportReplicaExchanges() (in FEPReportMaker)	reverse_iter() (in LinkedList)
read_dE_file() (in schrodinger.application.desmond.fepana)	reportReplicaPairEnergies() (in FEPReportMaker)	revert() (in EditDialog)
read_dE_Replicas() (in replica_container)	reportSet() (in ProteinReportCheck)	revert_to_original() (in Rama)
read_exp_dg() (in EnsembleSelection)	reportSimulationDetails() (in FEPReportMaker)	revert_to_saved() (in Rama)
read_fep_cms() (in schrodinger.application.desmond.struc)	reposition() (in _ScrolledDouble)	revertCollection() (in SimpleEnumDockPanel)
read_FEP_REST_energetics() (in FEPReportMaker)	REPRESENTATION (in schrodinger.application.matsci.nano.particle)	revertCombLib() (in SimpleEnumDockPanel)
read_FEPSimulation() (in FEPReportMaker)	REPRESENTATION_KEY (in schrodinger.application.matsci.nano.particle)	revertInitialRunParams() (in WriteInputs)
read_fragbox() (in Packing)	rept_file_ext (in Calculator)	reviseDatabase() (in PhpProject)
read_fragment() (in Packing)	request (in schrodinger.application.desmond.ana)	reviseIonizedGroup() (in Ionizer)
read_frame() (in _FepTrajectory)	requestCpus() (in Pipeline)	REVOLUTION (in ReactionCoords)
read_keys() (in schrodinger.utils.ligfilter)	requestHelpInfoSignal() (in sketcherScene)	REVOLUTIONTHRESH (in ReactionCoords)
read_keywords_file() (in schrodinger.application.glide.glide)	require_argument() (in schrodinger.job.hunt_stub)	rewind() (in DebugEventListener)
read_license_file() (in schrodinger.application.licensing.flexlm)	require_display() (in schrodinger.test.test_markers)	rewind() (in DebugEventSocketProxy)
read_LigandInfo() (in FEPReportMaker)	requireApiKey() (in TestUtility)	rewind() (in DebugTokenStream)
read_meta_cfg() (in schrodinger.application.desmond.meta)	required_datanames (in Lattice)	rewind() (in ANTLRStringStream)
read_mode (in CMSReader)	REQUIRED_MAJOR_VERSION (in schrodinger.application.licensing.licadmin)	rewind() (in CommonTokenStream)
read_mode (in MaestroReader)	REQUIRED_MINOR_VERSION (in schrodinger.application.licensing.licadmin)	rewind() (in IntStream)
read_mode (in MaestroTextReader)	requiredProduct() (in Stage)	rewind() (in CommonTreeNodeStream)
read_only (in ProjectRow)	requiredProductRuntime() (in Stage)	rewrite() (in ChmCSVTools)
read_output (in schrodinger.application.mcpro)	requirement (in LocalhostJob)	rewriteByIndex() (in ChmCSVTools)
read_prob() (in Packing)	requirement (in RequirementsJob)	rewriteByName() (in ChmCSVTools)
read_ProteinInfo() (in FEPReportMaker)	RequirementsJob (in schrodinger.job.queue)	RewriteCardinalityException (in schrodinger.application.desmond.antlr3.tree)
read_pw() (in schrodinger.test.canvas_utils)	requires_energy() (in _KeywordProcessor)	RewriteEarlyExitException (in schrodinger.application.desmond.antlr3.tree)
read_readme() (in TestScript)	reroot() (in schrodinger.application.desmond.reorder_atom)	RewriteEmptyStreamException (in schrodinger.application.desmond.antlr3.tree)
read_REST_exchanges() (in FEPReportMaker)	res_can_be_capped() (in schrodinger.protein.captermini)	RewriteOperation (in schrodinger.application.desmond.antlr3.streams)
read_stats() (in Packing)	RES_RE (in ModelCheck)	RewriteRuleElementStream (in schrodinger.application.desmond.antlr3.tree)
read_text() (in SystemBuilderInput)	RESCALE (in schrodinger.application.desmond.fep_edge_report_maker)	RewriteRuleNodeStream (in schrodinger.application.desmond.antlr3.tree)
read_trj_idx_file() (in schrodinger.trajectory.analyze_trajectories)	RESCALE (in schrodinger.application.desmond.fep_scholar_util)	RewriteRuleSubtreeStream (in schrodinger.application.desmond.antlr3.tree)
read_unique_field() (in schrodinger.pipeline.pipeutils)	rescale_ff() (in schrodinger.application.desmond.remd)	RewriteRuleTokenStream (in schrodinger.application.desmond.antlr3.tree)
read_yaml() (in schrodinger.application.glide.glide)	rescale_ff_solute_tempering() (in schrodinger.application.desmond.remd)	rgb() (in Color)
read_zmat() (in Zmat)	ResData (in schrodinger.application.desmond.fep_edge_data)	rgb() (in Color)
readActionSelected() (in GuiApp)	RESELECT_CURRENT_TEMPLATE (in schrodinger.application.matsci.builderwidgets)	rgb_float() (in Color)
readAgain() (in Job)	reserve (in SwigDoubleVector)	RGroupException (in schrodinger.application.canvas.r_group)
readColorRampFile() (in MM_ColorRamp)	reserve (in SwigDoubleVector3)	RGroupFinder (in schrodinger.application.canvas.r_group)
readColorSchemeFile() (in ColorSchemeManager)	reserve (in SwigIntVector)	RGroupStructureToolTip (in schrodinger.application.matsci.builderwidgets)
readCommand() (in GuiApp)	reserve (in SwigStringVector)	RIBBON_RAINBOW_COLORS (in schrodinger.application.bioluminate.pml_menus)
readData() (in schrodinger.infra.propedit)	reserve (in SwigUInt64Vector)	RIBBON_SCHEME (in ShowCartoon)
readDb() (in JoiningRules)	reserve (in SwigUnsignedIntVector)	RIBBON_SCHEME (in ShowCartoonOrRibbon)
ReadDialog (in schrodinger.ui.appframework)	reserve (in SwigUnsignedIntVector2)	RIBBON_SCHEME (in ShowRibbon)
ReadEditMixin (in schrodinger.application.jaguar.gui.base_panel)	reserve (in SwigVectorIntIntPair)	RIBBON_STYLE (in schrodinger.application.bioluminate.pml_menus)
readFile() (in Adduct)	reserve (in SwigDoubleVector)	right() (in WidgetTable)
readFile() (in JoiningRules)	reserve (in SwigDoubleVector3)	RIGHT_ANGLE (in CheckInput)
readFile() (in Substrate)	reserve (in SwigIntVector)	RIGHT_CLICK_CALLBACK (in schrodinger.maestro.maestro)
readFile() (in Pipeline)	reserve (in SwigStringVector)	right_click_callback_add() (in schrodinger.maestro.maestro)
ReadFileDialog (in schrodinger.application.jaguar.gui.filedialog)	reserve (in SwigUInt64Vector)	right_click_callback_remove() (in schrodinger.maestro.maestro)
readFilterCriteria() (in LigfilterFrame)	reserve (in SwigUnsignedIntVector)	rightButton() (in sketcherScene)
readFragmentLibrary() (in Ionizer)	reserve (in SwigUnsignedIntVector2)	rigidify_geo_vars() (in Zmat)
readFromIndex() (in StructureFileReader)	reserve (in SwigVectorIntIntPair)	ring (in Structure)
readFromOffset() (in MaestroReader)	reserve() (in SwigDoubleVector)	ring() (in TextualStructure)
README2TEST (in schrodinger.test.stu.testscripts)	reserve() (in SwigDoubleVector3)	ring_atoms() (in SchrodStruc)
READMESyntaxError (in schrodinger.test.stu.testscripts)	reserve() (in SwigIntVector)	ring_atoms() (in Struc)
readNewFormat() (in Pipeline)	reserve() (in SwigStringVector)	RING_MUTATION (in schrodinger.application.desmond.fep_gui)
readNewFormatStage() (in Pipeline)	reserve() (in SwigUInt64Vector)	ringspear (in schrodinger.structutils)
readNewFormatVariable() (in Pipeline)	reserve() (in SwigUnsignedIntVector)	RMSD (in schrodinger.application.desmond.mdpose.mdpose_analysis)
readNext() (in StructureFileReader)	reserve() (in SwigUnsignedIntVector2)	rmsd (in schrodinger.application.jaguar)
readRulesFromFile() (in MM_CScheme)	reserve() (in SwigVectorIntIntPair)	rmsd (in schrodinger.application.vsw.stages)
readSpecFile() (in Ionizer)	reserve() (in DoubleDoubleList)	rmsd (in schrodinger.pipeline.stages)
readStereoChemistry() (in sketcherBond)	reserve() (in DoubleList)	rmsd (in schrodinger.structutils)
readTemplateStructure() (in SketcherBox)	reserve() (in StringList)	RMSD (in schrodinger.trajectory.analysis)
readValueList() (in SubSetStage)	reserve() (in SwigAtomList)	rmsd() (in schrodinger.test.stu.outcomes.structure_comparisons)
readyToRun() (in StageJob)	reserve() (in SwigAtomPairList)	rmsd2d (in schrodinger.trajectory)
REAL (in schrodinger.application.jaguar.validation)	reserve() (in SwigAtomPairWithValueList)	rmsd_comb() (in EnsembleSelection)
real_to_int() (in schrodinger.application.desmond.gconfig)	reserve() (in SwigAtomQueryParamsList)	rmsd_in_place() (in schrodinger.test.stu.outcomes.structure_comparisons)
RealSpaceFit (in schrodinger.protein._reliability)	reserve() (in SwigDcNonPbcAtomIdxList)	RMSDCalculator (in schrodinger.trajectory.rmsd2d)
reassignHets() (in FixForPrime)	reserve() (in SwigDcPbcAtomList)	RMSDMultiprocessing (in schrodinger.trajectory.rmsd2d)
reassignResNums() (in FixForPrime)	reserve() (in SwigPiCationList)	RmsdStage (in schrodinger.pipeline.stages.rmsd)
rebuild_scripts_menu() (in schrodinger.maestro.maestro)	reserve() (in SwigPiPiInteractionList)	RMSDSyntax (in schrodinger.application.desmond.enhanced_sampling.FcnTypes)
rebuild_workflows_menu() (in schrodinger.maestro.maestro)	reserve() (in SwigRingList)	RMSDThreading (in schrodinger.trajectory.rmsd2d)
recalc() (in _StructureChainIterator)	reserve() (in SwigSaltBridgeList)	RMSF (in schrodinger.trajectory.analysis)
recalc() (in _StructureMoleculeIterator)	reserve() (in SwigDoubleVector)	RMSF_PROPERTY (in schrodinger.application.desmond.mdpose.mdpose_average_structure)
recalc() (in _StructureRingIterator)	reserve() (in SwigDoubleVector3)	RobustSubmissionJob (in schrodinger.application.matsci.jaguarworkflows)
RECAP_PATTERNS (in schrodinger.structutils.createfragments)	reserve() (in SwigIntVector)	rock_data (in schrodinger.application.bioluminate.pml_menus)
RECAP_PROP_PREFIX (in schrodinger.structutils.createfragments)	reserve() (in SwigStringVector)	rock_workspace() (in schrodinger.application.bioluminate.pml_menus)
receivers() (in RowModel)	reserve() (in SwigUInt64Vector)	RockData (in schrodinger.application.bioluminate.pml_menus)
receivers() (in DendrogramGraphicNode)	reserve() (in SwigUnsignedIntVector)	rollback() (in TokenRewriteStream)
receivers() (in DendrogramGraphicTree)	reserve() (in SwigUnsignedIntVector2)	rollback() (in CfgAtom)
receivers() (in DendrogramScene)	reserve() (in SwigVectorIntIntPair)	rollback() (in Key)
receivers() (in DendrogramView)	reset() (in FrameworkModel)	rolmp2() (in schrodinger.application.jaguar.output)
receivers() (in MM_StructMonitor)	reset() (in TableView)	rotamers (in schrodinger.protein)
receivers() (in MM_UICompactPropertySelector)	reset() (in PresetAction)	Rotamers (in schrodinger.protein.rotamers)
receivers() (in MM_UIComponent)	reset() (in ConnectionStorage)	rotamers (in Rotamers)
receivers() (in MM_UIForm)	reset() (in BaseRecognizer)	rotatable_bonds_iterator() (in schrodinger.structutils.analyze)
receivers() (in MM_UIVBoxLayout)	reset() (in Lexer)	rotate_double_bonds() (in schrodinger.application.matsci.nano.util)
receivers() (in sketcher)	reset() (in Parser)	rotate_structure() (in schrodinger.structutils.transform)
receivers() (in sketcherGUIMultiColumnToolBar)	reset() (in ANTLRStringStream)	rotateNanoSheet() (in NanoSheet)
receivers() (in sketcherScene)	reset() (in CommonTokenStream)	rotateProteinToMembrane() (in Membrane_Model)
receivers() (in sketcherView)	reset() (in CommonTreeNodeStream)	rotateTube() (in NanoTube)
RECENT_TEMPLATE_FILE (in schrodinger.application.matsci.builderwidgets)	reset() (in RewriteRuleElementStream)	rotation_points_add() (in schrodinger.maestro.maestro)
RecentCarbonColorSubMenu (in schrodinger.application.bioluminate.pml_menus)	reset() (in TreeParser)	ROTATION_POINTS_CALLBACK (in schrodinger.maestro.maestro)
RecentColorSubMenu (in schrodinger.application.bioluminate.pml_menus)	reset() (in Engine)	rotation_points_remove() (in schrodinger.maestro.maestro)
RecentHydrogenColorSubMenu (in schrodinger.application.bioluminate.pml_menus)	reset() (in Queue)	rotational_strength_precision (in NormalMode)
RecentObjectColorSubMenu (in schrodinger.application.bioluminate.pml_menus)	reset() (in RetryTimer)	ROUGH_CUT_DISTANCE (in schrodinger.structutils.ringspear)
receptor_b_factor() (in FEPEdgeData)	reset() (in _DesmondProt)	ROULETTE_WHEEL_SELECTION (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
receptor_chain_names() (in FEPEdgeData)	reset() (in _McproProt)	round() (in WriteInputs)
receptor_charge() (in FEPEdgeData)	reset() (in _ProtItem)	row (in WidgetTable)
receptor_residue_sequence_list() (in FEPEdgeData)	reset() (in GuiApp)	row_charge() (in ProjEntry)
receptor_residue_sequence_tags() (in FEPEdgeData)	reset() (in InputGroup)	row_number() (in ProjectRow)
receptor_residues_interaction_ligand1() (in FEPEdgeData)	reset() (in RestraintsTab)	RowActionItem (in schrodinger.application.bioluminate.bwidgets)
receptor_residues_interaction_ligand2() (in FEPEdgeData)	reset() (in _BaseAdvancedDialog)	rowCount() (in FrameworkModel)
receptor_sid_rmsd_backbone_lambda0() (in FEPEdgeData)	reset() (in Guide)	rowCount() (in CriteriaListModel)
receptor_sid_rmsd_backbone_lambda1() (in FEPEdgeData)	reset() (in SystemBuilderInput)	rowCount() (in DataModel)
receptor_sid_rmsd_ligand_lambda0() (in FEPEdgeData)	reset() (in Counter)	rowCount() (in PathModel)
receptor_sid_rmsd_ligand_lambda1() (in FEPEdgeData)	reset() (in BaseJaguarPanel)	rowCount() (in ResiduesModel)
receptor_sid_rmsf_backbone_lambda0() (in FEPEdgeData)	reset() (in InputEntriesModel)	rowCount() (in StrucListModel)
receptor_sid_rmsf_backbone_lambda1() (in FEPEdgeData)	reset() (in ProjEntry)	rowCount() (in AtomGroupModel)
receptor_st() (in FEPEdgeData)	reset() (in ProjEntryPka)	rowCount() (in PosResModel)
receptor_title() (in FEPEdgeData)	reset() (in BaseTab)	rowCount() (in TableModel)
receptor_total_atom() (in FEPEdgeData)	reset() (in CoordinatesModel)	rowCount() (in InputEntriesModel)
receptor_total_heavy() (in FEPEdgeData)	reset() (in BaseSubTab)	rowCount() (in CoordinatesModel)
receptor_total_residues() (in FEPEdgeData)	reset() (in InputTabBase)	rowCount() (in SubTabModel)
receptor_total_residues_in_chains() (in FEPEdgeData)	reset() (in InputTabHB)	rowCount() (in ChooseLigandModel)
RecognitionException (in schrodinger.application.desmond.antlr3.exceptions)	reset() (in InputTabWithSubTabs)	rowCount() (in CriteriaListModel)
recognitionException() (in DebugEventListener)	reset() (in MoleculeTabPka)	rowCount() (in PatternModel)
recognitionException() (in DebugEventSocketProxy)	reset() (in MultiStructureTab)	rowGetExpanded() (in Table)
recognizers (in schrodinger.application.desmond.antlr3)	reset() (in ReactionPropertiesTab)	rowGetVisible() (in Table)
RecognizerSharedState (in schrodinger.application.desmond.antlr3.recognizers)	reset() (in ReactionTab)	RowIterator (in schrodinger.ui.widgettable)
recolorPlot() (in HomologyRama)	reset() (in ScanTabNextGeom)	RowModel (in schrodinger.infra.projectmodel)
recombineInputLigands() (in DockingStage)	reset() (in ScfTabConsistentOrbitals)	rowPos() (in _Cell)
recombineInputLigands() (in LigPrepStage)	reset() (in SubTabModel)	rowPos() (in _Row)
recombineInputLigands() (in ConfSearchStage)	reset() (in ItemRow)	RowProxy (in schrodinger.utils.pymol)
recombineInputLigands() (in QikPropStage)	reset() (in ItemRowWithTemplates)	rowSetExpanded() (in Table)
recombineInputLigands() (in SemiEmpStage)	reset() (in SketcherBox)	rowSetVisible() (in Table)
RecombineStage (in schrodinger.pipeline.stages.gencodes)	reset() (in CompactSolventSelector)	rowsForEid() (in SubTabModel)
record() (in RecordDebugEventListener)	reset() (in EmbeddedSolventWidget)	rrho() (in ComUtil)
record() (in TraceDebugEventListener)	reset() (in MultiStageArea)	rsh_errors_re (in schrodinger.job.remote_command)
record_error() (in _Evalor)	reset() (in StageFrame)	rsh_exec (in schrodinger.job.remote_command)
record_error() (in _Evalor)	reset() (in ReorderAtomFrame)	rsh_max_retries (in schrodinger.job.remote_command)
RecordDebugEventListener (in schrodinger.application.desmond.antlr3.debug)	reset() (in StructureFrame)	rsh_src (in schrodinger.job.remote_command)
recover() (in BaseRecognizer)	reset() (in StructurePic)	rsh_test() (in schrodinger.job.remote_command)
recover() (in Lexer)	reset() (in DrawDdgPanel)	rsh_timeout (in schrodinger.job.remote_command)
recover_macro() (in CfgAtom)	reset() (in DrawFepPanel)	rsh_warning_issued (in schrodinger.job.remote_command)
recover_macro() (in Key)	reset() (in DrawLrmPanel)	RSI (in Icons)
recoverFromMismatchedSet() (in BaseRecognizer)	reset() (in DrawMcPanel)	RT (in schrodinger.application.ligprep.ionizer)
recoverFromMismatchedToken() (in BaseRecognizer)	reset() (in DrawMiniPanel)	RT_COLOR_LABEL_END (in schrodinger.application.bioluminate.pml_menus)
recoverFromScratch() (in TestScript)	reset() (in ModelSystem)	RT_COLOR_LABEL_START (in schrodinger.application.bioluminate.pml_menus)
Rectangle (in schrodinger.application.matsci.nano.tube)	reset() (in DrawSolventPanel)	RT_LN_10 (in schrodinger.application.ligprep.ionizer)
RED (in schrodinger.application.bioluminate.pml_menus)	reset() (in AnalyzeEnergyWidget)	RT_TO_MAESTRO_COLORS (in schrodinger.application.bioluminate.pml_menus)
RED (in schrodinger.application.matsci.amorphous)	reset() (in RowModel)	RULE (in DesmondTyper)
red (in Color)	reset() (in HuntCache)	RULE (in McproTyper)
redefineLatticeVecs() (in NanoTubeSheet)	reset() (in ModelCheck)	RULE (in TyperBase)
redraw (in InputEntriesProxyModel)	reset() (in StructuralInteractionFingerprintGenerator)	RULE (in WatermapTyper)
redraw() (in ClusterStatisticsPlotDialog)	reset_colors() (in schrodinger.application.combiglide.connection_storage)	rulePostProcessing() (in DebugTreeAdaptor)
redraw() (in DendrogramPlotDialog)	reset_protein() (in _ChopCap)	rulePostProcessing() (in BaseTreeAdaptor)
redraw() (in DistanceMatrixPlotDialog)	reset_protein() (in _Neut)	rulePostProcessing() (in TreeAdaptor)
redraw() (in schrodinger.maestro.maestro)	reset_tag() (in Sea)	RuleReturnScope (in schrodinger.application.desmond.antlr3.recognizers)
redraw_request() (in schrodinger.maestro.maestro)	RESET_TO_DEFAULT_CUSTOM_DIR (in schrodinger.application.matsci.builderwidgets)	run (in schrodinger.test.stu)
redraw_sphere() (in DrawSolventPanel)	reset_workspace_transformations() (in schrodinger.maestro.maestro)	run() (in SimulatedAnnealing)
reduced_mass_precision (in NormalMode)	resetAcceptedRow() (in FullProxyModel)	run() (in Queue)
reduced_set() (in Zmat)	resetAllColorSchemeRules() (in ColorSchemeManager)	run() (in ProteinCheckThread)
reduceToSingleOperationPerIndex() (in TokenRewriteStream)	resetAtomGroupTable() (in AtomGroupFrame)	run() (in Contact)
REDUCTION (in schrodinger.application.matsci.optoelectronics)	resetColorSchemes() (in ColorSchemeManager)	run() (in ContactCmd)
redundant_server() (in License)	resetData() (in CriteriaListModel)	run() (in MDPoseAnalysis)
ref_keys() (in SiteMatchLookup)	resetEnsClass() (in EnsembleTab)	run() (in RMSD)
REF_LICENSE_CHECK_FILE (in schrodinger.test.stu.constants)	resetfp() (in CanvasFingerprintGeneratorGUI)	run() (in Tanimoto)
refAtomFromCompAtom() (in ReorderAtomFrame)	resetFromModel() (in AtomGroupFrame)	run() (in MDPoseGlideJob)
refcount (in _StructureDeleter)	resetFromModel() (in InteractionTab)	run() (in MDPoseStrainJob)
REFERENCE (in schrodinger.application.matsci.nano.interface_mod)	resetFromModel() (in MdcMiscTab)	run() (in MDSimulation)
REFERENCE (in schrodinger.application.matsci.reordergui)	resetFromModel() (in RestraintsTab)	run() (in RestInput)
REFERENCE_FILTERS (in SequenceFileDialog)	resetFromModel() (in _BaseAdvancedDialog)	run() (in AnalysisJob)
referenceFragChanged() (in _Pert)	resetGroup() (in Preferences)	run() (in FepanaJob)
ReferenceFrame (in schrodinger.application.matsci.reordergui)	resetInputContext() (in DendrogramView)	run() (in MetadynamicsAnalysisJob)
ReferenceListWidget (in schrodinger.application.matsci.reordergui)	resetInputContext() (in sketcher)	run() (in SeaJob)
refill_queue() (in Queue)	resetInputContext() (in sketcherGUIMultiColumnToolBar)	run() (in TimeSeriesAnalysisJob)
refine_structure() (in schrodinger.application.desmond.mdpose.mdpose_average_structure)	resetInputContext() (in sketcherView)	run() (in WaterMapAnaJob)
refinePrime() (in Refiner)	resetInternalData() (in RowModel)	run() (in Starter)
Refiner (in schrodinger.application.bioluminate.protein)	resetLabelOptions() (in WorkspaceLabeler)	run() (in SystemBuilderInput)
refresh() (in _MdcBase)	resetMap() (in ReorderAtomFrame)	run() (in TestSuite)
refresh() (in LicenseResource)	resetMaxIter() (in MinimizationTab)	run() (in JaguarInput)
refresh() (in schrodinger.application.licensing.licadmin)	resetMaxIter() (in MinimizerFrame)	run() (in MopacLauncher)
refreshFragList() (in _Pert)	resetMode() (in DrawSolventPanel)	run() (in MopacLauncher2012)
refreshMarkers (in CoordinateTab)	resetPanel() (in _App)	run() (in MopacLauncher71)
refreshTable() (in Project)	resetParentProperties() (in StructureGenome)	run() (in StructureLauncher)
reg_checking() (in schrodinger.application.desmond.cmj)	resetPosResTable() (in RestraintsTab)	run() (in _CommonProblemsFixer)
reg_xcheck() (in schrodinger.application.desmond.mdkey)	resetSlots() (in ComplexBuilder)	run() (in PicturePrinter)
reg_xcheck() (in schrodinger.utils.sea)	resetStructure() (in JaguarInput)	run() (in WaterMapInput)
regenerate_markers() (in schrodinger.maestro.maestro)	resetThermoTemp() (in EnsembleTab)	run() (in App)
regeneratePic() (in _StructViewItem)	resID_to_asl() (in schrodinger.protein._reliability)	run() (in BaseJob)
regeneratePic() (in _zoomViewItem)	resID_to_atoms() (in schrodinger.protein._reliability)	run() (in JobDJ)
regeneratePicture() (in ReactionParticipant)	residue (in Sequence)	run() (in Pipeline)
REGEXS (in schrodinger.application.bioluminate.propka_parse)	residue (in Structure)	run() (in Stage)
RegionInfo (in schrodinger.application.bioluminate.pml_menus)	residue (in _Chain)	run() (in FrameLoader)
registerItem() (in Hierarchy)	residue (in _Molecule)	run() (in RMSDCalculator)
registerJob() (in JobApp)	residue() (in TextualStructure)	run_align() (in schrodinger.application.ska)
regularized_structure() (in Ligand)	RESIDUE_CALCULATIONS (in PropertyCalculator)	run_analysis() (in steric_clash_data_set)
Reinitialize (in schrodinger.application.bioluminate.pml_menus)	residue_charge (in ColorBy)	run_apbs() (in schrodinger.application.desmond.fep_net_charge)
reject() (in ValueSelectionDialog)	residue_hydrophobicity (in ColorBy)	run_bennett() (in schrodinger.application.desmond.fepana)
reject() (in DEE_Backtracking)	residue_indices() (in Consensus)	run_bennett() (in replica_container)
reject() (in _BaseAdvancedDialog)	residue_interaction (in schrodinger.application.prime)	run_bennett_orig() (in schrodinger.application.desmond.fepana)
reject() (in ReorderAtomsDialog)	residue_is_nonpolar() (in schrodinger.application.bioluminate.protein)	run_check() (in schrodinger.protein.reliability)
rejected() (in AddDefinitionDialog)	residue_is_polar() (in schrodinger.application.bioluminate.protein)	run_cleanup() (in schrodinger.application.mopac.utils)
RelaxFrame (in schrodinger.application.desmond.gui)	residue_position (in ColorBy)	run_comparison() (in schrodinger.test.stu.workup)
release() (in DebugTokenStream)	RESIDUE_ROTOR_COUNT (in schrodinger.application.bioluminate.protein)	run_desmond_ff_builder() (in schrodinger.application.desmond.fepdiff)
release() (in ANTLRStringStream)	residue_score (in schrodinger.application.desmond.mdpose.mdpose_neutralize)	run_hmc() (in BondRotator)
release() (in CommonTokenStream)	residue_type (in ColorBy)	run_kwargs (in JaguarInput)
release() (in IntStream)	residue_zscores() (in Packing)	run_lmdiag() (in schrodinger.application.licensing.licadmin)
release() (in CommonTreeNodeStream)	ResidueGroups (in schrodinger.ui.residueselector)	run_lmstat() (in schrodinger.application.licensing.licadmin)
release() (in StageBase)	residues() (in Consensus)	run_maestro_cmd() (in schrodinger.application.desmond.mdpose.mdpose_analysis)
release() (in Concluder)	residuesChanged() (in MM_StructMonitor)	run_mcs() (in schrodinger.test.canvas_utils)
releaseOwnership() (in Structure)	residueSelectionChanged() (in MM_StructMonitor)	run_mcs_pw() (in schrodinger.test.canvas_utils)
reliability (in schrodinger.protein)	residueselector (in schrodinger.ui)	run_mop_file() (in MopacAPI)
reload (in JaguarInput)	ResiduesModel (in schrodinger.application.desmond.fep_gui)	run_postmortem() (in schrodinger.test.stu.run)
reloadTemplateList() (in ItemRowWithTemplates)	residuetools (in schrodinger.application.mcpro)	run_propka (in schrodinger.application.bioluminate.protein)
relpath() (in schrodinger.application.desmond.util)	ResidueTools (in schrodinger.application.mcpro.residuetools)	run_propka (in schrodinger.application.bioluminate)
REMAINDER (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	residueWasClicked() (in sketcherScene)	run_propka() (in schrodinger.application.bioluminate.run_propka)
REMAINDER_FILE_EXT (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	resize (in SwigDoubleVector)	run_protein_reliability() (in schrodinger.application.desmond.feputils)
remap_members() (in Ensemble)	resize (in SwigDoubleVector3)	run_quick_check() (in schrodinger.protein.reliability)
REMD (in DEFAULT_SETTING)	resize (in SwigIntVector)	run_requested (in EditDialog)
REMD (in schrodinger.application.desmond.config)	resize (in SwigStringVector)	run_rga() (in schrodinger.application.desmond.fep_mapping)
remd (in schrodinger.application.desmond)	resize (in SwigUInt64Vector)	run_ska() (in schrodinger.infra._ska)
remediate (in schrodinger.protein)	resize (in SwigUnsignedIntVector)	run_structure() (in MopacAPI)
remediate_ct() (in schrodinger.protein.remediate)	resize (in SwigUnsignedIntVector2)	run_system_builder() (in schrodinger.application.matsci.desmondutils)
REMOTE (in schrodinger.test.stu.sysinfo)	resize (in SwigVectorIntIntPair)	run_workflows() (in schrodinger.application.matsci.jaguarworkflows)
remote_command (in schrodinger.job)	resize (in SwigDoubleVector)	runCluFile() (in CluUtil)
remote_command() (in schrodinger.job.remote_command)	resize (in SwigDoubleVector3)	runEditedInput() (in ReadEditMixin)
remote_mmshare_dir() (in schrodinger.utils.fileutils)	resize (in SwigIntVector)	runIt() (in GeneticOptimization)
remote_scripts_dir() (in schrodinger.utils.fileutils)	resize (in SwigStringVector)	runIt() (in Interface)
remotehost() (in ResultReporter)	resize (in SwigUInt64Vector)	runIt() (in Nanoparticle)
REMOVE (in schrodinger.application.mopac.utils)	resize (in SwigUnsignedIntVector)	runIt() (in Surface)
remove() (in SlidableLine)	resize (in SwigUnsignedIntVector2)	runIt() (in Interfaces)
remove() (in JobOutput)	resize (in SwigVectorIntIntPair)	runIt() (in Surfaces)
remove() (in _MdcBase)	Resize() (in schrodinger.analysis.visanalysis.volumedatautils)	runIt() (in SurfacesInterfaces)
remove() (in Group)	resize() (in Bitset)	runIt() (in ReactionPath)
remove() (in LinkedList)	resize() (in SwigDoubleVector)	runJob() (in EditDialog)
remove() (in RunningJobs)	resize() (in SwigDoubleVector3)	runJobDJ() (in Stage)
remove() (in _Callback)	resize() (in SwigIntVector)	runJobs() (in TestUtility)
remove() (in _Column)	resize() (in SwigStringVector)	runMaestro() (in JobApp)
remove() (in Preferences)	resize() (in SwigUInt64Vector)	Runner (in schrodinger.test.stu.run)
remove_basename_ext() (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	resize() (in SwigUnsignedIntVector)	RUNNING (in JobStatus)
remove_dummy_atoms() (in Membrane_Model)	resize() (in SwigUnsignedIntVector2)	RUNNING (in schrodinger.pipeline.pipeline)
remove_dupes() (in schrodinger.structutils.smilesfilter)	resize() (in SwigVectorIntIntPair)	RunningJobs (in schrodinger.job.queue)
remove_extra_rotable_atoms() (in schrodinger.application.desmond.r_group_asl)	resize() (in DoubleDoubleList)	runpKa() (in PropertyCalculator)
remove_file() (in schrodinger.application.desmond.util)	resize() (in DoubleList)	runPrimeLoopPrediction() (in Refiner)
remove_hypo_if_present() (in schrodinger.application.phase.hypothesis)	resize() (in StringList)	runPrimeMinimization() (in Refiner)
remove_object() (in schrodinger.maestro.maestro)	resize() (in SwigAtomList)	runPrimeResidue() (in Refiner)
remove_option() (in SingleDashOptionParser)	resize() (in SwigAtomQueryParamsList)	runPrimeSidechain() (in Refiner)
remove_plugin() (in schrodinger.application.desmond.config)	resize() (in SwigDcNonPbcAtomIdxList)	runPrimeSidechainBB() (in Refiner)
remove_plugin() (in schrodinger.application.desmond.mdkey)	resize() (in SwigDcPbcAtomList)	runPrimeSidechainCBeta() (in Refiner)
remove_stereo_annotation() (in schrodinger.structutils.smiles)	resize() (in SwigRingList)	runPythonMinimize() (in Refiner)
remove_tag() (in Sea)	resize() (in _Column)	runRefinement() (in Refiner)
remove_temp_dir() (in schrodinger.application.desmond.mplchart)	resize() (in SwigDoubleVector)	runSingleStruc() (in AnalyzeEnergyWidget)
remove_unconn_core_atoms() (in FEPScholarMapper)	resize() (in SwigDoubleVector3)	runsLocally() (in BaseJob)
removeAction() (in Factory)	resize() (in SwigIntVector)	runsLocally() (in JobControlJob)
removeAllFeatures() (in PhaseFeatureMixin)	resize() (in SwigStringVector)	runsLocally() (in TestJCJob)
removeAllFeaturesForEntry() (in PhaseFeatureMixin)	resize() (in SwigUInt64Vector)	runsRemotely() (in TestScript)
removeAllRows() (in WidgetTable)	resize() (in SwigUnsignedIntVector)	runSuperposition() (in ReactionCoords)
removeAminoAcids() (in schrodinger.trajectory.automatic_analysis_generator)	resize() (in SwigUnsignedIntVector2)	runTabValidation() (in BaseJaguarPanel)
removeAndRenumber() (in Nanoparticle)	resize() (in SwigVectorIntIntPair)	runTransmutations() (in Alchemist)
removeBadOptions() (in schrodinger.application.bioluminate.workspacelabeler)	resize_restr_block() (in _AtomGroup)	runTransmutations() (in StructureAlchemist)
removeColorsForMissingPoints() (in SliderPlot)	resize_restr_block() (in schrodinger.application.desmond.mdkey)	runWorkup() (in TestScript)
removeCoordinate() (in CoordinatesModel)	RESIZE_THRESHOLD (in schrodinger.ui.widgettable)	runXCluFile() (in CluUtil)
removed() (in DictDiffer)	resize_window() (in schrodinger.application.desmond.util)	rxn_channel (in schrodinger.application.matsci)
removeFeature() (in PhaseFeatureMixin)	resize_window2() (in schrodinger.application.desmond.util)	rxn_channel (in schrodinger.application.matsci.rxn_channel)
removeFFProperties() (in ItemRow)	resizeCells() (in WidgetTable)	rxn_coord_precision (in JaguarResults)
RemoveHydrogens (in schrodinger.application.bioluminate.pml_menus)	resizeEvent() (in _StructView)	RXN_KEY (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
removeHydrogens() (in NanoTube)	resizeEvent() (in DendrogramView)	rxn_path (in schrodinger.application.matsci)
removeIgnoredClashes() (in BuilderWithClashDetection)	resizeEvent() (in structure_view)	RXN_REPRESENTATION_KEY (in Products)
removeIgnorePair() (in ConnectionStorage)	resizeEvent() (in sketcher)	RXNCOORD (in ReactionPath)
removeKey() (in Definition)	resizeEvent() (in sketcherGUIMultiColumnToolBar)	RXNINDEX (in ReactionPath)
removeMarker (in BaseSubTab)	resizeEvent() (in sketcherView)