[ 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

p (in schrodinger.application.lid.ligand_interaction_diagram_gui)	pipi_colors (in schrodinger.application.lid.ligand_interaction_diagram)	PRIMEX_MAIN (in schrodinger.infra.licensing)
pack() (in Table)	PiPiInteraction (in schrodinger.structutils.interactions)	Primitive (in schrodinger.graphics3d.common)
pack() (in schroPmwWrapper)	pixels_size_changed() (in SaveFileDialog)	print_debug() (in schrodinger.application.desmond.cmj)
pack() (in GroundClass)	planar_groups (in schrodinger.protein.analysis)	print_help() (in Help)
pack() (in schroWidget)	PlanarAngle (in schrodinger.trajectory.analysis)	print_if() (in schrodinger.application.desmond.util)
pack_stage() (in StageBase)	PLATNOTLIC (in schrodinger.infra.licensing)	print_job_info() (in schrodinger.application.macromodel.paraUtils)
PACKAGE_SUFFIX (in schrodinger.application.desmond.cmj)	plot (in schrodinger.application.desmond.mplchart)	print_last_lines_of_file() (in schrodinger.pipeline.stages.phase)
paint() (in EditableDelegate)	plot() (in Plotter)	print_pathway() (in schrodinger.application.desmond.fepana)
paint_asl() (in Workspace)	plot() (in EnergyGroup)	print_quiet() (in schrodinger.application.desmond.cmj)
paint_mol() (in Workspace)	plot() (in Reporter)	print_report() (in schrodinger.application.canvas.driverutils)
PaintDeviceMetric	plot() (in Angle)	print_silent() (in schrodinger.application.desmond.cmj)
paintEvent() (in RowActionItem)	plot() (in AverageStructure)	print_tonull() (in schrodinger.application.desmond.cmj)
paintEvent() (in LegendDialog)	plot() (in CenterOfMass)	print_usage() (in Startup)
paintEvent() (in TwoDWidget)	plot() (in CenterOfMotion)	print_usage() (in schrodinger.application.desmond.simulation_block_data)
paintEvent() (in sketcher)	plot() (in CovarianceMatrix)	print_usage() (in schrodinger.application.desmond.simulation_block_test)
paintEvent() (in sketcherGUIMultiColumnToolBar)	plot() (in Dihedral)	print_usage() (in SingleDashOptionParser)
paintEvent() (in sketcherView)	plot() (in Distance)	print_val() (in Test)
pair() (in _FFIO)	plot() (in HydrogenBondTracker)	print_verbose() (in schrodinger.application.desmond.cmj)
pair_builtin_prop (in schrodinger.trajectory.ffstructure)	plot() (in PlanarAngle)	print_version() (in Help)
PairDict (in schrodinger.application.desmond.energygroup)	plot() (in Position)	print_version() (in Startup)
pairmap() (in _FEPIO)	plot() (in RMSD)	print_Zmat() (in Zmat)
pairwise_align_ct() (in schrodinger.application.ska)	plot() (in RMSF)	printAction() (in Pipeline)
pairwise_align_pdb() (in schrodinger.application.ska)	plot() (in RadiusOfGyration)	printAction() (in StageJob)
paletteChange() (in sketcher)	plot() (in Ramachandran)	printNode() (in IntervalTreeNode)
paletteChange() (in sketcherGUIMultiColumnToolBar)	plot() (in SecondaryStructure)	printout() (in InputConfig)
paletteChange() (in sketcherView)	plot() (in AnalysisTool)	printout() (in JobParameters)
PanedWidget (in schrodinger.ui.widget.pmwwidget)	plot2D() (in AnalysisTool)	printout() (in JobParameters)
PanedWindow (in schrodinger.ui.widget.tkinterwidget)	plot_2d() (in Reporter)	printParameters() (in Minimizer)
panel() (in schrodinger.antibody_db_manage_gui)	plot_lambda_window_overlap() (in schrodinger.application.desmond.fepana)	printStatus() (in JobDJ)
panel() (in schrodinger.application.bioluminate.protein_report_widget)	PLOT_TYPES (in ClusterStatisticsPlotDialog)	printStructure() (in FirstSecondaryStructure)
panel() (in schrodinger.application.lid.ligand_interaction_diagram_gui)	PLOT_TYPES (in DistanceMatrixPlotDialog)	printStructure() (in SecondSecondaryStructure)
PARAM (in schrodinger.application.desmond.cmj)	PLOTALEA (in MopacCalculation)	printSubTree() (in IntervalTreeNode)
PARAM() (in StageBase)	PLOTALIE (in MopacCalculation)	printSwapZmatAtom() (in ZmatAtom)
param() (in Key)	PLOTESP (in MopacCalculation)	printTransform() (in schrodinger.application.lid.lid2d.draw)
PARAM() (in Analysis)	Plotter (in schrodinger.analysis.enrichment)	printTransform() (in schrodinger.application.lid.ligand_interaction_diagram)
PARAM() (in AssignForcefield)	plus() (in Rama)	printTree() (in IntervalTree)
PARAM() (in BuildGeometry)	PM3 (in schrodinger.application.mopac)	printTree() (in DefinitionViewerDialog)
PARAM() (in Extern)	pml_menus (in schrodinger.application.bioluminate)	printvals() (in schrodinger.infra.propedit)
PARAM() (in FepAnalysis)	PML_PRESET_SURFACE (in schrodinger.application.bioluminate.pml_menus)	printZmatAtom() (in ZmatAtom)
PARAM() (in FepVrun)	PML_SURFACE (in schrodinger.application.bioluminate.pml_menus)	Priority
PARAM() (in LambdaHopping)	PMLContextMenu (in schrodinger.application.bioluminate.pml_menus)	PRO_COLOR (in Rama)
PARAM() (in McproSimulate)	PMLMenu (in schrodinger.application.bioluminate.pml_menus)	PRO_MARKER (in _ProMut)
PARAM() (in McproSystemBuilder)	pmode() (in Sea)	prob (in schrodinger.application.desmond.ana)
PARAM() (in Minimize)	Pmw_initialise() (in schrodinger.ui.widget.tkinterwidget)	probe_checkpoint() (in schrodinger.application.desmond.cmj)
PARAM() (in Multisim)	pmwwidget (in schrodinger.ui.widget)	process_ark() (in _KeywordProcessor)
PARAM() (in ReplicaExchange)	PNAME (in _McproProt)	process_chunks() (in schrodinger.application.desmond.simulation_block_test)
PARAM() (in Simulate)	PNAME0 (in _DesmondProt)	process_option_strings() (in SingleDashOption)
PARAM() (in SolvatePocket)	PNAME1 (in _DesmondProt)	process_pending_events() (in schrodinger.maestro.maestro)
PARAM() (in SystemBuilder)	PNAME2 (in _DesmondProt)	process_sequence() (in schrodinger.protein.helix)
PARAM() (in Task)	PO2_TAR (in _RingMut)	processEvents() (in AppFramework)
PARAM() (in Trajectory)	PO3_TAR (in _RingMut)	processFrame() (in EnergyGroup)
PARAM() (in Trim)	PO4_TAR (in _RingMut)	processFrame() (in Angle)
PARAM() (in Vrun)	point_group() (in schrodinger.application.jaguar.output)	processFrame() (in AverageStructure)
PARAM() (in WaterMap)	point_group_used() (in schrodinger.application.jaguar.output)	processFrame() (in CenterOfMass)
PARAM() (in WaterMapCluster)	point_inside_rectangle() (in schrodinger.application.lid.lid2d.utils)	processFrame() (in CenterOfMotion)
PARAM() (in WaterMapPostAnalysis)	pointForIndex() (in Grid3D)	processFrame() (in CovarianceMatrix)
param_in_parfile (in schrodinger.application.mcpro.writeinputs)	pointIsOutOfBounds() (in Grid3D)	processFrame() (in Dihedral)
parameters_c (in schrodinger.infra.mopac)	POLAR_CARBONS (in schrodinger.structutils.interactions)	processFrame() (in Distance)
parameters_dict (in schrodinger.application.lid.ligand_interaction_diagram_test)	POLAR_NOT_CHARGED_RESIDUES (in schrodinger.structutils)	processFrame() (in HydrogenBondFinder)
paraUtils (in schrodinger.application.macromodel)	POLAR_POS (in StructuralInteractionFingerprintGenerator)	processFrame() (in HydrogenBondTracker)
parent() (in Sea)	POLAR_RESIDUE (in StructuralInteractionFingerprintGenerator)	processFrame() (in PlanarAngle)
parent_dir() (in schrodinger.application.desmond.util)	POLAR_RESIDUES (in schrodinger.application.bioluminate.protein)	processFrame() (in Position)
parent_structure (in FFStructure)	POLAR_RESIDUES (in schrodinger.structutils)	processFrame() (in RMSD)
parse() (in TreeWizard)	POLAR_RESIDUES (in StructuralInteractionFingerprintGenerator)	processFrame() (in RMSF)
parse() (in TextParser)	PolarContactsObject (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in RadiusOfGyration)
parse() (in Scan)	PolarContactsOnlyMainchain (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in Ramachandran)
parse() (in CriterionParser)	PolarContactsOnlySidechain (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in SecondaryStructure)
parse() (in DefinitionParser)	PolarContactsSubMenu (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in VolumeMapper)
parse() (in _MySplit)	PolarContactsToAnyAtoms (in schrodinger.application.bioluminate.pml_menus)	processFrame() (in AnalysisTool)
parse_args() (in SingleDashOptionParser)	PolarContactsToAnyNonSolvent (in schrodinger.application.bioluminate.pml_menus)	processJobOutputs() (in GeneratePropsStage)
parse_command_line() (in schrodinger.application.vsw.vswinput)	PolarContactsToEntry (in schrodinger.application.bioluminate.pml_menus)	processJobOutputs() (in LigFilterStage)
parse_eneseq() (in schrodinger.application.desmond.fepana)	PolarContactsToEntryWithoutSolvent (in schrodinger.application.bioluminate.pml_menus)	processJobOutputs() (in DockingStage)
parse_geometry() (in schrodinger.application.desmond.util)	PolarContactsWithoutIntraMainchain (in schrodinger.application.bioluminate.pml_menus)	processJobOutputs() (in LigPrepStage)
parse_indices() (in schrodinger.application.desmond.enhsamp)	PolarContactsWithoutMainchain (in schrodinger.application.bioluminate.pml_menus)	processJobOutputs() (in ConfSearchStage)
parse_lambda() (in schrodinger.application.desmond.config)	PolarContactsWithoutSolvent (in schrodinger.application.bioluminate.pml_menus)	processJobOutputs() (in SampleRingsStage)
parse_meta() (in schrodinger.application.desmond.meta)	PolarContactsWithSidechains (in schrodinger.application.bioluminate.pml_menus)	processJobOutputs() (in MMGBSAStage)
parse_mexpr() (in schrodinger.application.desmond.enhsamp)	PolarContactsWithSolvent (in schrodinger.application.bioluminate.pml_menus)	processJobOutputs() (in PrimeStage)
parse_msj() (in schrodinger.application.desmond.cmj)	POLARIZABILITY (in schrodinger.application.moldescriptors)	processJobOutputs() (in QikPropStage)
parse_sba() (in schrodinger.application.desmond.simulation_block_data)	polygon (in schrodinger.graphics3d)	processJobOutputs() (in QSiteStage)
parse_sbt() (in schrodinger.application.desmond.simulation_block_test)	Polygon (in schrodinger.graphics3d.polygon)	processJobOutputs() (in SemiEmpStage)
parse_slice() (in schrodinger.application.desmond.util)	polyhedron (in schrodinger.graphics3d)	processResults() (in ThreadedJob)
parseCanvasCsv() (in Calculator)	Polyhedron (in schrodinger.graphics3d.polyhedron)	procText() (in schrodinger.application.desmond.enhsamp)
ParseError (in schrodinger.application.desmond.cmj)	PolyhedronCore (in schrodinger.graphics3d.polyhedron)	productsInstalled() (in Stage)
parseInput() (in Calculator)	POLYMER (in schrodinger.application.bioluminate.pml_menus)	PROG (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)
parseLine() (in Criterion)	POOL (in schrodinger.infra.licensing)	PROG (in schrodinger.application.desmond.enhanced_sampling.mexpParser)
parseNode() (in TreePatternParser)	pop() (in CommonTreeNodeStream)	prog() (in mexpParser)
parseOptions() (in CanvasFingerprintClusterCLI)	pop() (in PairDict)	prog_return (in mexpParser)
parseOptions() (in CanvasFingerprintGeneratorCLI)	pop() (in List)	progress_set() (in App)
parseOptions() (in CanvasFingerprintSimilarityCLI)	pop_errors() (in ErrorHandler)	project (in schrodinger)
parseOptions() (in _Main)	pop_level() (in ErrorHandler)	Project (in schrodinger.project)
Parser (in schrodinger.application.desmond.antlr3.recognizers)	pop_level() (in schrodinger.infra.mmerr)	project_close_callback_add() (in schrodinger.maestro.maestro)
parser (in schrodinger.application.desmond.system_builder_util)	POPEN (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)	project_close_callback_remove() (in schrodinger.maestro.maestro)
parser (in schrodinger.application.glide.newxp_reorg_fit)	POPEN (in schrodinger.application.desmond.enhanced_sampling.mexpParser)	project_close_cancel() (in schrodinger.maestro.maestro)
parser (in schrodinger.application.watermap.watermap_inp)	Popen() (in schrodinger.utils.subprocess)	project_get() (in schrodinger.maestro.maestro)
ParserMain (in schrodinger.application.desmond.antlr3.main)	popitem() (in PairDict)	project_rename_callback_add() (in schrodinger.maestro.maestro)
ParserRuleReturnScope (in schrodinger.application.desmond.antlr3.recognizers)	populateButtonClicked() (in _ProMut)	project_rename_callback_remove() (in schrodinger.maestro.maestro)
parseSolvent() (in DrawSolventPanel)	PoseLibrary (in schrodinger.application.glide.glideanalysis)	PROJECT_SUFFIXES (in schrodinger.ui.qt.filedialog)
parseStr() (in schrodinger.application.desmond.enhsamp)	poseviewconvert (in schrodinger.application.glide)	PROJECT_TABLE (in JobInputFrame)
parseStream() (in LexerMain)	posfbhw() (in _FFIO)	PROJECT_TABLE (in JobInputFrame)
parseStream() (in ParserMain)	Position (in schrodinger.trajectory.analysis)	project_table_get() (in schrodinger.maestro.maestro)
parseStream() (in WalkerMain)	position (in _DesmondFrame)	project_table_synchronize() (in schrodinger.maestro.maestro)
parseStream() (in _Main)	POSITION_SCHEME (in schrodinger.application.bioluminate.pml_menus)	project_table_update() (in schrodinger.maestro.maestro)
parseTree() (in TreePatternParser)	POSITIONAL (in schrodinger.application.glide.glide)	project_update_callback_add() (in schrodinger.maestro.maestro)
PARTIAL (in GenOptions)	PositionalConstraint (in schrodinger.application.glide.glide)	project_update_callback_remove() (in schrodinger.maestro.maestro)
PARTIAL (in schrodinger.ui.widget.tkinterwidget)	POSITIVES (in schrodinger.structutils.interactions)	projectClosedCallback() (in _App)
partial_charge (in _StructureAtom)	PosResDelegate (in schrodinger.application.desmond.gui)	ProjectOpenDialog (in schrodinger.ui.qt.filedialog)
PARTIAL_CHARGE_4D (in schrodinger.application.bioluminate.pml_menus)	PosResModel (in schrodinger.application.desmond.gui)	ProjectRow (in schrodinger.project)
particle_position (in _DesmondFrame)	PosResRow (in schrodinger.application.desmond.gui)	PROJECTS_FILTER (in schrodinger.ui.qt.filedialog)
particle_total (in _DesmondFrame)	post() (in PMLContextMenu)	PROJET_TABLE (in SimplifiedSequenceViewer)
particle_velocity (in _DesmondFrame)	post() (in _Cell)	PromptDialog (in schrodinger.ui.widget.pmwwidget)
PasswordRetryException (in schrodinger.utils.urllib)	postCommand() (in BaseJob)	prop (in schrodinger.structure)
PATH_MAX (in schrodinger.infra.mm)	PostLigPrepStage (in schrodinger.pipeline.stages.ligprep)	PROP_BOOLEAN (in schrodinger.structure)
PathModel (in schrodinger.application.desmond.fep_gui)	postProcess() (in AverageStructure)	PROP_CONVERSIONS (in schrodinger.application.bioluminate.protein)
pathModified() (in FileEntry)	postProcess() (in CovarianceMatrix)	PROP_FLOAT (in schrodinger.structure)
pathname() (in schrodinger.utils.sea)	postProcess() (in AnalysisTool)	PROP_INTEGER (in schrodinger.structure)
pattern() (in TreePatternParser)	poststage() (in StageBase)	PROP_LONG_NAME (in schrodinger.structure)
PatternModel (in schrodinger.ui.ligfilter)	poststage() (in FepAnalysis)	prop_RE (in schrodinger.infra.propedit)
PCLOSE (in schrodinger.application.desmond.enhanced_sampling.mexpLexer)	poststage() (in Stop)	PROP_REAL (in schrodinger.structure)
PCLOSE (in schrodinger.application.desmond.enhanced_sampling.mexpParser)	poststage() (in SystemBuilder)	PROP_SHORT_NAME (in schrodinger.structure)
PDB (in schrodinger.antibody_db_manage_gui)	poststage() (in WaterMapCluster)	PROP_STRING (in schrodinger.structure)
PDB (in schrodinger.utils.fileutils)	PotentialEnergy (in schrodinger.application.desmond.simulation_block_test)	prop_type_names (in schrodinger.application.desmond.ffiostructure)
PDB_STRING (in SimplifiedSequenceViewer)	PotentialFrame (in schrodinger.ui.macromodel)	prop_value (in Array_Prop)
pdbcode (in _StructureAtom)	PR_NAME (in TimeSeriesAnalysisJob)	propedit (in schrodinger.infra)
pdbname (in _StructureAtom)	pre_score_pairs() (in hbond_cluster)	properties (in schrodinger.application.medchem.property)
PDBReader (in schrodinger.structure)	pre_score_self() (in hbond_cluster)	properties_c (in schrodinger.infra.mopac)
pdbres (in _Residue)	pre_treat() (in changeable)	property (in _Element)
pdbres (in _StructureAtom)	pre_treat_1() (in amide_changeable)	property (in _FEPIO)
pdbres (in Ligand)	pre_treat_1() (in amine_changeable)	property (in _FEPIOSubBlock)
PDBWriter (in schrodinger.structure)	pre_treat_1() (in carboxyl_changeable)	property (in _FFIO)
PENALIZE (in schrodinger.application.glide.glide)	pre_treat_1() (in changeable)	property (in _FFIOSubBlock)
PEOE_INTERVAL (in schrodinger.application.moldescriptors)	pre_treat_1() (in histidine_changeable)	property (in schrodinger.application.medchem)
peptide_planarity_data_set (in Report)	pre_treat_1() (in rotatable_changeable)	property (in Structure)
PERCENT (in schrodinger.application.desmond.antlr3.treewizard)	pre_treat_2() (in amide_changeable)	property (in TextualStructure)
Percent_helix() (in schrodinger.utils.ligfilter)	pre_treat_2() (in amine_changeable)	property (in _StructureAtom)
Percent_loop() (in schrodinger.utils.ligfilter)	pre_treat_2() (in carboxyl_changeable)	property (in _StructureBond)
Percent_strand() (in schrodinger.utils.ligfilter)	pre_treat_2() (in changeable)	property (in _FFAngle)
percentage() (in _Rotamer)	pre_treat_2() (in histidine_changeable)	property (in _FFBond)
periodic_callback_add() (in schrodinger.maestro.maestro)	pre_treat_2() (in rotatable_changeable)	property (in _FFConstraint)
periodic_callback_remove() (in schrodinger.maestro.maestro)	PRECISION (in CanvasFingerprintGenerator)	property (in _FFDihedral)
periodicfix (in schrodinger.application.desmond)	precision (in BondCharge)	property (in _FFExclusion)
permanent_arrays (in schrodinger.infra.mopac)	precision (in Dipole)	property (in _FFPair)
PERMANENT_LICENSE_FAILURE (in JobStatus)	precision (in FukuiIndices)	property (in _FFPseudo)
perp() (in schrodinger.application.lid.lid2d.utils)	precision (in Orbital)	property (in _FFRestraint)
PERT_NAME (in ModelSystem)	precision (in ThermoCollection)	property (in _FFSite)
PertID (in schrodinger.application.mcpro.perturbations)	precision (in ThermoProp)	property (in _FFVdwtype)
PertReorder (in schrodinger.application.mcpro.perturbations)	precision (in ZVariables)	property (in _FFVirtual)
perturbation_databases (in schrodinger.application.mcpro.perturbations)	precision (in Scan)	PROPERTY (in schrodinger.utils.ligfilter)
perturbations (in schrodinger.application.mcpro)	PRECISION (in schrodinger.application.watermap.watermap_scoring)	property_dict (in schrodinger.maestro.maestro)
Perturbations (in schrodinger.application.mcpro.perturbations)	preCommand() (in BaseJob)	PropertyCalculator (in schrodinger.application.bioluminate.protein)
PFF_2005 (in schrodinger.structutils.minimize)	PREDEFINED (in schrodinger.utils.ligfilter)	PropertyCriterion (in schrodinger.utils.ligfilter)
PFILE (in _McproProt)	PREDEFINED_ATOM_GROUP (in schrodinger.application.desmond.mdkey)	PropertyDictionary (in schrodinger.project)
PFILE0 (in _DesmondProt)	predefined_function_dict (in schrodinger.utils.ligfilter)	PropertyName (in schrodinger.structure)
PFILE1 (in _DesmondProt)	PREDEFINED_GROUP_NAME (in _AtomGroup)	propertyselector (in schrodinger.ui)
PFILE2 (in _DesmondProt)	PREDEFINED_KEYS (in schrodinger.utils.ligfilter)	PropertySelector (in schrodinger.ui.propertyselector)
pH_high (in schrodinger.protein.assignment)	PREDEFINED_STAGE_FAMILY (in schrodinger.application.desmond.stage)	PropertySelectorMenu (in schrodinger.ui.propertyselector)
pH_low (in schrodinger.protein.assignment)	PredefinedCriterion (in schrodinger.utils.ligfilter)	PropertySelectorWithRanges (in schrodinger.application.bioluminate.propfilter)
pH_neutral (in schrodinger.protein.assignment)	predict() (in DFA)	propfilter (in schrodinger.application.bioluminate)
pH_vlow (in schrodinger.protein.assignment)	predict_remd_temp (in schrodinger.application.desmond)	propfilter_ui (in schrodinger.application.bioluminate)
phase (in schrodinger.application)	predict_temperature() (in schrodinger.application.desmond.predict_remd_temp)	PropFilterDialog (in schrodinger.application.bioluminate.propfilter)
phase (in schrodinger.application.vsw.stages)	predict_temperature_ladder() (in schrodinger.application.desmond.remd)	PropkaError (in schrodinger.application.bioluminate.protein)
PHASE (in schrodinger.infra.mm)	predict_with_nreplica_and_exch() (in schrodinger.application.desmond.remd)	PropKaException (in schrodinger.protein.assignment)
phase (in schrodinger.pipeline.stages)	predict_with_temp_and_exch() (in schrodinger.application.desmond.remd)	PROT_AND_DNA_SELE (in schrodinger.application.bioluminate.pml_menus)
PHASE (in schrodinger.utils.preferences)	predict_with_temp_and_nreplica() (in schrodinger.application.desmond.remd)	PROT_FINAL_NAME (in ModelSystem)
PHASE_CORE_HOPPING (in schrodinger.infra.licensing)	PREF_ACTIVE_DATABASES (in schrodinger.application.bioluminate.antibody.utils)	PROT_NAME (in ModelSystem)
PHASE_DBCREATE (in schrodinger.infra.licensing)	PREF_ALL_DATABASES (in schrodinger.application.bioluminate.antibody.utils)	PROT_ONLY (in ModelSystem)
PHASE_DBSEARCH (in schrodinger.infra.licensing)	pref_dir (in schrodinger.application.bioluminate.pml_menus)	prot_toggle() (in _Flex)
PHASE_ELEMENTS (in schrodinger.infra.licensing)	PREFERENCE_GROUP (in schrodinger.antibody_db_manage_gui)	ProtAssign (in schrodinger.protein.assignment)
PHASE_FEATURE (in schrodinger.infra.licensing)	preferences (in schrodinger.application.bioluminate.antibody.utils)	protein (in schrodinger.application.bioluminate)
PHASE_FQSAR (in schrodinger.infra.licensing)	preferences (in schrodinger.utils)	protein (in schrodinger)
PHASE_PARTITION (in schrodinger.infra.licensing)	Preferences (in schrodinger.utils.preferences)	protein_dictionary() (in schrodinger.structutils.interactions)
PHASE_QSAR (in schrodinger.infra.licensing)	PREFIX_NAME (in _AtomGroup)	PROTEIN_MUTATION (in schrodinger.application.desmond.fep_gui)
PHASE_SCORING (in schrodinger.infra.licensing)	PREFIX_NAME_LEN (in _AtomGroup)	protein_report_widget (in schrodinger.application.bioluminate)
PHASE_SELECTIVITY (in schrodinger.infra.licensing)	premul() (in schrodinger.application.lid.lid2d.utils)	protein_sequences (in SimplifiedSequenceViewer)
PhaseDatabaseIconProvider (in schrodinger.ui.qt.filedialog)	prep_struc() (in schrodinger.application.desmond.mdkey)	protein_structure_quality (in schrodinger.application.bioluminate)
PhaseDatabaseOpenDialog (in schrodinger.ui.qt.filedialog)	prepActive() (in PrimeConfig)	protein_structure_quality_ui (in schrodinger.application.bioluminate)
PHASEDB (in schrodinger.application.vsw.vswinput)	prepAntibodyLoop() (in PrimeConfig)	proteinHandler (in schrodinger.application.mcpro.zmat)
PHASEDB (in schrodinger.pipeline.pipeio)	prepare() (in SysType)	ProteinStructureQualityViewer (in schrodinger.application.bioluminate.protein_structure_quality)
PhaseDB (in schrodinger.pipeline.pipeio)	prepare() (in TyperBase)	PROTOCOL_VERSION (in DebugEventListener)
PHASEDB_FILTER (in schrodinger.ui.qt.filedialog)	prepare() (in WatermapTyper)	protonateResidue() (in ResidueTools)
PHASEDB_SUFFIXES (in schrodinger.ui.qt.filedialog)	prepare_for_epik() (in schrodinger.application.prepwizard)	ProxyBasicAuthHandler (in schrodinger.utils.urllib)
PHI (in schrodinger.graphics3d.polyhedron)	prepareInputLigands() (in SampleRingsStage)	ProxyDigestAuthHandler (in schrodinger.utils.urllib)
phi0 (in _FFIOImproperFBHW)	prepareStructures() (in WaterMapInput)	ProxyHandler (in schrodinger.utils.urllib)
PhotoImage (in schrodinger.ui.widget.tkinterwidget)	prepBldStruct() (in PrimeConfig)	ProxyPasswordManager (in schrodinger.utils.urllib)
pi (in schrodinger.protein.assignment)	prepDatabase() (in DBManagePanel)	ProxyPasswordManagerQt (in schrodinger.utils.urllib)
picat_c (in schrodinger.application.lid.ligand_interaction_diagram)	prepEnergy() (in PrimeConfig)	ProxyTunnelError (in schrodinger.utils.urllib)
picat_c_bw (in schrodinger.application.lid.ligand_interaction_diagram)	prepickBondCallback() (in _LigMut)	Pseudo (in schrodinger.application.desmond.cms)
picat_colors (in schrodinger.application.lid.ligand_interaction_diagram)	prepickLigCallback() (in _ProMut)	pseudo() (in _FFIO)
pick_best_pose_prop() (in ReorgFitting)	prepickResidueCallback() (in _ProMut)	pseudo_builtin_prop (in schrodinger.trajectory.ffstructure)
pick_best_pose_prop_() (in ReorgFitting)	prepickRingAtomCallback() (in _RingMut)	pseudo_charge (in FFStructure)
pick_by_atom() (in Rama)	prepLoop() (in PrimeConfig)	pseudo_mass (in FFStructure)
pick_by_point() (in Rama)	prepMinimize() (in PrimeConfig)	pseudospectral() (in schrodinger.application.jaguar.output)
pick_category (in MaestroArrow)	prepMultiLoop() (in PrimeConfig)	PSP (in schrodinger.infra.mm)
pick_category (in MaestroSphere)	prepSidechain() (in PrimeConfig)	PSP (in schrodinger.utils.preferences)
pick_id (in MaestroArrow)	prepSidechainBB() (in PrimeConfig)	PSP_ADMET (in schrodinger.infra.licensing)
pick_id (in MaestroSphere)	prepSidechainCBeta() (in PrimeConfig)	PSP_BB (in schrodinger.infra.licensing)
PickAtomToggle (in schrodinger.application.desmond.fep_gui)	prepwizard (in schrodinger.application)	PSP_FR (in schrodinger.infra.licensing)
PickAtomToggle (in schrodinger.ui.picking)	PRESET_GCR (in schrodinger.application.bioluminate.protein_structure_quality)	PSP_GPGPU (in schrodinger.infra.licensing)
PickAtomToggle (in schrodinger.ui.widget.tkinterwidget)	PRESET_RT (in schrodinger.application.bioluminate.protein_structure_quality)	PSP_PLOP (in schrodinger.infra.licensing)
pickBondCallback() (in _LigMut)	PRESET_RYW (in schrodinger.application.bioluminate.protein_structure_quality)	PSP_PLOP_MEMBRANE (in schrodinger.infra.licensing)
PickBondToggle (in schrodinger.application.desmond.fep_gui)	PresetAction (in schrodinger.application.bioluminate.pml_menus)	PSP_RB (in schrodinger.infra.licensing)
PickBondToggle (in schrodinger.ui.picking)	PRESETS (in schrodinger.application.bioluminate.protein_structure_quality)	PSP_SKA (in schrodinger.infra.licensing)
PickBondToggle (in schrodinger.ui.widget.tkinterwidget)	PresetSubMenu (in schrodinger.application.bioluminate.pml_menus)	PSP_SSP (in schrodinger.infra.licensing)
picked() (in ColorChooserPanel)	Pressure (in schrodinger.application.desmond.simulation_block_test)	PSP_STA (in schrodinger.infra.licensing)
picking (in schrodinger.ui)	prestage() (in StageBase)	PSP_STA_GPCR (in schrodinger.infra.licensing)
picking_atom_start() (in schrodinger.maestro.maestro)	prestage() (in Stop)	pt_enclosed_by() (in schrodinger.application.lid.lid2d.utils)
picking_bond_start() (in schrodinger.maestro.maestro)	prestage() (in SystemBuilder)	ptSegDistSq() (in schrodinger.application.lid.lid2d.utils)
picking_loss_notify() (in schrodinger.maestro.maestro)	prestartCommand() (in GuiApp)	ptSegDistSqPT() (in schrodinger.application.lid.lid2d.utils)
picking_stop() (in schrodinger.maestro.maestro)	PrettyPubPreset (in schrodinger.application.bioluminate.pml_menus)	PUBKEY_ERROR (in schrodinger.infra.licensing)
Picklable (in schrodinger.application.desmond.picklejar)	prev() (in _Step)	pull (in schrodinger.application.vsw.stages)
picklejar (in schrodinger.application.desmond)	prevent_overlapping_x_labels() (in schrodinger.application.bioluminate.sliderchart)	pull (in schrodinger.pipeline.stages)
PickleJar (in schrodinger.application.desmond.picklejar)	prevent_overlapping_x_labels() (in schrodinger.application.desmond.mplchart)	pullCompounds() (in PullStage)
PickleState (in schrodinger.application.desmond.picklejar)	prewriteCommand() (in GuiApp)	PullStage (in schrodinger.pipeline.stages.pull)
pickLigCallback() (in _ProMut)	prime (in schrodinger.application)	push() (in CommonTreeNodeStream)
pickResidueCallback() (in _ProMut)	Prime (in schrodinger.application.prime.input)	push() (in Queue)
pickRingAtomCallback() (in _RingMut)	prime (in schrodinger.pipeline.stages)	push() (in StageBase)
PickToggle (in schrodinger.ui.widget.tkinterwidget)	prime' (in schrodinger.application.vsw.stages)	push_level() (in ErrorHandler)
PINF (in schrodinger.protein.assignment)	PRIME_ANTIB_LOOP_PRED (in Refiner)	push_level() (in schrodinger.infra.mmerr)
PINFO (in _McproProt)	PRIME_LOOP_PRED (in Refiner)	putToM2ioFile() (in Structure)
PINK (in schrodinger.application.bioluminate.pml_menus)	PRIME_MINIMIZE (in Refiner)	putToM2ioFile() (in TextualStructure)
PIPE (in schrodinger.utils.subproc)	PRIME_MULTILOOP_PRED (in Refiner)	PV (in schrodinger.application.glide.glide)
PIPE (in schrodinger.utils.subprocess)	PRIME_SIDECHAIN (in Refiner)	pv2complex() (in schrodinger.application.glide.poseviewconvert)
pipeio (in schrodinger.pipeline)	PRIME_SIDECHAIN_BB (in Refiner)	PV_SD (in schrodinger.application.glide.glide)
PipeIO (in schrodinger.pipeline.pipeio)	PRIME_SIDECHAIN_CBETA (in Refiner)	PYMOL (in schrodinger.infra.mm)
pipeline (in schrodinger)	prime_specs (in schrodinger.application.prime.input)	PYMOL (in schrodinger.utils.preferences)
pipeline (in schrodinger.pipeline)	PrimeConfig (in schrodinger.application.bioluminate.protein)	PYMOL_COLOR_CYCLE (in schrodinger.application.bioluminate.pml_menus)
Pipeline (in schrodinger.pipeline.pipeline)	primefix (in schrodinger.application.prime)	PYMOL_IONS (in schrodinger.application.bioluminate.pml_menus)
pipeutils (in schrodinger.application.vsw)	Primer	pysupport (in schrodinger.infra.mopac)
pipeutils (in schrodinger.pipeline)	PrimeStage (in schrodinger.pipeline.stages.prime)	PYTHON_MINIMIZE (in Refiner)
pipi_c (in schrodinger.application.lid.ligand_interaction_diagram)	PrimeStructure (in schrodinger.application.bioluminate.protein)	PZERO (in schrodinger.protein.assignment)
pipi_c_bw (in schrodinger.application.lid.ligand_interaction_diagram)	PRIMEX_LIGPREP_EPIK (in schrodinger.infra.licensing)