[ 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 _ ]

P

P1_SPACE_GROUP_SYMBOL (in schrodinger.application.matsci.nano.xtal)	PhpProject_getHypoSitesStrings() (in _phase')	prepareGeometryChange() (in DendrogramGraphicTree)
pack() (in schroPmwWrapper)	PhpProject_getInFileType() (in _phase')	prepareGeometryChange() (in sketcherAtom)
pack() (in GroundClass)	PhpProject_getLigand() (in _phase')	prepareGeometryChange() (in sketcherBond)
pack() (in schroWidget)	PhpProject_getLigandCount() (in _phase')	prepareGeometryChange() (in sketcherGraphicalObject)
pack_stage() (in StageBase)	PhpProject_getLigandIDs() (in _phase')	prepareGeometryChange() (in sketcherResidue)
Package (in schrodinger.application.licensing.flexlm)	PhpProject_getMatchedSites() (in _phase')	prepareGeometryChange() (in sketcherResidueInteraction)
PACKAGE_SUFFIX (in schrodinger.application.desmond.cmj)	PhpProject_getMatchedSitesStrings() (in _phase')	prepareInputLigands() (in SampleRingsStage)
packages (in schrodinger.application.combiglide)	PhpProject_getMolSites() (in _phase')	prepareStructureForMinimization() (in ItemRow)
Packing (in schrodinger.protein._reliability)	PhpProject_getMolSitesStrings() (in _phase')	prepareStructureForMinimization() (in TMLigandRowMixin)
padAlignment() (in BaseAlignment)	PhpProject_getMustMatch() (in _phase')	prepareStructures() (in WaterMapInput)
PAGE_MARGIN (in PicturePrinter)	PhpProject_getPatternMatches() (in _phase')	prepBldStruct() (in PrimeConfig)
paint() (in _StructViewItem)	PhpProject_getPharmSet() (in _phase')	prepend_mmfile_path() (in schrodinger.application.ligprep.ionizer)
paint() (in _zoomViewItem)	PhpProject_getProjectPath() (in _phase')	prepend_path() (in schrodinger.utils.env)
paint() (in WorkspaceInclusionDelegate)	PhpProject_getQsarAlignments() (in _phase')	prepEnergy() (in PrimeConfig)
paint() (in BarHeightDelegate)	PhpProject_getQsarCount() (in _phase')	prepLoop() (in PrimeConfig)
paint() (in BaseRowDelegate)	PhpProject_getQsarHypoIDs() (in _phase')	prepMinimize() (in PrimeConfig)
paint_asl() (in Workspace)	PhpProject_getQsarIDs() (in _phase')	prepResidue() (in PrimeConfig)
paint_asl() (in schrodinger.application.desmond.maestro)	PhpProject_getQsarModel() (in _phase')	preprocessMatchAtoms() (in NanoTube)
paint_mol() (in Workspace)	PhpProject_getQsarModelClassDescription() (in _phase')	prepSidechain() (in PrimeConfig)
paintCell() (in createFragmentDelegate)	PhpProject_getQsarModelClasses() (in _phase')	prepSidechainBB() (in PrimeConfig)
paintCell() (in simpleEnumDockDelegate)	PhpProject_getQsarModelClassFraction() (in _phase')	prepSidechainCBeta() (in PrimeConfig)
PaintDeviceMetric	PhpProject_getQsarModelCoeff() (in _phase')	prepwizard (in schrodinger.application)
paintEvent() (in RowActionItem)	PhpProject_getQsarModelCoeffRange() (in _phase')	present_tense (in TestUtility)
paintEvent() (in WorkspaceInclusionCheckBox)	PhpProject_getQsarModelFactorCount() (in _phase')	PRESERVE_BONDING_KEY (in schrodinger.application.matsci.nano.xtal)
paintEvent() (in DendrogramView)	PhpProject_getQsarModelGridLimits() (in _phase')	PRESET_GCR (in schrodinger.application.bioluminate.protein_structure_quality)
paintEvent() (in SHView)	PhpProject_getQsarModelGridSpacing() (in _phase')	PRESET_RT (in schrodinger.application.bioluminate.protein_structure_quality)
paintEvent() (in sketcher)	PhpProject_getQsarModelRegF() (in _phase')	PRESET_RYW (in schrodinger.application.bioluminate.protein_structure_quality)
paintEvent() (in sketcherGUIMultiColumnToolBar)	PhpProject_getQsarModelRegP() (in _phase')	PresetAction (in schrodinger.application.bioluminate.pml_menus)
paintEvent() (in sketcherView)	PhpProject_getQsarModelRegRsqr() (in _phase')	PRESETS (in schrodinger.application.bioluminate.protein_structure_quality)
pair() (in _FFIO)	PhpProject_getQsarModelRegRsqrCv() (in _phase')	PresetSubMenu (in schrodinger.application.bioluminate.pml_menus)
pair_builtin_prop (in schrodinger.trajectory.ffstructure)	PhpProject_getQsarModelRegRsqrScramble() (in _phase')	Pressure (in schrodinger.application.desmond.simulation_block_test)
PairDict (in schrodinger.application.desmond.energygroup)	PhpProject_getQsarModelRegSD() (in _phase')	pressure_tensor_pattern (in MSEnergyGroupAnalysis)
pairmap() (in _FEPIO)	PhpProject_getQsarModelRegStability() (in _phase')	prestage() (in StageBase)
PairMarker (in schrodinger.maestro.markers)	PhpProject_getQsarModelStyle() (in _phase')	prestage() (in FepMapperReport)
PAIRS (in CheckInput)	PhpProject_getQsarModelVolBitCount() (in _phase')	prestage() (in Stop)
pairwise_align_ct() (in schrodinger.application.ska)	PhpProject_getQsarModelVolClasses() (in _phase')	prestage() (in SystemBuilder)
paletteChange() (in DendrogramView)	PhpProject_getQsarModelVolCoords() (in _phase')	PRESUMED_TS (in ParserWrapper)
paletteChange() (in SHView)	PhpProject_getQsarModelVolOnBits() (in _phase')	PRESUMED_TS_CHOICES (in ParserWrapper)
paletteChange() (in sketcher)	PhpProject_getQsarProps() (in _phase')	PrettyPubPreset (in schrodinger.application.bioluminate.pml_menus)
paletteChange() (in sketcherGUIMultiColumnToolBar)	PhpProject_getQsarSet() (in _phase')	prev() (in _Step)
paletteChange() (in sketcherView)	PhpProject_getQsarStats() (in _phase')	PREV_ROW (in schrodinger.application.msv.gui.viewmodel)
paletteChanged() (in SimpleEnumDockPanel)	PhpProject_getRuntimeName() (in _phase')	prevent_overlapping_x_labels() (in schrodinger.application.bioluminate.sliderchart)
paletteRefreshed() (in SimpleEnumDockPanel)	PhpProject_getSiteFragment() (in _phase')	prevent_overlapping_x_labels() (in schrodinger.application.desmond.mplchart)
PAM250 (in schrodinger.application.msv.domain.constants)	PhpProject_getSiteMasks() (in _phase')	preview() (in EditDialog)
PanedWidget (in schrodinger.ui.widget.pmwwidget)	PhpProject_getSitesConformer() (in _phase')	PREVIOUS (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
PanedWindow (in schrodinger.ui.widget.tkinterwidget)	PhpProject_getSitesConformers() (in _phase')	previous() (in SwigPyIterator)
panel() (in schrodinger.application.bioluminate.protein_report_widget)	PhpProject_getSlash() (in _phase')	previous() (in SwigPyIterator)
panel() (in schrodinger.application.matsci.reordergui)	PhpProject_getStep() (in _phase')	previous() (in SwigPyIterator)
PanelModality	PhpProject_getTitle() (in _phase')	previous() (in SwigPyIterator)
panels (in schrodinger.application.combiglide.combenumdock)	PhpProject_haveMasterDiffs() (in _phase')	previous() (in SwigPyIterator)
Parallelepiped (in schrodinger.application.matsci.shapes)	PhpProject_isValidArchiveName() (in _phase')	previous() (in SwigPyIterator)
PARALLELEPIPED_SIDE_FACES (in schrodinger.application.matsci.nano.slab)	PhpProject_isValidProjectName() (in _phase')	previous() (in SwigPyIterator)
PARAM (in schrodinger.application.desmond.cmj)	PhpProject_logActivity() (in _phase')	previous() (in SwigPyIterator)
PARAM() (in StageBase)	PhpProject_needSyncFeatureDef() (in _phase')	PRIMARY (in SpaceGroups)
param() (in Key)	PhpProject_newProject() (in _phase')	PRIMARY_ALIGNMENT_DEFAULT (in schrodinger.application.matsci.nano.particle)
PARAM() (in Aacg_SiteMap_Multijob)	PhpProject_openProject() (in _phase')	PRIMARY_ALIGNMENT_DEFAULT_LIST (in schrodinger.application.matsci.nano.particle)
PARAM() (in AlignCore)	PhpProject_restoreMasterData() (in _phase')	PRIMARY_OPERATIONS_TAG (in SpaceGroup)
PARAM() (in Analysis)	PhpProject_reviseDatabase() (in _phase')	PRIMARY_OPERS (in SpaceGroup)
PARAM() (in AssignForcefield)	PhpProject_sampleActives() (in _phase')	prime (in schrodinger.application)
PARAM() (in BuildGeometry)	PhpProject_saveFeatureDef() (in _phase')	Prime (in schrodinger.application.prime.input)
PARAM() (in CalcDdg)	PhpProject_saveFeatureDefToFile() (in _phase')	prime (in schrodinger.application.vsw.stages)
PARAM() (in CovalentFepMapper)	PhpProject_saveFeatureFreq() (in _phase')	prime (in schrodinger.pipeline.stages)
PARAM() (in DesmondExtend)	PhpProject_saveFeatureRadii() (in _phase')	PRIME_ANTIB_LOOP_PRED (in Refiner)
PARAM() (in Extern)	PhpProject_saveFeatureTol() (in _phase')	PRIME_ENTROPY (in _mmutil')
PARAM() (in FepAnalysis)	PhpProject_saveFind() (in _phase')	PRIME_ENTROPY (in schrodinger.utils.mmutil)
PARAM() (in FepLauncher)	PhpProject_saveMasterData() (in _phase')	PRIME_LOOP_PRED (in Refiner)
PARAM() (in FepMapper)	PhpProject_saveQsar() (in _phase')	PRIME_MINIMIZE (in Refiner)
PARAM() (in FepMapperCleanup)	PhpProject_saveSiteMasks() (in _phase')	PRIME_RESIDUE (in Refiner)
PARAM() (in FepMapperReport)	PhpProject_scaleActivity() (in _phase')	prime_search_and_scan() (in BondRotator)
PARAM() (in FepMapping)	PhpProject_setActivity() (in _phase')	PRIME_SIDECHAIN (in Refiner)
PARAM() (in FepVrun)	PhpProject_setActivityMissing() (in _phase')	PRIME_SIDECHAIN_BB (in Refiner)
PARAM() (in ForcefieldBuilder)	PhpProject_setGroup() (in _phase')	PRIME_SIDECHAIN_CBETA (in Refiner)
PARAM() (in LambdaHopping)	PhpProject_setMustMatch() (in _phase')	prime_specs (in schrodinger.application.prime.input)
PARAM() (in MatSciAnalysis)	PhpProject_setPharmSet() (in _phase')	prime_workups (in schrodinger.test.stu.outcomes)
PARAM() (in McproSimulate)	PhpProject_setQsarSet() (in _phase')	PrimeConfig (in schrodinger.application.bioluminate.protein)
PARAM() (in McproSystemBuilder)	PhpProject_setupFind() (in _phase')	primefix (in schrodinger.application.prime)
PARAM() (in Minimize)	PhpProject_setupQsar() (in _phase')	Primer
PARAM() (in Multisim)	PhpProject_siteToStrings() (in _phase')	PrimeStage (in schrodinger.pipeline.stages.prime)
PARAM() (in PLAnalysis)	PhpProject_swiginit() (in _phase')	PrimeStructure (in schrodinger.application.bioluminate.protein)
PARAM() (in ProteinFepMapper)	PhpProject_swigregister() (in _phase')	PRIMEX_LIGPREP_EPIK (in schrodinger.infra.mm)
PARAM() (in ProteinMutationGenerator)	PhpProject_syncFeatureDef() (in _phase')	PRIMEX_MAIN (in schrodinger.infra.mm)
PARAM() (in ReplicaExchange)	PhpProject_testQsarModel() (in _phase')	primex_steric_clash_data_set (in Report)
PARAM() (in Simulate)	PhpProject_unzipArchive() (in _phase')	Primitive (in schrodinger.graphics3d.common)
PARAM() (in SolvatePocket)	PhpProject_unzipProject() (in _phase')	print_1() (in AlchemicalInteractions)
PARAM() (in SystemBuilder)	PhpProject_writeHypoFiles() (in _phase')	print_all() (in AlchemicalInteractions)
PARAM() (in Task)	PhpProject_zipDirectory() (in _phase')	print_allow_adsorption_onto() (in schrodinger.application.matsci.rxn_channel.rxn_channel)
PARAM() (in Trajectory)	PhpProject_zipProject() (in _phase')	print_attachment_points() (in Data)
PARAM() (in Trim)	PhpSite (in schrodinger.infra.phase)	print_attachment_points_ct() (in Data)
PARAM() (in VacuumReport)	PhpSite___eq__() (in _phase')	print_bad_jobs() (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
PARAM() (in Vrun)	PhpSite___ne__() (in _phase')	print_debug() (in schrodinger.application.desmond.cmj)
PARAM() (in WaterMap)	PhpSite_calculateSimilarity() (in _phase')	print_deprecate() (in schrodinger.application.watermap.watermap_inp)
PARAM() (in WaterMapCluster)	PhpSite_distance() (in _phase')	print_fields() (in Feature)
PARAM() (in WaterMapPostAnalysis)	PhpSite_getProjectedOnly() (in _phase')	print_fields() (in LicenseLine)
param_in_parfile (in schrodinger.application.mcpro.writeinputs)	PhpSite_getSiteNumber() (in _phase')	print_fields() (in Package)
parameters_c (in schrodinger.infra.mopac)	PhpSite_getSiteSimilarity() (in _phase')	print_fields() (in Server)
PARAMS (in Jcoupling)	PhpSite_getSiteStatus() (in _phase')	print_fields() (in Vendor)
ParaStyle (in schrodinger.application.desmond.report_helper)	PhpSite_getSiteType() (in _phase')	print_help() (in Help)
paraUtils (in schrodinger.application.macromodel)	PhpSite_getSiteTypeChar() (in _phase')	print_help() (in Help)
parent() (in Node)	PhpSite_getXCoord() (in _phase')	print_if() (in schrodinger.application.desmond.util)
parent() (in NonNestedProxy)	PhpSite_getYCoord() (in _phase')	PRINT_INFO (in ParserWrapper)
parent() (in Sea)	PhpSite_getZCoord() (in _phase')	print_job_info() (in schrodinger.application.macromodel.paraUtils)
parent_dir() (in schrodinger.application.desmond.util)	PhpSite_setCoordinates() (in _phase')	print_pathway() (in schrodinger.application.desmond.fepana)
parent_structure (in FFStructure)	PhpSite_setProjectedOnly() (in _phase')	print_quiet() (in schrodinger.application.desmond.cmj)
pargph() (in schrodinger.application.desmond.report_helper)	PhpSite_setProjectedOnlyOff() (in _phase')	print_report() (in schrodinger.application.canvas.driverutils)
parse() (in TreeWizard)	PhpSite_setProjectedOnlyOn() (in _phase')	print_silent() (in schrodinger.application.desmond.cmj)
parse() (in TextParser)	PhpSite_setSiteNumber() (in _phase')	print_summary() (in schrodinger.test.stu.workup)
parse() (in Scan)	PhpSite_setSiteSimilarity() (in _phase')	print_tonull() (in schrodinger.application.desmond.cmj)
parse() (in CriterionParser)	PhpSite_setSiteStatusOff() (in _phase')	print_tree() (in Node)
parse() (in DefinitionParser)	PhpSite_setSiteStatusOn() (in _phase')	print_usage() (in Startup)
parse() (in _MySplit)	PhpSite_setSiteType() (in _phase')	print_usage() (in schrodinger.application.desmond.simulation_block_data)
parse_args() (in schrodinger.application.licensing.licadmin)	PhpSite_setSiteTypeChar() (in _phase')	print_usage() (in schrodinger.application.desmond.simulation_block_test)
parse_args() (in CmdlineParser)	PhpSite_setStatus() (in _phase')	print_usage() (in UI)
parse_args() (in MopacAPI)	PhpSite_setXCoord() (in _phase')	print_usage() (in SingleDashOptionParser)
parse_args() (in HuntOptions)	PhpSite_setYCoord() (in _phase')	print_val() (in Test)
parse_args() (in SingleDashOptionParser)	PhpSite_setZCoord() (in _phase')	print_verbose() (in schrodinger.application.desmond.cmj)
parse_arguments() (in schrodinger.protein.getpdb_utility)	PhpSite_SiteStatusOff (in _phase')	print_version() (in Help)
parse_basis() (in schrodinger.application.jaguar.basis)	PhpSite_SiteStatusOn (in _phase')	print_version() (in Startup)
parse_checkpoint_file() (in schrodinger.application.desmond.starter.generator.fep_plus)	PhpSite_swiginit() (in _phase')	print_version() (in Help)
parse_command_line() (in schrodinger.application.vsw.vswinput)	PhpSite_swigregister() (in _phase')	print_version() (in UI)
parse_components() (in schrodinger.application.licensing.flexlm)	PI (in schrodinger.application.matsci.shapes)	print_Zmat() (in Zmat)
parse_date() (in schrodinger.application.licensing.flexlm)	pi (in schrodinger.protein.assignment)	printAction() (in Pipeline)
parse_eneseq() (in schrodinger.application.desmond.fepana)	pi (in schrodinger.structutils.interactions)	printAction() (in StageJob)
parse_expiration() (in schrodinger.application.licensing.flexlm)	PI_CAT_INTERACTION() (in sketcherStyle)	printAllChannels() (in ChannelDefinitions)
parse_fep_data() (in FEPReportMaker)	PI_PI_INTERACTION() (in sketcherStyle)	printAllSpgInfo() (in SpaceGroups)
parse_file() (in Mopac2012TextParser)	PiCationInteraction (in schrodinger.infra.structure)	printChannelDefs() (in Channels)
parse_geometry() (in schrodinger.application.desmond.util)	PiCationParams (in schrodinger.infra.structure)	printCrystalParams() (in Crystal)
parse_indices() (in schrodinger.application.desmond.enhsamp)	Pick3DObjectToggle (in schrodinger.ui.picking)	printDatabaseEntry() (in SpaceGroup)
parse_it() (in schrodinger.application.desmond.title_to_hex)	PICK_ATOMS (in schrodinger.application.jaguar.gui.tabs.coordinates)	printFailureMessage() (in StageJob)
parse_keyword_list() (in schrodinger.application.matsci.jobutils)	PICK_ATOMS_AND_BONDS (in schrodinger.application.jaguar.gui.tabs.coordinates)	printFiltered() (in Channels)
parse_lambda() (in schrodinger.application.desmond.config)	pick_by_atom() (in Rama)	printFooter() (in TestUtility)
parse_lambda() (in schrodinger.application.desmond.gconfig)	pick_by_point() (in Rama)	printHeader() (in TestUtility)
parse_line() (in schrodinger.application.licensing.flexlm)	pick_category (in MaestroArrow)	printHeader() (in TestQueue)
parse_lmdiag_entry() (in schrodinger.application.licensing.licadmin)	pick_category (in MaestroSphere)	printInfo() (in replica_container)
parse_lmdiag_output() (in schrodinger.application.licensing.licadmin)	pick_category (in MaestroTorus)	printInternals() (in InternalCoords)
parse_lmgrd_event() (in schrodinger.application.licensing.licadmin)	PICK_COMBO_ATOMS (in schrodinger.application.jaguar.gui.tabs.coordinates)	printJobParams() (in NanoSheets)
parse_lmgrd_lines() (in schrodinger.application.licensing.licadmin)	PICK_COMBO_BONDS (in schrodinger.application.jaguar.gui.tabs.coordinates)	printJobParams() (in NanoTubes)
parse_lmgrd_log() (in schrodinger.application.licensing.licadmin)	pick_id (in MaestroArrow)	printline() (in schrodinger.test.stu.outcomes.jaguar)
parse_lmhostid_output() (in schrodinger.application.licensing.licadmin)	pick_id (in MaestroSphere)	printMultiWalledTubes() (in NanoTubes)
parse_lmstat_output() (in schrodinger.application.licensing.licadmin)	pick_id (in MaestroTorus)	printNotMinimized() (in Channels)
parse_log_file() (in schrodinger.test.stu.outcomes.standard_workups)	PICK_MAX_ATOMS (in CoordinatePicker)	printOnlyFailed() (in TestUtility)
parse_meta() (in schrodinger.application.desmond.meta)	PICK_TYPES (in schrodinger.application.jaguar.gui.tabs.coordinates)	printout() (in InputConfig)
parse_mexpr() (in schrodinger.application.desmond.enhsamp)	PickAtomToggle (in schrodinger.application.desmond.fep_gui)	printout() (in JobParameters)
parse_msj() (in schrodinger.application.desmond.cmj)	PickAtomToggle (in schrodinger.ui.picking)	printout() (in JobParameters)
parse_res_tag() (in schrodinger.application.desmond.fep_edge_report_maker)	PickAtomToggle (in schrodinger.ui.widget.tkinterwidget)	printOverlapTable() (in schrodinger.trajectory.prody.compare)
parse_restart_parameters_file() (in schrodinger.application.matsci.jobutils)	PickBondToggle (in schrodinger.application.desmond.fep_gui)	printParameters() (in Minimizer)
parse_sba() (in schrodinger.application.desmond.simulation_block_data)	PickBondToggle (in schrodinger.ui.picking)	printParams() (in GeneticOptimization)
parse_sbt() (in schrodinger.application.desmond.simulation_block_test)	PickBondToggle (in schrodinger.ui.widget.tkinterwidget)	printParams() (in Nanoparticle)
parse_slice() (in schrodinger.application.desmond.util)	pickCompleted() (in CoordinatePicker)	printParams() (in Surface)
parse_tokens() (in schrodinger.application.licensing.flexlm)	pickCompleted() (in OptimizationTab)	printProperties() (in GeneticOptimization)
parseArgs() (in ParserWrapper)	pickCompleted() (in ScanTab)	printProps() (in MultiWalledNanoTube)
parseArgs() (in ParserWrapper)	picked() (in ColorChooserPanel)	printProps() (in NanoTube)
parseArgs() (in ParserWrapper)	picking (in schrodinger.ui)	printRunSummary() (in TestUtility)
parseArgs() (in ParserWrapper)	picking_atom_start() (in schrodinger.maestro.maestro)	printRxnReprs() (in Channels)
parseArgs() (in ParserWrapper)	picking_bond_start() (in schrodinger.maestro.maestro)	printSingleWalledTubes() (in NanoTubes)
parseArgs() (in ParserWrapper)	picking_lasso_start() (in schrodinger.maestro.maestro)	printStatus() (in NewEntryGroup)
parseAtomText() (in StructureListWidget)	picking_loss_notify() (in schrodinger.maestro.maestro)	printStatus() (in JobDJ)
parseCanvasCsv() (in Calculator)	picking_stop() (in schrodinger.maestro.maestro)	printStatus() (in TestQueue)
parseCodes() (in FastaAlignmentReader)	Picklable (in schrodinger.application.desmond.picklejar)	printSwapZmatAtom() (in ZmatAtom)
parseConfigFile() (in schrodinger.test.stu.outcomes.jaguar)	picklejar (in schrodinger.application.desmond)	printSymmetryOpers() (in SpaceGroup)
ParseError (in schrodinger.application.desmond.cmj)	PickleJar (in schrodinger.application.desmond.picklejar)	printTestNumbers() (in TestUtility)
parseHeader() (in FastaAlignmentReader)	PickleState (in schrodinger.application.desmond.picklejar)	printTree() (in DefinitionViewerDialog)
parseInput() (in Calculator)	PickMixedToggle (in schrodinger.ui.picking)	printvals() (in schrodinger.infra.propedit)
parseInputFile() (in MMKVSettings)	pickProjTableAtom() (in MoleculeTabPka)	printZmatAtom() (in ZmatAtom)
parseLine() (in Criterion)	pickThisAtom() (in MoleculeTabPka)	Priority
parseNode() (in TreePatternParser)	PickToggle (in schrodinger.ui.widget.tkinterwidget)	Priority
parseOptions() (in CanvasFingerprintClusterCLI)	PickTorsionToggle (in schrodinger.ui.picking)	priority() (in LicenseResource)
parseOptions() (in CanvasFingerprintGeneratorCLI)	PicturePrinter (in schrodinger.application.report2d)	PriorityQueue (in schrodinger.job.queue)
parseOptions() (in CanvasFingerprintSimilarityCLI)	PINF (in schrodinger.protein.assignment)	PRISM (in schrodinger.application.matsci.shapes)
parseOptions() (in _Main)	PINFO (in _McproProt)	PRO_COLOR (in Rama)
parsePropertyString() (in Property)	PINK (in schrodinger.application.bioluminate.pml_menus)	prob (in schrodinger.application.desmond.ana)
Parser (in schrodinger.application.desmond.antlr3.recognizers)	PINK (in CoordinatePicker)	probe_checkpoint() (in schrodinger.application.desmond.cmj)
parser (in schrodinger.application.desmond.cns_io)	PINK (in schrodinger.application.matsci.amorphous)	process_ark() (in _KeywordProcessor)
parser (in schrodinger.application.desmond.system_builder_util)	pink (in Color)	process_attributes() (in schrodinger.application.licensing.licadmin)
parser (in schrodinger.application.licensing.licadmin)	pipeio (in schrodinger.pipeline)	process_bennett_log() (in replica_container)
parser (in schrodinger.application.watermap.watermap_inp)	PipeIO (in schrodinger.pipeline.pipeio)	process_chunks() (in schrodinger.application.desmond.simulation_block_test)
ParserMain (in schrodinger.application.desmond.antlr3.main)	pipeline (in schrodinger)	process_highlights() (in schrodinger.utils.pymol)
ParserRuleReturnScope (in schrodinger.application.desmond.antlr3.recognizers)	pipeline (in schrodinger.pipeline)	process_hypothesis() (in schrodinger.utils.pymol)
ParserWrapper (in schrodinger.application.matsci.nano.interface_mod)	Pipeline (in schrodinger.pipeline.pipeline)	process_management (in schrodinger.test.stu)
ParserWrapper (in schrodinger.application.matsci.nano.particle)	pipeline_init_wrapper() (in schrodinger.pipeline.compiled_functions)	process_measurements() (in schrodinger.utils.pymol)
ParserWrapper (in schrodinger.application.matsci.nano.slab)	pipeutils (in schrodinger.application.vsw)	process_option_strings() (in SingleDashOption)
ParserWrapper (in schrodinger.application.matsci.nano.surfaces_interfaces_mod)	pipeutils (in schrodinger.pipeline)	process_pending_events() (in schrodinger.maestro.maestro)
ParserWrapper (in schrodinger.application.matsci.nano.xtal)	PIPI_EDGE_TO_FACE_MAXIMUM_DISTANCE (in _structure')	process_prj() (in schrodinger.utils.pymol)
ParserWrapper (in schrodinger.application.matsci.rxn_path)	PIPI_EDGE_TO_FACE_MAXIMUM_DISTANCE (in schrodinger.infra.structure)	process_row() (in schrodinger.utils.pymol)
parseSolvent() (in DrawSolventPanel)	PIPI_EDGE_TO_FACE_MINIMUM_ANGLE (in _structure')	process_status() (in schrodinger.test.stu.process_management)
parseStr() (in schrodinger.application.desmond.enhsamp)	PIPI_EDGE_TO_FACE_MINIMUM_ANGLE (in schrodinger.infra.structure)	process_surface() (in schrodinger.utils.pymol)
parseStream() (in LexerMain)	PIPI_FACE_TO_FACE_MAXIMUM_ANGLE (in _structure')	processContextAction() (in ParticipantView)
parseStream() (in ParserMain)	PIPI_FACE_TO_FACE_MAXIMUM_ANGLE (in schrodinger.infra.structure)	processEvents() (in AppFramework)
parseStream() (in WalkerMain)	PIPI_FACE_TO_FACE_MAXIMUM_DISTANCE (in _structure')	processFrame() (in EnergyGroup)
parseStream() (in _Main)	PIPI_FACE_TO_FACE_MAXIMUM_DISTANCE (in schrodinger.infra.structure)	processFrame() (in MSEnergyGroup)
parseTree() (in TreePatternParser)	PiPiInteraction (in schrodinger.infra.structure)	processFrame() (in Angle)
parseWorkup() (in TestScript)	PiPiInteraction (in schrodinger.structutils.interactions.pi)	processFrame() (in AverageStructure)
PART_FILL (in Partition)	PiPiParams (in schrodinger.infra.structure)	processFrame() (in CenterOfMass)
PARTIAL (in GenOptions)	PK_THRESH_DEF (in schrodinger.application.ligprep.ionizer)	processFrame() (in CenterOfMotion)
PARTIAL (in schrodinger.ui.widget.tkinterwidget)	PKA_ATOM (in InputEntriesColumnsPka)	processFrame() (in CovarianceMatrix)
partial_charge (in _StructureAtom)	pka_atom (in ProjEntryTuplePka)	processFrame() (in Dihedral)
partial_charge (in ColorBy)	PKA_ATOM_PROP (in ProjEntryPka)	processFrame() (in Distance)
PARTIAL_CHARGE_4D (in schrodinger.application.bioluminate.pml_menus)	PKA_ATOM_PROP (in MoleculeTabPka)	processFrame() (in HydrogenBondFinder)
partial_structure_reader() (in schrodinger.test.stu.outcomes.prime_workups)	PKA_ATOM_ROLE (in schrodinger.application.jaguar.gui.input_tab_widgets_pka)	processFrame() (in HydrogenBondTracker)
participants (in ReactionTab)	PKA_INVALID (in ProjEntryPka)	processFrame() (in LigandRMSD)
ParticipantView (in schrodinger.application.jaguar.gui.tabs.reaction_tab)	PKA_MISSING (in ProjEntryPka)	processFrame() (in MolecularSurfaceArea)
particle (in schrodinger.application.matsci.nano)	pka_property (in schrodinger.protein.assignment)	processFrame() (in PlanarAngle)
particle_position (in _DesmondFrame)	PKA_VALID (in ProjEntryPka)	processFrame() (in PolarSurfaceArea)
particle_total (in _DesmondFrame)	pl_image_tools (in schrodinger.application.desmond.event_analysis)	processFrame() (in Position)
particle_velocity (in _DesmondFrame)	PL_INTERACTIONS (in schrodinger.application.desmond.fep_edge_report_maker)	processFrame() (in RMSD)
Partition (in schrodinger.application.combiglide.packages.hierarchy)	placeStructureInCell() (in AmorphousCellBuilder)	processFrame() (in RMSF)
partitionAtoms() (in Nanoparticle)	PLAIN_FORMAT (in schrodinger.job.jobapi)	processFrame() (in RadiusOfGyration)
Partitioning (in schrodinger.application.combiglide.packages.hierarchy)	PLAnalysis	processFrame() (in Ramachandran)
partitioning_names_at_levels (in CoreClassifier)	planar_groups (in schrodinger.protein.analysis_params)	processFrame() (in SecondaryStructure)
PasswordRetryException (in schrodinger.utils.urllib)	PlanarAngle (in schrodinger.trajectory.analysis)	processFrame() (in SolventAccessibleSurfaceArea)
past_tense (in TestUtility)	plane (in schrodinger.application.matsci.nano)	processFrame() (in SolventAccessibleSurfaceAreaByResidue)
patch() (in _BaseClient)	PLATFORM_WARNING (in schrodinger.application.desmond.gui)	processFrame() (in VolumeMapper)
PATCH_ANALYZER (in _mmutil')	PLATONIC (in schrodinger.application.matsci.shapes)	processFrame() (in AnalysisTool)
PATCH_ANALYZER (in schrodinger.utils.mmutil)	plot (in schrodinger.application.desmond.mplchart)	processFrame() (in HydrophobicContactFinder)
patch_count (in Surface)	plot() (in Plotter)	processFrame() (in Jcoupling)
patch_vertices (in Surface)	plot() (in EnergyGroup)	processFrame() (in AreaPerLipid)
PATH (in schrodinger.utils.env)	plot() (in Reporter)	processFrame() (in PhospholipidBilayerThickness)
path_geometry() (in schrodinger.application.jaguar.output)	plot() (in Angle)	processFrame() (in OrderParameter)
PATH_MAX (in _mmutil')	plot() (in AverageStructure)	processFrame() (in ProtLigInteractionFinder)
PATH_MAX (in schrodinger.infra.mm)	plot() (in CenterOfMass)	processFrame() (in SaltBridgeFinder)
PATH_MAX (in schrodinger.utils.mmutil)	plot() (in CenterOfMotion)	processHbFrame() (in ProtLigInteractionFinder)
PathModel (in schrodinger.application.desmond.fep_gui)	plot() (in CovarianceMatrix)	processHydrophobic() (in ProtLigInteractionFinder)
pathModified() (in FileEntry)	plot() (in Dihedral)	processHydrophobicFrame() (in HydrophobicContactFinder)
pathname() (in Vendor)	plot() (in Distance)	processJobOutputs() (in GeneratePropsStage)
pathname() (in LicenseResource)	plot() (in HydrogenBondTracker)	processJobOutputs() (in LigFilterStage)
pathname() (in schrodinger.utils.sea)	plot() (in LigandRMSD)	processJobOutputs() (in DockingStage)
PATTERN (in ChannelDefinition)	plot() (in MolecularSurfaceArea)	processJobOutputs() (in LigPrepStage)
pattern() (in TreePatternParser)	plot() (in PlanarAngle)	processJobOutputs() (in ConfSearchStage)
PatternModel (in schrodinger.ui.ligfilter)	plot() (in PolarSurfaceArea)	processJobOutputs() (in SampleRingsStage)
PB_BOX_FACTOR (in schrodinger.application.desmond.fep_net_charge)	plot() (in Position)	processJobOutputs() (in MMGBSAStage)
PBC (in schrodinger.infra.structure)	plot() (in RMSD)	processJobOutputs() (in PrimeStage)
PBC_BOND_COLOR (in PBCBond)	plot() (in RMSF)	processJobOutputs() (in QikPropStage)
PBC_BOND_COLOR_KEY (in PBCBond)	plot() (in RadiusOfGyration)	processJobOutputs() (in QSiteStage)
PBC_BOND_KEY (in schrodinger.application.matsci.desmondutils)	plot() (in Ramachandran)	processJobOutputs() (in SemiEmpStage)
PBC_BOND_KEY (in PBCBond)	plot() (in SecondaryStructure)	processMetalFrame() (in ProtLigInteractionFinder)
PBC_BOND_THRESHOLD (in PBCBond)	plot() (in SolventAccessibleSurfaceArea)	processOldDBs() (in ActiveDatabaseDialog)
PBC_BONDING (in ParserWrapper)	plot() (in SolventAccessibleSurfaceAreaByResidue)	processPiCationFrame() (in HydrophobicContactFinder)
pbc_manager (in schrodinger.trajectory)	plot() (in AnalysisTool)	processPiFrame() (in ProtLigInteractionFinder)
PBCBond (in schrodinger.application.matsci.nano.xtal)	plot() (in PhospholipidBilayerThickness)	processPiPiFrame() (in HydrophobicContactFinder)
PBCBonds (in schrodinger.application.matsci.nano.xtal)	plot() (in OrderParameter)	processProducts() (in Channels)
PBCMeasureMananger (in schrodinger.trajectory.pbc_manager)	plot2D() (in AnalysisTool)	processSbFrame() (in ProtLigInteractionFinder)
pca (in schrodinger.trajectory.prody)	plot_2d() (in Reporter)	processWatersFrame() (in ProtLigInteractionFinder)
PCA (in schrodinger.trajectory.prody.pca)	plot_lambda_window_overlap() (in schrodinger.application.desmond.fepana)	PROCS_COL (in MultiHostTableModel)
PCLOSE (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)	PLOT_TYPES (in ClusterStatisticsPlotDialog)	procText() (in schrodinger.application.desmond.enhsamp)
PCLOSE (in schrodinger.application.desmond.enhanced_sampling.mexpParser)	PLOT_TYPES (in DistanceMatrixPlotDialog)	PRODUCT (in MultiStructureTab)
PDB (in schrodinger.utils.fileutils)	PLOTALEA (in MopacResults71)	PRODUCT (in ParserWrapper)
PDB_ATOM_NAME_KEY (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	PLOTALIE (in MopacResults71)	PRODUCT (in PerformanceTestCase)
PDB_COMMON_NAMELEN (in _structure')	PLOTESP (in MopacResults71)	product (in schrodinger.test.stu.constants)
PDB_COMMON_NAMELEN (in schrodinger.infra.structure)	Plotter (in schrodinger.analysis.enrichment)	product_dependencies (in schrodinger.test.stu.constants)
PDB_CRYSTAL_PROPS (in schrodinger.application.matsci.desmondutils)	plum (in Color)	PRODUCT_LIKE (in ParserWrapper)
PDB_R (in schrodinger.protein._reliability)	plus() (in Rama)	PRODUCT_NAME_BASE (in Products)
PDB_RES_NAME_KEY (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	PLUS_ICON (in schrodinger.application.matsci.msicons.controlicons)	PRODUCT_PREFIX (in schrodinger.application.jaguar.gui.tabs.reaction_molecules_tab)
PDB_RESOL (in schrodinger.protein._reliability)	pml_menus (in schrodinger.application.bioluminate)	PRODUCTPREFIX (in ReactionCoords)
PDB_RFREE (in schrodinger.protein._reliability)	PML_PRESET_SURFACE (in schrodinger.application.bioluminate.pml_menus)	Products (in schrodinger.application.matsci.rxn_channel.rxn_channel)
PDB_STRING (in SimplifiedSequenceViewer)	PML_SURFACE (in schrodinger.application.bioluminate.pml_menus)	prody (in schrodinger.trajectory)
pdbcode (in _StructureAtom)	PMLContextMenu (in schrodinger.application.bioluminate.pml_menus)	profile_get_current_parent() (in schrodinger.maestro.maestro)
PdbMmpdbxAtom (in schrodinger.infra.structure)	PMLMenu (in schrodinger.application.bioluminate.pml_menus)	profiling (in schrodinger.job.hunt_stub)
pdbname (in schrodinger.application.prepwizard)	pmode() (in Sea)	profiling (in schrodinger.job.jobcontrol)
pdbname (in _StructureAtom)	Pmw_initialise() (in schrodinger.ui.widget.tkinterwidget)	PROG (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)
PDBNAME_ELEMENT_DICT (in schrodinger.application.prepwizard)	pmwwidget (in schrodinger.ui.widget)	PROG (in schrodinger.application.desmond.enhanced_sampling.mexpParser)
PdbReader (in schrodinger.infra.structure)	PNAME (in _McproProt)	prog() (in mexpParser)
PDBReader (in schrodinger.structure)	PNAME0 (in _DesmondProt)	prog_return (in mexpParser)
pdbres (in _Residue)	PNAME1 (in _DesmondProt)	PROJ_DIR (in ProjectTestCase)
pdbres (in _StructureAtom)	PNAME2 (in _DesmondProt)	project (in schrodinger)
pdbres (in Ligand)	Point (in schrodinger.application.matsci.rxn_path)	Project (in schrodinger.project)
PDBWriter (in schrodinger.structure)	point_group() (in schrodinger.application.jaguar.output)	PROJECT_CLOSE_CALLBACK (in schrodinger.maestro.maestro)
PENALIZE (in schrodinger.application.glide.glide)	POINT_GROUP_NAME (in SpaceGroup)	project_close_callback_add() (in schrodinger.maestro.maestro)
PENALIZE_CHOICES (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	POINT_GROUP_TAG (in SpaceGroup)	project_close_callback_remove() (in schrodinger.maestro.maestro)
PENALIZE_DEFAULT (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	point_group_used() (in schrodinger.application.jaguar.output)	project_close_cancel() (in schrodinger.maestro.maestro)
PENALIZE_PROTOCOLS (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	pointForIndex() (in Grid3D)	project_get() (in schrodinger.maestro.maestro)
PENALTYWEIGHT (in ParserWrapper)	pointInside() (in ConvexPolyhedron)	PROJECT_RENAME_CALLBACK (in schrodinger.maestro.maestro)
PEOE_INTERVAL (in schrodinger.application.moldescriptors)	pointInside() (in Cylinder)	project_rename_callback_add() (in schrodinger.maestro.maestro)
PEPTIDE_BOND_LENGTH_CUTOFF (in schrodinger.protein._reliability)	pointInside() (in Sphere)	project_rename_callback_remove() (in schrodinger.maestro.maestro)
peptide_planarity_data_set (in Report)	pointIsOutOfBounds() (in Grid3D)	PROJECT_SUFFIXES (in schrodinger.ui.qt.filedialog)
PER_ATOM_BASIS_ROLE (in schrodinger.application.jaguar.gui.input_tab_widgets)	POLAR_NOT_CHARGED_RESIDUES (in schrodinger.structutils)	PROJECT_TABLE (in JobInputFrame)
perAtomBasisChanged() (in InputEntriesModel)	POLAR_POS (in StructuralInteractionFingerprintGenerator)	PROJECT_TABLE (in JobInputFrame)
perAtomBasisForEid() (in BasisSetModel)	POLAR_RESIDUE (in StructuralInteractionFingerprintGenerator)	project_table_get() (in schrodinger.maestro.maestro)
PerAtomBasisRow (in schrodinger.application.jaguar.gui.tabs.sub_tab_widgets.basis_set_widgets)	POLAR_RESIDUE() (in sketcherStyle)	project_table_synchronize() (in schrodinger.maestro.maestro)
perAtomBasisSetsPresent() (in BasisSetSubTab)	POLAR_RESIDUES (in schrodinger.application.bioluminate.protein)	project_table_update() (in schrodinger.maestro.maestro)
perAtomBasisSetsPresent() (in InputTabWithSubTabs)	POLAR_RESIDUES (in schrodinger.structutils)	PROJECT_UPDATE_CALLBACK (in schrodinger.maestro.maestro)
PERCENT (in schrodinger.application.desmond.antlr3.treewizard)	POLAR_RESIDUES (in StructuralInteractionFingerprintGenerator)	project_update_callback_add() (in schrodinger.maestro.maestro)
Percent_helix() (in schrodinger.utils.ligfilter)	PolarContactsObject (in schrodinger.application.bioluminate.pml_menus)	project_update_callback_remove() (in schrodinger.maestro.maestro)
Percent_loop() (in schrodinger.utils.ligfilter)	PolarContactsOnlyMainchain (in schrodinger.application.bioluminate.pml_menus)	PROJECT_V4 (in _mmutil')
PERCENT_METAL_THRESHOLD (in schrodinger.application.matsci.nano.xtal)	PolarContactsOnlySidechain (in schrodinger.application.bioluminate.pml_menus)	PROJECT_V4 (in schrodinger.utils.mmutil)
Percent_strand() (in schrodinger.utils.ligfilter)	PolarContactsSubMenu (in schrodinger.application.bioluminate.pml_menus)	projectClosed() (in ReactionTab)
percentage() (in _Rotamer)	PolarContactsToAnyAtoms (in schrodinger.application.bioluminate.pml_menus)	projectClosedCallback() (in _App)
perceptual_diff (in schrodinger.test.stu.outcomes.custom)	PolarContactsToAnyNonSolvent (in schrodinger.application.bioluminate.pml_menus)	ProjectException (in schrodinger.project)
perceptual_diff() (in schrodinger.test.stu.outcomes.custom.perceptual_diff)	PolarContactsToEntry (in schrodinger.application.bioluminate.pml_menus)	projectmodel (in schrodinger.infra)
perform_transmutations() (in schrodinger.application.matsci.enumeration)	PolarContactsToEntryWithoutSolvent (in schrodinger.application.bioluminate.pml_menus)	ProjectOpenDialog (in schrodinger.ui.qt.filedialog)
performance (in schrodinger.test)	PolarContactsWithoutIntraMainchain (in schrodinger.application.bioluminate.pml_menus)	ProjectRow (in schrodinger.project)
performance_api_url() (in schrodinger.test.performance.reporter)	PolarContactsWithoutMainchain (in schrodinger.application.bioluminate.pml_menus)	PROJECTS_FILTER (in schrodinger.ui.qt.filedialog)
PerformanceTestCase (in schrodinger.test.performance.api)	PolarContactsWithoutSolvent (in schrodinger.application.bioluminate.pml_menus)	ProjectSurface (in schrodinger.surface)
performSVD() (in PCA)	PolarContactsWithSidechains (in schrodinger.application.bioluminate.pml_menus)	ProjectTableButton (in schrodinger.application.jaguar.gui.input_tab_widgets)
performTransmutation() (in Alchemist)	PolarContactsWithSolvent (in schrodinger.application.bioluminate.pml_menus)	ProjectTestCase (in schrodinger.test.custom_test_classes)
performTransmutation() (in ElementAlchemist)	POLARIZABILITY (in schrodinger.application.moldescriptors)	projectUpdated() (in InputTabMixin)
performTransmutation() (in VacancyAlchemist)	POLARIZABILITY_ROW (in schrodinger.application.jaguar.gui.tabs.properties_tab)	projectUpdated() (in MultiStructureMixin)
PERIODIC_CALLBACK (in schrodinger.maestro.maestro)	PolarizabilitySubTab (in schrodinger.application.jaguar.gui.tabs.properties_tab)	projectUpdated() (in SubTabMixin)
periodic_callback_add() (in schrodinger.maestro.maestro)	polarization (in _Basis)	projectUpdated() (in InputEntriesModel)
periodic_callback_remove() (in schrodinger.maestro.maestro)	PolarSurfaceArea (in schrodinger.trajectory.analysis)	projectUpdated() (in InputTabBase)
periodicfix (in schrodinger.application.desmond)	polygon (in schrodinger.graphics3d)	projectUpdated() (in InputTabWithSubTabs)
PERL5LIB (in schrodinger.utils.env)	Polygon (in schrodinger.graphics3d.polygon)	projectUpdated() (in MultiStructureTab)
PERL_FEATURE_FLAGS (in schrodinger.utils.mmutil)	polyhedron (in schrodinger.graphics3d)	ProjEntry (in schrodinger.application.jaguar.gui.input_tab_widgets)
permanent_arrays (in schrodinger.infra.mopac)	Polyhedron (in schrodinger.graphics3d.polyhedron)	ProjEntryPka (in schrodinger.application.jaguar.gui.input_tab_widgets_pka)
PERMANENT_LICENSE_FAILURE (in JobStatus)	POLYHEDRON_TYPES (in schrodinger.application.matsci.shapes)	ProjEntryTuple (in schrodinger.application.jaguar.gui.input_tab_widgets)
persistentIndexList() (in RowModel)	POLYMER (in schrodinger.application.bioluminate.pml_menus)	ProjEntryTuplePka (in schrodinger.application.jaguar.gui.input_tab_widgets_pka)
PERSONAL_FRAGS_DIR (in schrodinger.application.combiglide.combenumdock)	pop() (in CommonTreeNodeStream)	PROJET_TABLE (in SimplifiedSequenceViewer)
PERSONAL_PALS_DIR (in schrodinger.application.combiglide.combenumdock)	pop() (in PairDict)	ProjTableLikeView (in schrodinger.application.jaguar.gui.utils)
PERT_NAME (in ModelSystem)	pop() (in stringvector)	PROLINE (in schrodinger.application.msv.domain.residue)
PertID (in schrodinger.application.mcpro.perturbations)	pop() (in SwigDoubleVector)	promoteShowToolTip() (in InputEntriesProxyModel)
PertReorder (in schrodinger.application.mcpro.perturbations)	pop() (in SwigDoubleVector3)	PromptDialog (in schrodinger.ui.widget.pmwwidget)
perturbation_databases (in schrodinger.application.mcpro.perturbations)	pop() (in SwigIntVector)	prop (in schrodinger.structure)
perturbations (in schrodinger.application.mcpro)	pop() (in SwigStringVector)	PROP_BOOLEAN (in schrodinger.structure)
Perturbations (in schrodinger.application.mcpro.perturbations)	pop() (in SwigUInt64Vector)	PROP_CONVERSIONS (in schrodinger.application.bioluminate.protein)
PFILE (in _McproProt)	pop() (in SwigUnsignedIntVector)	PROP_FLOAT (in schrodinger.structure)
PFILE0 (in _DesmondProt)	pop() (in SwigUnsignedIntVector2)	PROP_INTEGER (in schrodinger.structure)
PFILE1 (in _DesmondProt)	pop() (in SwigVectorIntIntPair)	PROP_LONG_NAME (in schrodinger.structure)
PFILE2 (in _DesmondProt)	pop() (in SwigDoubleVector)	prop_RE (in schrodinger.infra.propedit)
PH_DEF (in schrodinger.application.ligprep.ionizer)	pop() (in SwigDoubleVector3)	PROP_REAL (in schrodinger.structure)
PH_DIFF_TOL (in schrodinger.application.ligprep.ionizer)	pop() (in SwigIntVector)	PROP_SHORT_NAME (in schrodinger.structure)
pH_high (in schrodinger.protein.assignment)	pop() (in SwigStringVector)	PROP_STRING (in schrodinger.structure)
pH_low (in schrodinger.protein.assignment)	pop() (in SwigUInt64Vector)	prop_type_names (in schrodinger.application.desmond.ffiostructure)
pH_neutral (in schrodinger.protein.assignment)	pop() (in SwigUnsignedIntVector)	prop_value (in Array_Prop)
PH_PRECISION (in schrodinger.application.ligprep.ionizer)	pop() (in SwigUnsignedIntVector2)	propedit (in schrodinger.infra)
PH_THRESH_DEF (in schrodinger.application.ligprep.ionizer)	pop() (in SwigVectorIntIntPair)	properties (in schrodinger.application.medchem.property)
pH_vlow (in schrodinger.protein.assignment)	pop() (in SwigDoubleVector)	properties_c (in schrodinger.infra.mopac)
phase (in schrodinger.application)	pop() (in SwigDoubleVector3)	properties_do_not_exist() (in schrodinger.test.stu.outcomes.custom.glide)
phase (in schrodinger.application.vsw.stages)	pop() (in SwigIntVector)	PROPERTIES_NOT_IN_TABLE_1_FILE (in schrodinger.infra.mmproj)
PHASE (in schrodinger.infra.mm)	pop() (in SwigStringVector)	properties_tab (in schrodinger.application.jaguar.gui.tabs)
phase (in schrodinger.infra)	pop() (in SwigUInt64Vector)	properties_tab_ui (in schrodinger.application.jaguar.gui.ui)
phase (in schrodinger.pipeline.stages)	pop() (in SwigUnsignedIntVector)	PropertiesMixin (in schrodinger.application.jaguar.gui.base_panel)
PHASE (in schrodinger.utils.preferences)	pop() (in SwigUnsignedIntVector2)	PropertiesTab (in schrodinger.application.jaguar.gui.tabs.properties_tab)
PHASE_CORE_HOPPING (in schrodinger.infra.mm)	pop() (in SwigVectorIntIntPair)	PropertiesTabBase (in schrodinger.application.jaguar.gui.tabs.properties_tab)
PHASE_DATABASE_EXE (in schrodinger.pipeline.stages.phase)	pop() (in DoubleDoubleList)	PropertiesTabIGO (in schrodinger.application.jaguar.gui.tabs.properties_tab)
PHASE_DBCREATE (in schrodinger.infra.mm)	pop() (in DoubleList)	PropertiesTableWidget (in schrodinger.application.jaguar.gui.utils)
PHASE_DBSEARCH (in schrodinger.infra.mm)	pop() (in StringList)	PropertiesValidatorMixin (in schrodinger.application.jaguar.gui.base_panel)
PHASE_DEVELOP_HYPOTHESIS_SPEC (in PhaseHypothesisInputConfig)	pop() (in SwigAtomList)	property (in _Element)
PHASE_ELEMENTS (in schrodinger.infra.mm)	pop() (in SwigAtomPairList)	property (in _FEPIO)
PHASE_FEATURE (in schrodinger.infra.mm)	pop() (in SwigAtomPairWithValueList)	property (in _FEPIOSubBlock)
PHASE_FQSAR (in schrodinger.infra.mm)	pop() (in SwigAtomQueryParamsList)	property (in _FFIO)
phase_markers (in schrodinger.application.phase)	pop() (in SwigDcNonPbcAtomIdxList)	property (in _FFIOSubBlock)
PHASE_MULTI_EXE (in schrodinger.pipeline.stages.phase)	pop() (in SwigDcPbcAtomList)	Property (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
PHASE_PARTITION (in schrodinger.infra.mm)	pop() (in SwigPiCationList)	property (in schrodinger.application.medchem)
PHASE_QSAR (in schrodinger.infra.mm)	pop() (in SwigPiPiInteractionList)	property (in Structure)
PHASE_SCORING (in schrodinger.infra.mm)	pop() (in SwigRingList)	property (in TextualStructure)
PHASE_SELECTIVITY (in schrodinger.infra.mm)	pop() (in SwigSaltBridgeList)	property (in _StructureAtom)
PHASE_SIMPLE_PHOBIC (in _mmutil')	pop() (in OneIndexedList)	property (in _StructureBond)
PHASE_SIMPLE_PHOBIC (in schrodinger.utils.mmutil)	pop() (in PriorityQueue)	property (in _FFAngle)
phase_widgets (in schrodinger.application.phase)	pop() (in SwigDoubleVector)	property (in _FFBond)
PhaseDatabaseIconProvider (in schrodinger.ui.qt.filedialog)	pop() (in SwigDoubleVector3)	property (in _FFConstraint)
PhaseDatabaseOpenDialog (in schrodinger.ui.qt.filedialog)	pop() (in SwigIntVector)	property (in _FFDihedral)
PHASEDB (in schrodinger.application.vsw.vswinput)	pop() (in SwigStringVector)	property (in _FFExclusion)
PHASEDB (in schrodinger.pipeline.pipeio)	pop() (in SwigUInt64Vector)	property (in _FFPair)
PhaseDB (in schrodinger.pipeline.pipeio)	pop() (in SwigUnsignedIntVector)	property (in _FFPseudo)
PHASEDB_FILTER (in schrodinger.ui.qt.filedialog)	pop() (in SwigUnsignedIntVector2)	property (in _FFRestraint)
PHASEDB_SUFFIXES (in schrodinger.ui.qt.filedialog)	pop() (in SwigVectorIntIntPair)	property (in _FFSite)
PhaseFeatureMarker (in schrodinger.application.phase.phase_markers)	pop() (in List)	property (in _FFVdwtype)
PhaseFeatureMixin (in schrodinger.application.phase.phase_markers)	pop_back() (in stringvector)	property (in _FFVirtual)
PhaseHypothesisInputConfig (in schrodinger.application.phase.input)	pop_back() (in SwigDoubleVector)	PROPERTY (in schrodinger.utils.ligfilter)
PHENYLALANINE (in schrodinger.application.msv.domain.residue)	pop_back() (in SwigDoubleVector3)	property_dict (in schrodinger.maestro.maestro)
PHI (in schrodinger.graphics3d.polyhedron)	pop_back() (in SwigIntVector)	property_is_consistent() (in schrodinger.test.stu.outcomes.custom.glide)
phi0 (in _FFIOImproperFBHW)	pop_back() (in SwigStringVector)	PROPERTY_METHOD (in PolarizabilitySubTab)
PhospholipidBilayerThickness (in schrodinger.trajectory.lipid_analysis)	pop_back() (in SwigUInt64Vector)	property_names (in schrodinger.application.matsci)
PhotoImage (in schrodinger.ui.widget.tkinterwidget)	pop_back() (in SwigUnsignedIntVector)	PropertyCalculator (in schrodinger.application.bioluminate.protein)
PhpAlignCore (in schrodinger.infra.phase)	pop_back() (in SwigUnsignedIntVector2)	PropertyCriterion (in schrodinger.utils.ligfilter)
PhpAlignCore_getAlignedB() (in _phase')	pop_back() (in SwigVectorIntIntPair)	PropertyDictionary (in schrodinger.project)
PhpAlignCore_getMappings() (in _phase')	pop_back() (in SwigDoubleVector)	PropertyName (in schrodinger.structure)
PhpAlignCore_getNumMappings() (in _phase')	pop_back() (in SwigDoubleVector3)	propertyselector (in schrodinger.ui)
PhpAlignCore_stereoFailure() (in _phase')	pop_back() (in SwigIntVector)	PropertySelector (in schrodinger.ui.propertyselector)
PhpAlignCore_swiginit() (in _phase')	pop_back() (in SwigStringVector)	PropertySelectorMenu (in schrodinger.ui.propertyselector)
PhpAlignCore_swigregister() (in _phase')	pop_back() (in SwigUInt64Vector)	PropertySelectorWithRanges (in schrodinger.application.bioluminate.propfilter)
PhpComplex (in schrodinger.infra.phase)	pop_back() (in SwigUnsignedIntVector)	propfilter (in schrodinger.application.bioluminate)
PhpComplex_create() (in _phase')	pop_back() (in SwigUnsignedIntVector2)	propfilter_ui (in schrodinger.application.bioluminate)
PhpComplex_getErrMesg() (in _phase')	pop_back() (in SwigVectorIntIntPair)	PropFilterDialog (in schrodinger.application.bioluminate.propfilter)
PhpComplex_getLimits() (in _phase')	pop_back() (in SwigDoubleVector)	propka_parse (in schrodinger.application.bioluminate)
PhpComplex_setDefaultLimits() (in _phase')	pop_back() (in SwigDoubleVector3)	PROPKA_SCRIPT (in schrodinger.application.bioluminate.run_propka)
PhpComplex_setLimits() (in _phase')	pop_back() (in SwigIntVector)	PropkaError (in schrodinger.application.bioluminate.protein)
PhpComplex_swiginit() (in _phase')	pop_back() (in SwigStringVector)	PropKaException (in schrodinger.protein.assignment)
PhpComplex_swigregister() (in _phase')	pop_back() (in SwigUInt64Vector)	PROT_AND_DNA_SELE (in schrodinger.application.bioluminate.pml_menus)
PhpException (in schrodinger.infra.phase)	pop_back() (in SwigUnsignedIntVector)	PROT_ANIONS (in SaltBridgeFinder)
PhpException_errCode_get() (in _phase')	pop_back() (in SwigUnsignedIntVector2)	PROT_CATIONS (in SaltBridgeFinder)
PhpException_errCode_set() (in _phase')	pop_back() (in SwigVectorIntIntPair)	PROT_FINAL_NAME (in ModelSystem)
PhpException_errMesg_get() (in _phase')	pop_back() (in DoubleDoubleList)	PROT_NAME (in ModelSystem)
PhpException_errMesg_set() (in _phase')	pop_back() (in DoubleList)	PROT_ONLY (in ModelSystem)
PhpException_swiginit() (in _phase')	pop_back() (in StringList)	prot_toggle() (in _Flex)
PhpException_swigregister() (in _phase')	pop_back() (in SwigAtomList)	ProtAssign (in schrodinger.protein.assignment)
PhpException_what() (in _phase')	pop_back() (in SwigAtomPairList)	protein (in schrodinger.application.bioluminate)
PhpFastShape (in schrodinger.infra.phase)	pop_back() (in SwigAtomPairWithValueList)	protein (in schrodinger)
PhpFastShape_alignCt() (in _phase')	pop_back() (in SwigAtomQueryParamsList)	PROTEIN_ASL (in schrodinger.application.matsci.nano.xtal)
PhpFastShape_alignCtPy() (in _phase')	pop_back() (in SwigDcNonPbcAtomIdxList)	PROTEIN_ASL (in schrodinger.trajectory.automatic_analysis_generator)
PhpFastShape_computeShapeSim() (in _phase')	pop_back() (in SwigDcPbcAtomList)	PROTEIN_ELEC_BLOCK (in schrodinger.application.desmond.fep_net_charge)
PhpFastShape_computeShapeSimPy() (in _phase')	pop_back() (in SwigPiCationList)	PROTEIN_MUTATION (in schrodinger.application.desmond.fep_gui)
PhpFastShape_setDebug() (in _phase')	pop_back() (in SwigPiPiInteractionList)	PROTEIN_REPORT_LABEL (in schrodinger.protein._reliability)
PhpFastShape_swiginit() (in _phase')	pop_back() (in SwigRingList)	protein_report_widget (in schrodinger.application.bioluminate)
PhpFastShape_swigregister() (in _phase')	pop_back() (in SwigSaltBridgeList)	protein_residue() (in FEPEdgeData)
PhpFastShapePair (in schrodinger.infra.phase)	pop_back() (in SwigDoubleVector)	PROTEIN_RIP (in schrodinger.application.desmond.fep_net_charge)
PhpFastShapePair_a_get() (in _phase')	pop_back() (in SwigDoubleVector3)	protein_sequences (in SimplifiedSequenceViewer)
PhpFastShapePair_a_set() (in _phase')	pop_back() (in SwigIntVector)	protein_structure_quality (in schrodinger.application.bioluminate)
PhpFastShapePair_b_get() (in _phase')	pop_back() (in SwigStringVector)	protein_structure_quality_ui (in schrodinger.application.bioluminate)
PhpFastShapePair_b_set() (in _phase')	pop_back() (in SwigUInt64Vector)	ProteinAlignment (in schrodinger.application.msv.domain.alignment)
PhpFastShapePair_c_get() (in _phase')	pop_back() (in SwigUnsignedIntVector)	ProteinAlignment (in schrodinger.application.msv.domain.undoable_alignment)
PhpFastShapePair_c_set() (in _phase')	pop_back() (in SwigUnsignedIntVector2)	ProteinAlignmentAnnotations (in schrodinger.application.msv.domain.annotation)
PhpFastShapePair_i1_get() (in _phase')	pop_back() (in SwigVectorIntIntPair)	ProteinAlignmentMsvWidget (in schrodinger.application.msv.gui.msv_widget)
PhpFastShapePair_i1_set() (in _phase')	pop_errors() (in ErrorHandler)	ProteinAlignmentView (in schrodinger.application.msv.gui.view)
PhpFastShapePair_i2_get() (in _phase')	pop_level() (in ErrorHandler)	ProteinCheckLabelSpinner (in schrodinger.application.desmond.feputils)
PhpFastShapePair_i2_set() (in _phase')	pop_level() (in schrodinger.infra.mmerr)	ProteinCheckParameters (in schrodinger.protein.reliability)
PhpFastShapePair_swiginit() (in _phase')	POPEN (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)	ProteinCheckThread (in schrodinger.application.desmond.feputils)
PhpFastShapePair_swigregister() (in _phase')	POPEN (in schrodinger.application.desmond.enhanced_sampling.mexpParser)	ProteinFepMapper
PhpFeatureData (in schrodinger.infra.phase)	Popen() (in schrodinger.utils.subprocess)	proteinHandler (in schrodinger.application.mcpro.zmat)
PhpFeatureData_clear() (in _phase')	popitem() (in PairDict)	ProteinMapperMsjGenerator (in schrodinger.application.desmond.mapper_msj_generator)
PhpFeatureData_exportToFile() (in _phase')	populate_from_file() (in MopacResults2012)	ProteinMutationGenerator
PhpFeatureData_exportToStream() (in _phase')	populateExcitedStatesType() (in ExcitedStateWidget)	ProteinReport (in schrodinger.application.desmond.replica_sid_generator)
PhpFeatureData_getDataColumn() (in _phase')	populateHostsTable() (in MultiHostSelector)	ProteinReportCheck (in schrodinger.test.structurecheck)
PhpFeatureData_getDataRow() (in _phase')	populatePickCombo() (in CoordinatePicker)	ProteinSequence (in schrodinger.application.msv.domain.sequence)
PhpFeatureData_getDataValue() (in _phase')	populateTypeCombo() (in CoordinatePicker)	ProteinSequence (in schrodinger.application.msv.domain.undoable_sequence)
PhpFeatureData_importFromFile() (in _phase')	populateWeights() (in _ChargeSelectorPopUp)	ProteinSequenceAnnotations (in schrodinger.application.msv.domain.annotation)
PhpFeatureData_importFromStream() (in _phase')	POPULATION (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	ProteinStructureQualityViewer (in schrodinger.application.bioluminate.protein_structure_quality)
PhpFeatureData_numDataColumns() (in _phase')	popup() (in AbstractMsvContextMenu)	protliginteractionfinder (in schrodinger.trajectory)
PhpFeatureData_setDataRow() (in _phase')	popup() (in DefaultContextMenu)	ProtLigInteractionFinder (in schrodinger.trajectory.protliginteractionfinder)
PhpFeatureData_setDataValue() (in _phase')	popUpUpdated() (in BasisSelectorLineEdit)	PROTOCOL_VERSION (in DebugEventListener)
PhpFeatureData_setDefaultDataRow() (in _phase')	popUpUpdated() (in MutationSelectorComboBox)	protonated_res_list (in schrodinger.protein.analysis)
PhpFeatureData_setDefaultDataValue() (in _phase')	popUpUpdated() (in MutationSelectorLineEdit)	protonated_residues (in schrodinger.protein.analysis_params)
PhpFeatureData_swiginit() (in _phase')	PopUpWidget (in schrodinger.ui.qt.appframework)	protonateResidue() (in ResidueTools)
PhpFeatureData_swigregister() (in _phase')	port() (in Vendor)	ProvidesBasisMixin (in schrodinger.application.jaguar.gui.tabs.base_tab)
PhpFeatureDefinition (in schrodinger.infra.phase)	pos() (in _fakeEvent)	ProvidesStructuresMetaclass (in schrodinger.application.jaguar.gui.tabs.base_tab)
PhpFeatureDefinition___eq__() (in _phase')	PoseLibrary (in schrodinger.application.glide.glideanalysis)	ProvidesStructuresMixin (in schrodinger.application.jaguar.gui.tabs.base_tab)
PhpFeatureDefinition___ne__() (in _phase')	poseviewconvert (in schrodinger.application.glide)	ProxyBasicAuthHandler (in schrodinger.utils.urllib)
PhpFeatureDefinition_clear() (in _phase')	posfbhw() (in _FFIO)	ProxyDigestAuthHandler (in schrodinger.utils.urllib)
PhpFeatureDefinition_getAllExcludes() (in _phase')	Position (in schrodinger.application.msv.gui.color)	ProxyHandler (in schrodinger.utils.urllib)
PhpFeatureDefinition_getAllIncludes() (in _phase')	Position (in schrodinger.trajectory.analysis)	ProxyMixin (in schrodinger.application.msv.gui.viewmodel)
PhpFeatureDefinition_getExcludePattern() (in _phase')	position (in _DesmondFrame)	ProxyPasswordManager (in schrodinger.utils.urllib)
PhpFeatureDefinition_getExtendDistance() (in _phase')	POSITION_SCHEME (in schrodinger.application.bioluminate.pml_menus)	ProxyPasswordManagerQt (in schrodinger.protein.getpdb_utility)
PhpFeatureDefinition_getFeatureComment() (in _phase')	POSITIONAL (in schrodinger.application.glide.glide)	ProxyTunnelError (in schrodinger.utils.urllib)
PhpFeatureDefinition_getFeatureName() (in _phase')	PositionalConstraint (in schrodinger.application.glide.glide)	Pseudo (in schrodinger.application.desmond.cms)
PhpFeatureDefinition_getFeatureNumber() (in _phase')	PositionScheme (in schrodinger.application.msv.gui.color)	pseudo() (in _FFIO)
PhpFeatureDefinition_getFeatureType() (in _phase')	POSITIVELY_CHARGED_RESIDUE() (in sketcherStyle)	pseudo_builtin_prop (in schrodinger.trajectory.ffstructure)
PhpFeatureDefinition_getIncludePattern() (in _phase')	PosResDelegate (in schrodinger.application.desmond.gui)	pseudo_charge (in FFStructure)
PhpFeatureDefinition_getNumExcludes() (in _phase')	PosResModel (in schrodinger.application.desmond.gui)	pseudo_mass (in FFStructure)
PhpFeatureDefinition_getNumIncludes() (in _phase')	PosResRow (in schrodinger.application.desmond.gui)	pseudo_position (in _DesmondFrame)
PhpFeatureDefinition_getProjectedType() (in _phase')	post() (in PMLContextMenu)	pseudospectral() (in schrodinger.application.jaguar.output)
PhpFeatureDefinition_getSasOptions() (in _phase')	post() (in JobAPI)	PSP (in schrodinger.infra.mm)
PhpFeatureDefinition_setAllExcludes() (in _phase')	post() (in _BaseClient)	PSP (in schrodinger.utils.preferences)
PhpFeatureDefinition_setAllIncludes() (in _phase')	post() (in _Cell)	PSP_BB (in schrodinger.infra.mm)
PhpFeatureDefinition_setExcludePattern() (in _phase')	post_system() (in schrodinger.test.performance.reporter)	PSP_FR (in schrodinger.infra.mm)
PhpFeatureDefinition_setExtendDistance() (in _phase')	PostAnnotationFilterProxyMixin (in schrodinger.application.msv.gui.viewmodel)	PSP_PLOP (in _licensing')
PhpFeatureDefinition_setFeatureComment() (in _phase')	postCommand() (in BaseJob)	PSP_PLOP (in schrodinger.infra.licensing)
PhpFeatureDefinition_setFeatureName() (in _phase')	PostLigPrepStage (in schrodinger.pipeline.stages.ligprep)	PSP_PLOP (in schrodinger.infra.mm)
PhpFeatureDefinition_setFeatureNumber() (in _phase')	postProcess() (in AverageStructure)	PSP_PLOP_MEMBRANE (in schrodinger.infra.mm)
PhpFeatureDefinition_setFeatureType() (in _phase')	postProcess() (in CovarianceMatrix)	PSP_RB (in schrodinger.infra.mm)
PhpFeatureDefinition_setIncludePattern() (in _phase')	postProcess() (in AnalysisTool)	PSP_SKA (in schrodinger.infra.mm)
PhpFeatureDefinition_setProjectedTypeOff() (in _phase')	PostReorderingProxyMixin (in schrodinger.application.msv.gui.viewmodel)	PSP_SSP (in schrodinger.infra.mm)
PhpFeatureDefinition_setProjectedTypeOn() (in _phase')	poststage() (in StageBase)	PSP_STA (in schrodinger.infra.mm)
PhpFeatureDefinition_setSasOptions() (in _phase')	poststage() (in FepAnalysis)	PSP_STA_GPCR (in schrodinger.infra.mm)
PhpFeatureDefinition_swiginit() (in _phase')	poststage() (in FepAnalysis2)	pt_entry_id (in ReactionParticipant)
PhpFeatureDefinition_swigregister() (in _phase')	poststage() (in FepMapperReport)	PT_IMPORT_TXT (in ParticipantView)
PhpFeaturePattern (in schrodinger.infra.phase)	poststage() (in Stop)	pull (in schrodinger.application.vsw.stages)
PhpFeaturePattern___eq__() (in _phase')	poststage() (in SystemBuilder)	pull (in schrodinger.pipeline.stages)
PhpFeaturePattern___ne__() (in _phase')	poststage() (in WaterMapCluster)	pull_ligand() (in schrodinger.application.glide.http_server)
PhpFeaturePattern_getAtomList() (in _phase')	postTreatBuiltCell() (in AmorphousCellBuilder)	pullCompounds() (in PullStage)
PhpFeaturePattern_getEditStatus() (in _phase')	postTreatMinimizedStructure() (in ItemRow)	pullHBonds() (in sketcherLID)
PhpFeaturePattern_getExtendDistance() (in _phase')	postTreatMinimizedStructure() (in TMLigandRowMixin)	pullPiInteractions() (in sketcherLID)
PhpFeaturePattern_getGeometry() (in _phase')	potential() (in BondRotator)	pullSaltBridges() (in sketcherLID)
PhpFeaturePattern_getPattern() (in _phase')	PotentialEnergy (in schrodinger.application.desmond.simulation_block_test)	PullStage (in schrodinger.pipeline.stages.pull)
PhpFeaturePattern_getPatternID() (in _phase')	PotentialFrame (in schrodinger.ui.macromodel)	purgeRecord() (in Job)
PhpFeaturePattern_getPattyHandle() (in _phase')	POWER_LAW_SCALING (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	push() (in CommonTreeNodeStream)
PhpFeaturePattern_getProjectedType() (in _phase')	PR_NAME (in TimeSeriesAnalysisJob)	push() (in Queue)
PhpFeaturePattern_getType() (in _phase')	pre_score_pairs() (in hbond_cluster)	push() (in StageBase)
PhpFeaturePattern_getTypeSimilarity() (in _phase')	pre_score_self() (in hbond_cluster)	push() (in PriorityQueue)
PhpFeaturePattern_getUsedStatus() (in _phase')	pre_treat() (in changeable)	push_back() (in stringvector)
PhpFeaturePattern_setAtomList() (in _phase')	pre_treat_1() (in amide_changeable)	push_back() (in SwigDoubleVector)
PhpFeaturePattern_setEditOff() (in _phase')	pre_treat_1() (in amine_changeable)	push_back() (in SwigDoubleVector3)
PhpFeaturePattern_setEditOn() (in _phase')	pre_treat_1() (in carboxyl_changeable)	push_back() (in SwigIntVector)
PhpFeaturePattern_setExtendDistance() (in _phase')	pre_treat_1() (in changeable)	push_back() (in SwigStringVector)
PhpFeaturePattern_setGeometry() (in _phase')	pre_treat_1() (in histidine_changeable)	push_back() (in SwigUInt64Vector)
PhpFeaturePattern_setPattern() (in _phase')	pre_treat_1() (in rotatable_changeable)	push_back() (in SwigUnsignedIntVector)
PhpFeaturePattern_setPatternID() (in _phase')	pre_treat_2() (in amide_changeable)	push_back() (in SwigUnsignedIntVector2)
PhpFeaturePattern_setPattyHandle() (in _phase')	pre_treat_2() (in amine_changeable)	push_back() (in SwigVectorIntIntPair)
PhpFeaturePattern_setProjectedType() (in _phase')	pre_treat_2() (in carboxyl_changeable)	push_back() (in SwigDoubleVector)
PhpFeaturePattern_setType() (in _phase')	pre_treat_2() (in changeable)	push_back() (in SwigDoubleVector3)
PhpFeaturePattern_setTypeSimilarity() (in _phase')	pre_treat_2() (in histidine_changeable)	push_back() (in SwigIntVector)
PhpFeaturePattern_setUsedOff() (in _phase')	pre_treat_2() (in rotatable_changeable)	push_back() (in SwigStringVector)
PhpFeaturePattern_setUsedOn() (in _phase')	PRECISION (in CanvasFingerprintGenerator)	push_back() (in SwigUInt64Vector)
PhpFeaturePattern_swiginit() (in _phase')	precision (in BondCharge)	push_back() (in SwigUnsignedIntVector)
PhpFeaturePattern_swigregister() (in _phase')	precision (in Dipole)	push_back() (in SwigUnsignedIntVector2)
PhpIntCoord (in schrodinger.infra.phase)	precision (in FukuiIndices)	push_back() (in SwigVectorIntIntPair)
PhpIntCoord_atoms_get() (in _phase')	precision (in Orbital)	push_back() (in SwigDoubleVector)
PhpIntCoord_atoms_set() (in _phase')	precision (in ThermoCollection)	push_back() (in SwigDoubleVector3)
PhpIntCoord_coords_get() (in _phase')	precision (in ThermoProp)	push_back() (in SwigIntVector)
PhpIntCoord_coords_set() (in _phase')	precision (in ZVariables)	push_back() (in SwigStringVector)
PhpIntCoord_swiginit() (in _phase')	precision (in Scan)	push_back() (in SwigUInt64Vector)
PhpIntCoord_swigregister() (in _phase')	PRECISION (in schrodinger.application.watermap.watermap_scoring)	push_back() (in SwigUnsignedIntVector)
PhpProject (in schrodinger.infra.phase)	preCommand() (in BaseJob)	push_back() (in SwigUnsignedIntVector2)
PhpProject_addLigands() (in _phase')	preCommand() (in TestSPJob)	push_back() (in SwigVectorIntIntPair)
PhpProject_afterStep() (in _phase')	PREDEFINED (in schrodinger.utils.ligfilter)	push_back() (in DoubleDoubleList)
PhpProject_alignLigands() (in _phase')	PREDEFINED_ATOM_GROUP (in schrodinger.application.desmond.mdkey)	push_back() (in DoubleList)
PhpProject_assignActives() (in _phase')	predefined_function_dict (in schrodinger.utils.ligfilter)	push_back() (in StringList)
PhpProject_assignDefaultGroups() (in _phase')	PREDEFINED_GROUP_NAME (in _AtomGroup)	push_back() (in SwigAtomList)
PhpProject_assignGroups() (in _phase')	PREDEFINED_KEYS (in schrodinger.utils.ligfilter)	push_back() (in SwigAtomPairList)
PhpProject_assignInactives() (in _phase')	PREDEFINED_STAGE_FAMILY (in schrodinger.application.desmond.stage)	push_back() (in SwigAtomPairWithValueList)
PhpProject_assignQsarSet() (in _phase')	PredefinedCriterion (in schrodinger.utils.ligfilter)	push_back() (in SwigAtomQueryParamsList)
PhpProject_beforeStep() (in _phase')	predict() (in DFA)	push_back() (in SwigDcNonPbcAtomIdxList)
PhpProject_buildQsarModel() (in _phase')	predict_correlation() (in schrodinger.application.desmond.correlation_tau)	push_back() (in SwigDcPbcAtomList)
PhpProject_closeProject() (in _phase')	predict_kendall_tau() (in schrodinger.application.desmond.correlation_tau)	push_back() (in SwigPiCationList)
PhpProject_combineFragmentCts() (in _phase')	predict_remd_temp (in schrodinger.application.desmond)	push_back() (in SwigPiPiInteractionList)
PhpProject_commitMasterData() (in _phase')	predict_temperature() (in schrodinger.application.desmond.predict_remd_temp)	push_back() (in SwigRingList)
PhpProject_compareFeatureDef() (in _phase')	predict_temperature_ladder() (in schrodinger.application.desmond.remd)	push_back() (in SwigSaltBridgeList)
PhpProject_copyFile() (in _phase')	predict_with_nreplica_and_exch() (in schrodinger.application.desmond.remd)	push_back() (in SwigDoubleVector)
PhpProject_createSites() (in _phase')	predict_with_temp_and_exch() (in schrodinger.application.desmond.remd)	push_back() (in SwigDoubleVector3)
PhpProject_deleteHypotheses() (in _phase')	predict_with_temp_and_nreplica() (in schrodinger.application.desmond.remd)	push_back() (in SwigIntVector)
PhpProject_deleteLigands() (in _phase')	PREF_AB_SCHEME (in schrodinger.application.bioluminate.antibody.utils)	push_back() (in SwigStringVector)
PhpProject_deleteQsarModels() (in _phase')	PREF_ACTIVE_DATABASES (in schrodinger.application.bioluminate.antibody.utils)	push_back() (in SwigUInt64Vector)
PhpProject_expActivity() (in _phase')	PREF_ALL_DATABASES (in schrodinger.application.bioluminate.antibody.utils)	push_back() (in SwigUnsignedIntVector)
PhpProject_getAbsolutePath() (in _phase')	pref_dir (in schrodinger.application.bioluminate.pml_menus)	push_back() (in SwigUnsignedIntVector2)
PhpProject_getActivity() (in _phase')	PREF_GROUP (in schrodinger.application.matsci.builderwidgets)	push_back() (in SwigVectorIntIntPair)
PhpProject_getActivityMissing() (in _phase')	preferences (in schrodinger.application.bioluminate.antibody.utils)	push_level() (in ErrorHandler)
PhpProject_getBindingModes() (in _phase')	preferences (in schrodinger.utils)	push_level() (in schrodinger.infra.mmerr)
PhpProject_getConformer() (in _phase')	Preferences (in schrodinger.utils.preferences)	push_ligand() (in schrodinger.application.glide.http_server)
PhpProject_getConformerCount() (in _phase')	PREFIX_CALLOUTS (in schrodinger.utils.pymol)	put() (in _BaseClient)
PhpProject_getConformers() (in _phase')	PREFIX_MAPS (in schrodinger.utils.pymol)	putToM2ioFile() (in Structure)
PhpProject_getDbID() (in _phase')	PREFIX_MEASUREMENTS (in schrodinger.utils.pymol)	putToM2ioFile() (in TextualStructure)
PhpProject_getDefaultFdFile() (in _phase')	PREFIX_NAME (in _AtomGroup)	PV (in schrodinger.application.glide.glide)
PhpProject_getDefaultFeatureDef() (in _phase')	PREFIX_NAME_LEN (in _AtomGroup)	pv2complex() (in schrodinger.application.glide.poseviewconvert)
PhpProject_getDefaultFeatureFreq() (in _phase')	PREFIX_SURFACES (in schrodinger.utils.pymol)	PV_SD (in schrodinger.application.glide.glide)
PhpProject_getDefaultFeatureRadii() (in _phase')	preflight() (in JaguarInput)	pxp_vdwr (in schrodinger.protein.analysis_params)
PhpProject_getDefaultFeatureTol() (in _phase')	preoptimizeIsChecked() (in ReactionPropertiesTab)	pyepik (in schrodinger.application.epik)
PhpProject_getDefaultSiteMasks() (in _phase')	prep_struc() (in schrodinger.application.desmond.mdkey)	PYEVOLVE_LOG_EXT (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)
PhpProject_getFdFile() (in _phase')	prepActive() (in PrimeConfig)	PYHELP_ERROR_MSG (in schrodinger.ui.qt.appframework)
PhpProject_getFeatureDef() (in _phase')	prepAntibodyLoop() (in PrimeConfig)	pymol (in schrodinger.application.msv.io.structure_model)
PhpProject_getFeatureDefFromProj() (in _phase')	prepare() (in SysType)	PYMOL (in schrodinger.infra.mm)
PhpProject_getFeatureFreq() (in _phase')	prepare() (in TyperBase)	PYMOL (in schrodinger.utils.preferences)
PhpProject_getFeatureRadii() (in _phase')	prepare() (in WatermapTyper)	pymol (in schrodinger.utils)
PhpProject_getFeatureTol() (in _phase')	prepare() (in ReactionCoords)	PYMOL_COLOR_CYCLE (in schrodinger.application.bioluminate.pml_menus)
PhpProject_getGroup() (in _phase')	prepare_command() (in RestInput)	PYMOL_IONS (in schrodinger.application.bioluminate.pml_menus)
PhpProject_getGroupCount() (in _phase')	prepare_for_epik() (in schrodinger.application.prepwizard)	PymolInstance (in schrodinger.utils.pymol)
PhpProject_getHypoAlignments() (in _phase')	prepare_msj() (in RestInput)	PymolScriptInstance (in schrodinger.utils.pymol)
PhpProject_getHypoIDs() (in _phase')	prepare_next_generation_dirs_callback() (in schrodinger.application.matsci.genetic_optimization.genetic_optimization)	pysupport (in schrodinger.infra.mopac)
PhpProject_getHypoMatches() (in _phase')	prepare_structure() (in RestInput)	PYTHON_MINIMIZE (in Refiner)
PhpProject_getHypoScores() (in _phase')	prepareGeometryChange() (in DendrogramGraphicNode)	PZERO (in schrodinger.protein.assignment)
PhpProject_getHypoSites() (in _phase')	prepareGeometryChange() (in DendrogramGraphicNodeLabel)