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 Z Y Z _ ]

A

Accept_cb() (in Dpf4InitLigand)	ADGetOutputGUI (in AutoDockTools.autoanalyzeCommands)	allowed_bonds (in AutoDockTools.Utilities24.prepare_ligand)
Accept_cb() (in DpfInitLigand)	adjustMarker() (in SetBoxParameters)	allowed_bonds (in AutoDockTools.Utilities24.prepare_ligand4)
Accept_cb() (in GA)	adjustMsms() (in ADShowBindingSite)	AppConfigType_Def (in nbcr_sdsc_edu_opal_types)
Accept_cb() (in LS)	adjustPt_cb() (in AF_SetHinge)	append() (in Clust)
Accept_cb() (in SetAutoDock4Parameters)	adjustSideLengths() (in SetBoxParameters)	append_to_outputfile (in AutoDockTools.Utilities24.summarize_results)
Accept_cb() (in SetDockingRunParms)	ADKill (in AutoDockTools.autostartCommands)	append_to_outputfile (in AutoDockTools.Utilities24.summarize_results4)
Accept_cb() (in SimAnneal)	ADMacroLigandChart (in AutoDockTools.autoanalyzeCommands)	append_to_outputfile (in AutoDockTools.Utilities24.summarize_wcg_docking)
Accept_cb() (in Gpf4SetMapTypes)	ADMacroLigandChartGUI (in AutoDockTools.autoanalyzeCommands)	applyState() (in ConformationPlayer)
Accept_cb() (in GpfInitLigand)	ADMakeAllGrids (in AutoDockTools.autoanalyzeCommands)	applyState() (in PopulationPlayer)
Accept_cb() (in SetBoxParameters)	ADMakeAllGridsGUI (in AutoDockTools.autoanalyzeCommands)	applyState() (in StatesPlayerWidget)
Accept_cb() (in SetMapTypes)	ADpilot_Cluster (in AutoDockTools.autopilotCommands)	AppMetadataType_Def (in nbcr_sdsc_edu_opal_types)
Accept_cb() (in SetOtherOptions)	ADpilot_ClusterGUI (in AutoDockTools.autopilotCommands)	AppService_services (in AutoDockTools)
Accept_cb() (in SetUpCovalentMap)	ADpilot_ClusterGUICommand (in AutoDockTools.autopilotCommands)	AppService_services_types (in AutoDockTools)
Accept_cb() (in PyAD4CalcInternalEnergies)	ADpilot_Template (in AutoDockTools.autopilotCommands)	AppServiceInterface (in AutoDockTools.AppService_services)
Accept_cb() (in PyADCalcAD3Energies)	ADpilot_TemplateGUI (in AutoDockTools.autopilotCommands)	AppServiceLocator (in AutoDockTools.AppService_services)
Accept_cb() (in PyADCalcClosestPairs)	ADpilot_TemplateGUICommand (in AutoDockTools.autopilotCommands)	AppServicePortSoapBindingSOAP (in AutoDockTools.AppService_services)
Accept_cb() (in PyADCalcVDWEnergies)	ADProcessManager (in AutoDockTools.autostartCommands)	AppServicePortType_address (in AppServiceLocator)
ad305scorer (in AutoDockTools.Utilities24.summarize_results)	ADProcessManagerGUI (in AutoDockTools.autostartCommands)	ArgumentsType_Def (in nbcr_sdsc_edu_opal_types)
AD3Dpf (in AutoDockTools.VisionInterface)	ADReadMacro (in AutoDockTools.autoanalyzeCommands)	AromaticCarbonManager (in AutoDockTools.atomTypeTools)
AD3Dpf (in AutoDockTools.VisionInterface.AD3Dpf)	ADReadMacroGUI (in AutoDockTools.autoanalyzeCommands)	aromDict (in AutoDockTools.LigandMixin)
AD3Gpf (in AutoDockTools.VisionInterface)	adscorer (in AutoDockTools.Utilities24.summarize_wcg_docking)	Assign_AD4Types (in AutoDockTools.VisionInterface.AdtNodes)
AD3Gpf (in AutoDockTools.VisionInterface.AD3Gpf)	ADSeeSpots (in AutoDockTools.autoanalyzeCommands)	at_types (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)
AD4_grid_parameter_list (in AutoDockTools.GridParameters_AD4)	ADSeeSpotsGUI (in AutoDockTools.autoanalyzeCommands)	atDict (in AutoDockTools.Utilities24.summarize_results)
AD4_typer (in AutoDockTools.Utilities24.pdbq_to_pdbqt)	ADSelectDLG (in AutoDockTools.autoanalyzeCommands)	atDict (in AutoDockTools.Utilities24.summarize_wcg_docking)
AD4_typer (in AutoDockTools.Utilities24.pdbqs_to_pdbqt)	ADSelectDLGGUI (in AutoDockTools.autoanalyzeCommands)	atom_ct (in AutoDockTools.Utilities24.summarize_wcg_docking)
AD4FlexibleDockingPreparation (in AutoDockTools.MoleculePreparation)	ADShowBindingSite (in AutoDockTools.autoanalyzeCommands)	atomtypes (in AutoDockTools.Utilities24.energy_average_maps)
AD4FlexibleReceptorPreparation (in AutoDockTools.MoleculePreparation)	ADShowBindingSiteGUI (in AutoDockTools.autoanalyzeCommands)	atomTypeTools (in AutoDockTools)
AD4LigandPreparation (in AutoDockTools.MoleculePreparation)	adthosts (in AutoDockTools)	Ators4MoleculeChooser (in AutoDockTools.autotorsCommands)
AD4LigandWriter (in AutoDockTools.MoleculePreparation)	adtlib (in AutoDockTools.VisionInterface.AdtNodes)	Ators4MoleculeChooserGUI (in AutoDockTools.autotorsCommands)
AD4ReceptorPreparation (in AutoDockTools.MoleculePreparation)	AdtNodes (in AutoDockTools.VisionInterface)	Ators4Reader (in AutoDockTools.autotorsCommands)
AD4ReceptorWriter (in AutoDockTools.MoleculePreparation)	AdtPrepareDpf3 (in AutoDockTools.VisionInterface.AdtNodes)	Ators4ReaderGUI (in AutoDockTools.autotorsCommands)
ad_scorer (in AutoDockTools.Utilities24.compute_AutoDock41_score)	AdtPrepareDpf4 (in AutoDockTools.VisionInterface.AdtNodes)	AtorsInit (in AutoDockTools.autotorsCommands)
ADChooseMacro (in AutoDockTools.autoanalyzeCommands)	AdtPrepareGpf3 (in AutoDockTools.VisionInterface.AdtNodes)	AtorsInitMol (in AutoDockTools.autotorsCommands)
ADChooseMacroGUI (in AutoDockTools.autoanalyzeCommands)	AdtPrepareGpf4 (in AutoDockTools.VisionInterface.AdtNodes)	AtorsMoleculeChooser (in AutoDockTools.autotorsCommands)
add() (in ConformationHandler)	adUpdate() (in ADProcessManager)	AtorsMoleculeChooserGUI (in AutoDockTools.autotorsCommands)
add() (in PopulationHandler)	AF_EditHinge (in AutoDockTools.autoflexCommands)	AtorsReader (in AutoDockTools.autotorsCommands)
add_bonds (in AutoDockTools.Utilities24.prepare_ligand)	AF_EditHingeGUI (in AutoDockTools.autoflexCommands)	AtorsReaderGUI (in AutoDockTools.autotorsCommands)
add_bonds (in AutoDockTools.Utilities24.prepare_ligand4)	AF_FlexFileWriter (in AutoDockTools.autoflexCommands)	AtorsRefWriter (in AutoDockTools.autotorsCommands)
Add_SolvationParameters (in AutoDockTools.VisionInterface.AdtNodes)	AF_FlexFileWriterGUI (in AutoDockTools.autoflexCommands)	AtorsRefWriterGUI (in AutoDockTools.autotorsCommands)
addAromatic() (in LigandMixin)	AF_LigandDirectoryWriter (in AutoDockTools.autoflexCommands)	autoanalyzeCommands (in AutoDockTools)
addAtom() (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	AF_LigandDirectoryWriterGUI (in AutoDockTools.autoflexCommands)	AutoAutoTors (in AutoDockTools.autotorsCommands)
AddAutoDockHost (in AutoDockTools.autostartCommands)	AF_MacroChooser (in AutoDockTools.autoflexCommands)	AutoAutoTorsGUI (in AutoDockTools.autotorsCommands)
AddAutoDockHostGUI (in AutoDockTools.autostartCommands)	AF_MacroChooserGUI (in AutoDockTools.autoflexCommands)	autoCenter() (in SetBoxParameters)
addButton() (in ADMacroLigandChart)	AF_MacroReader (in AutoDockTools.autoflexCommands)	autoCenterLig() (in SetBoxParameters)
addCharges() (in AutoDockMoleculePreparation)	AF_MacroReaderGUI (in AutoDockTools.autoflexCommands)	AutoDock4_AtomTyper (in AutoDockTools.atomTypeTools)
addColumnButton() (in ADMacroLigandChart)	AF_ProcessHingeResidues (in AutoDockTools.autoflexCommands)	AutoDockBondClassifier (in AutoDockTools)
addColumnRowButton() (in ADMacroLigandChart)	AF_ProcessHingeResiduesGUI (in AutoDockTools.autoflexCommands)	AutoDockBondClassifier (in AutoDockTools.AutoDockBondClassifier)
addConformations() (in Docking)	AF_ProcessResidues (in AutoDockTools.autoflexCommands)	autodockElementDict (in AutoDockTools.autogpfCommands)
addData() (in Histogram)	AF_ProcessResiduesGUI (in AutoDockTools.autoflexCommands)	autodockHosts (in AutoDockTools)
ADDeleteDLG (in AutoDockTools.autoanalyzeCommands)	AF_RigidFileWriter (in AutoDockTools.autoflexCommands)	AutoDockHosts (in AutoDockTools.autodockHosts)
ADDeleteDLGGUI (in AutoDockTools.autoanalyzeCommands)	AF_RigidFileWriterGUI (in AutoDockTools.autoflexCommands)	AutoDockMoleculePreparation (in AutoDockTools.MoleculePreparation)
addHost() (in AutoDockHosts)	AF_SelectResidues (in AutoDockTools.autoflexCommands)	AutoDockStarter (in AutoDockTools.autostartCommands)
addHost() (in ADProcessManager)	AF_SelectResiduesGUI (in AutoDockTools.autoflexCommands)	AutoDockStarterGUI (in AutoDockTools.autostartCommands)
addHydrogens() (in AutoDockMoleculePreparation)	AF_SetBondRotatableFlag (in AutoDockTools.autoflexCommands)	AutodockState (in AutoDockTools.Conformation)
addItem_cb() (in AddAutoDockHost)	AF_SetHinge (in AutoDockTools.autoflexCommands)	AutoDockTools
addKollman() (in LigandMixin)	AF_SetHingeGUI (in AutoDockTools.autoflexCommands)	autodpfCommands (in AutoDockTools)
ADDockingChooser (in AutoDockTools.autoanalyzeCommands)	AF_StepBack (in AutoDockTools.autoflexCommands)	autoflexCommands (in AutoDockTools)
ADDockingChooserGUI (in AutoDockTools.autoanalyzeCommands)	AF_StepBackGUI (in AutoDockTools.autoflexCommands)	autogpfCommands (in AutoDockTools)
addParameters() (in SolvationParameterizer)	afterAddingToNetwork() (in AD3Dpf)	AutoGridStarter (in AutoDockTools.autostartCommands)
addPopulation() (in Docking)	afterAddingToNetwork() (in AD3Gpf)	AutoGridStarterGUI (in AutoDockTools.autostartCommands)
addProcess() (in ADProcessManager)	afterAddingToNetwork() (in PrepareAD3Ligand)	autoMergeNPHS (in AutoDockTools.autotorsCommands)
ADDrawHistogram (in AutoDockTools.autoanalyzeCommands)	afterAddingToNetwork() (in PrepareAD3Receptor)	autopilotCommands (in AutoDockTools)
ADDrawHistogramGUI (in AutoDockTools.autoanalyzeCommands)	afterAddingToNetwork() (in PrepareAD4Ligand)	AutoRoot (in AutoDockTools.autotorsCommands)
addRowButton() (in ADMacroLigandChart)	afterAddingToNetwork() (in recluster)	autoroot() (in LigandMixin)
addSpheres() (in ADSeeSpots)	all_bnds (in AutoDockTools.Utilities24.prepare_flexdocking4)	autoroot() (in LigandPreparation)
ADEPDBMol (in AutoDockTools.autoanalyzeCommands)	all_bnds (in AutoDockTools.Utilities24.prepare_flexreceptor4)	autoroot() (in RotatableBondManager)
ADEPDBMolGUI (in AutoDockTools.autoanalyzeCommands)	all_lines (in AutoDockTools.Utilities24.energy_average_maps)	AutoRootGUI (in AutoDockTools.autotorsCommands)
ADGetAGrid (in AutoDockTools.autoanalyzeCommands)	all_maps (in AutoDockTools.Utilities24.energy_average_maps)	autostartCommands (in AutoDockTools)
ADGetAGridGUI (in AutoDockTools.autoanalyzeCommands)	all_res (in AutoDockTools.Utilities24.prepare_flexdocking4)	AutoStarter (in AutoDockTools.autostartCommands)
ADGetDirDLGs (in AutoDockTools.autoanalyzeCommands)	all_res (in AutoDockTools.Utilities24.prepare_flexreceptor4)	AUTOTORS4Writer (in AutoDockTools.autotorsCommands)
ADGetDirDLGsGUI (in AutoDockTools.autoanalyzeCommands)	all_stems (in AutoDockTools.Utilities24.energy_average_maps)	AUTOTORS4WriterGUI (in AutoDockTools.autotorsCommands)
ADGetDLG (in AutoDockTools.autoanalyzeCommands)	all_types (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	autotorsCommands (in AutoDockTools)
ADGetDLGGUI (in AutoDockTools.autoanalyzeCommands)	all_types (in AutoDockTools.Utilities24.energy_average_maps)	AUTOTORSWriter (in AutoDockTools.autotorsCommands)
ADGetOutput (in AutoDockTools.autoanalyzeCommands)	allAts (in AutoDockTools.Utilities24.repair_ligand4)	AUTOTORSWriterGUI (in AutoDockTools.autotorsCommands)

B

beforeAddingToNetwork() (in AD3Dpf)	build_hydrogen_bonds (in AutoDockTools.Utilities24.summarize_wcg_docking)	buildForm() (in SetTorsionNumberGUICommand)
beforeAddingToNetwork() (in AD3Gpf)	BuildAll_cb() (in ConformationPlayer)	buildForm() (in PyAD4CalcInternalEnergies)
beforeAddingToNetwork() (in ReadDockingParameterFile)	buildCenterMenu() (in SetBoxParameters)	buildForm() (in PyADCalcAD3Energies)
beforeAddingToNetwork() (in ReadGridParameterFile)	buildCloseAtoms() (in ADShowBindingSite)	buildForm() (in PyADCalcClosestPairs)
beforeAddingToNetwork() (in Docking)	buildCol() (in AF_ProcessHingeResidues)	buildForm() (in PyADCalcVDWEnergies)
beforeAddingToNetwork() (in PrepareAD3Ligand)	buildCol() (in AF_ProcessResidues)	buildFormDescr() (in WebServices)
beforeAddingToNetwork() (in PrepareAD3Receptor)	buildCol() (in AF_SetBondRotatableFlag)	buildFormDescr() (in ADpilot_ClusterGUICommand)
beforeAddingToNetwork() (in PrepareAD4Ligand)	buildCol() (in SetRotatableBonds)	buildFormDescr() (in ADpilot_TemplateGUICommand)
beforeAddingToNetwork() (in recluster)	buildConf() (in ConformationPlayer)	buildHbondDisplay() (in ADShowBindingSite)
bindEntries() (in AutoDockStarter)	buildConf() (in PopulationPlayer)	buildHBonds() (in ConformationPlayer)
BlockingOutputType_Def (in nbcr_sdsc_edu_opal_types)	buildDisplayForm() (in ADShowBindingSite)	buildHBonds() (in PopulationPlayer)
bnd_pairs (in AutoDockTools.Utilities24.prepare_flexdocking4)	buildEntry() (in AutoDockHosts)	buildHelpMenu() (in SetBoxParameters)
bnd_pairs (in AutoDockTools.Utilities24.prepare_flexreceptor4)	buildFileMenu() (in SetBoxParameters)	buildHostMenu() (in AutoStarter)
bonds_to_inactivate (in AutoDockTools.Utilities24.prepare_ligand)	buildForm() (in ADMacroLigandChart)	buildIcons() (in HistogramNodeSet)
bonds_to_inactivate (in AutoDockTools.Utilities24.prepare_ligand4)	buildFORM() (in MakeAutoDockCLUSTERING)	buildInteractiveGraph() (in ShowAutoDockStatesHISTOGRAM)
boundingBox() (in GraphObjects)	buildFORM() (in MakeAutoDockSubsetCLUSTERING)	buildIt() (in ADDrawHistogram)
boundingBox() (in GraphPoints)	buildFORM() (in StatesPlayerWidget)	buildIt() (in InteractiveGraphBuilder)
boundingBox() (in HistogramNodeSet)	buildForm() (in Dpf4InitLigand)	buildLigandDisplay() (in ADShowBindingSite)
box (in AutoDockTools.autogpfCommands)	buildForm() (in DpfInitLigand)	buildLogStr() (in AddAutoDockHost)
browse_dpf() (in WebServices)	buildForm() (in GA)	buildMacroMenu() (in AutoStarter)
browse_gpf() (in WebServices)	buildForm() (in LS)	buildMenu() (in SetBoxParameters)
browseAD() (in AddAutoDockHost)	buildForm() (in SetAutoDock4Parameters)	buildMenu() (in AutoStarter)
browseAG() (in AddAutoDockHost)	buildForm() (in SetDockingRunParms)	buildMolList() (in ShowAutoDockStatesBaseCmd)
browseEX() (in AutoStarter)	buildForm() (in SimAnneal)	buildMolList() (in WriteAutoDockStates)
browseLF() (in AutoStarter)	buildForm() (in AF_SetHinge)	buildNodeIcon() (in HistogramNode)
browsePF() (in AutoStarter)	buildForm() (in Gpf4SetMapTypes)	buildNodeIcon() (in InteractiveGraphObject)
build() (in ADShowBindingSite)	buildForm() (in GpfInitLigand)	buildPdb() (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)
build() (in Cluster)	buildForm() (in SetBoxParameters)	buildPlayModeMenu() (in ConformationPlayer)
Build_cb() (in ConformationPlayer)	buildForm() (in SetMapTypes)	buildProjectMenu() (in AutoStarter)
Build_cb() (in StatesPlayerWidget)	buildForm() (in SetOtherOptions)	buildTorsionTree() (in LigandMixin)
build_hydrogen_bonds (in AutoDockTools.Utilities24.summarize_results)	buildForm() (in SetUpCovalentMap)	buildVisiMenu() (in SetBoxParameters)
build_hydrogen_bonds (in AutoDockTools.Utilities24.summarize_results4)	buildForm() (in AutoAutoTors)

C

c (in AutoDockTools.Utilities24.compute_rms_between_methods)	chooseMolecule_cb() (in ADChooseMacro)	cluster_list (in AutoDockTools.DockingParameters)
c (in AutoDockTools.Utilities24.summarize_results)	chooseMolecule_cb() (in ShowAutoDockStatesBaseCmd)	cluster_list4 (in AutoDockTools.DockingParameters)
c (in AutoDockTools.Utilities24.summarize_wcg_docking)	chooseMolecule_cb() (in WriteAutoDockClustering)	ClusterDockingChooser (in AutoDockTools.autoanalyzeCommands)
calcChargeError() (in AutoDockMoleculePreparation)	chooseMolecule_cb() (in WriteAutoDockStates)	Clusterer (in AutoDockTools.cluster)
callDoit_cb() (in AutoDockStarter)	chooseMolecule_cb() (in Dpf4MacroChooser)	clustering (in AutoDockTools.Utilities24.write_largest_cluster_ligand)
callDoit_cb() (in AutoStarter)	chooseMolecule_cb() (in DpfMacroChooser)	Clustering (in AutoDockTools.cluster)
Cancel_cb() (in MakeAutoDockCLUSTERING)	chooseMolecule_cb() (in AF_MacroChooser)	cmdlib (in AutoDockTools)
cancel_cb() (in AutoAutoTors)	chooseMolecule_cb() (in Gpf4MacroChooser)	cmdlist (in AutoDockTools.cmdlib)
cenCross (in AutoDockTools.autogpfCommands)	chooseMolecule_cb() (in GpfAddSol)	color_cb() (in ADSeeSpots)
cenSph (in AutoDockTools.autogpfCommands)	chooseMolecule_cb() (in GpfMacroChooser)	colorButton() (in ADMacroLigandChart)
center (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	chooseMolecule_cb() (in GpfMergeNonPolarHs)	colorsList (in AutoDockTools.autoanalyzeCommands)
change_aromatic_criteria() (in AromaticCarbonManager)	chooseMolecule_cb() (in AutoAutoTors)	commandList (in AutoDockTools.WebServices)
ChangeAromaticCutOff (in AutoDockTools.autotorsCommands)	cl (in AutoDockTools.Utilities24.summarize_wcg_docking)	commandList (in AutoDockTools.autoanalyzeCommands)
ChangeAromaticCutOffGUI (in AutoDockTools.autotorsCommands)	classify() (in AutoDockBondClassifier)	commandList (in AutoDockTools.autodpfCommands)
changeFlexResCt() (in AF_ProcessHingeResidues)	cleanup (in AutoDockTools.Utilities24.prepare_ligand)	commandList (in AutoDockTools.autoflexCommands)
changeFlexResCt() (in AF_ProcessResidues)	cleanup (in AutoDockTools.Utilities24.prepare_ligand4)	commandList (in AutoDockTools.autogpfCommands)
changeFlexResCt() (in AF_SetHinge)	cleanup (in AutoDockTools.Utilities24.prepare_receptor)	commandList (in AutoDockTools.autopilotCommands)
changeHingeFlexResCt() (in AF_ProcessHingeResidues)	cleanup (in AutoDockTools.Utilities24.prepare_receptor4)	commandList (in AutoDockTools.autostartCommands)
changeInfo() (in ADMacroLigandChart)	cleanUpAtomTypes() (in AutoDockMoleculePreparation)	commandList (in AutoDockTools.autotorsCommands)
changePlanarityCriteria() (in LigandPreparation)	cleanUpResidues() (in AutoDockMoleculePreparation)	commandList (in AutoDockTools.pyAutoDockCommands)
charge_errorfile (in AutoDockTools.autotorsCommands)	clear() (in InteractiveGraphBuilder)	compute_AutoDock41_score (in AutoDockTools.Utilities24)
charges_to_add (in AutoDockTools.Utilities24.pdbqs_to_pdbqt)	clear_cb() (in AF_SetHinge)	compute_consensus_maps_from_dlgs (in AutoDockTools.Utilities24)
charges_to_add (in AutoDockTools.Utilities24.prepare_ligand)	clearAll_cb() (in AF_SetHinge)	compute_rms_between_methods (in AutoDockTools.Utilities24)
charges_to_add (in AutoDockTools.Utilities24.prepare_ligand4)	clearElem() (in DefineNewAtomParms)	computeGasteiger() (in LigandMixin)
charges_to_add (in AutoDockTools.Utilities24.prepare_receptor)	close() (in ADDrawHistogram)	conf0 (in AutoDockTools.Utilities24.write_lowest_energy_ligand)
charges_to_add (in AutoDockTools.Utilities24.prepare_receptor4)	close() (in ADMacroLigandChart)	conf_LC (in AutoDockTools.Utilities24.compute_rms_between_methods)
check_autogpf_geoms() (in AutoDockTools.autogpfCommands)	close() (in ADShowBindingSite)	configure() (in InteractiveGraphBuilder)
check_autotors_geoms() (in AutoDockTools.autotorsCommands)	Close_cb() (in ADMakeAllGrids)	confL (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)
check_for_fragments (in AutoDockTools.Utilities24.prepare_ligand)	Close_cb() (in StatesPlayerWidget)	Conformation (in AutoDockTools)
check_for_fragments (in AutoDockTools.Utilities24.prepare_ligand4)	Close_cb() (in Dpf4InitLigand)	Conformation (in AutoDockTools.Conformation)
check_torscount() (in AF_SetHinge)	Close_cb() (in DpfInitLigand)	ConformationHandler (in AutoDockTools.Conformation)
check_types() (in AutoDockTools.Utilities24.compute_AutoDock41_score)	Close_cb() (in GA)	ConformationPlayer (in AutoDockTools.ConfPlayer)
CheckAromatic (in AutoDockTools.autotorsCommands)	Close_cb() (in LS)	ConfPlayer (in AutoDockTools)
checkAromatic_cb() (in AF_ProcessResidues)	Close_cb() (in SetAutoDock4Parameters)	confs (in AutoDockTools.Utilities24.write_all_complexes)
CheckAromaticGUI (in AutoDockTools.autotorsCommands)	Close_cb() (in SetDockingRunParms)	construct_hydrogen_bonds() (in AutoDockTools.Utilities24.summarize_results4)
checkAromatics() (in LigandMixin)	Close_cb() (in SimAnneal)	continuousUpdate_cb() (in AF_EditHinge)
checkBonds() (in LigandMixin)	close_cb() (in AF_EditHinge)	continuousUpdate_cb() (in AF_SetHinge)
checkCharges() (in LigandMixin)	close_cb() (in AF_ProcessResidues)	coords (in AutoDockTools.Utilities24.compute_rms_between_methods)
checkFile() (in AutoDockTools.autogpfCommands)	close_cb() (in AF_SetHinge)	coords (in AutoDockTools.Utilities24.summarize_results)
checkHasDpo() (in AutoDockTools.autodpfCommands)	Close_cb() (in Gpf4SetMapTypes)	coords (in AutoDockTools.Utilities24.summarize_results4)
checkHasGpo() (in AutoDockTools.autogpfCommands)	Close_cb() (in GpfInitLigand)	coords (in AutoDockTools.Utilities24.summarize_wcg_docking)
checkHasInitializedDockings() (in AutoDockTools.autoanalyzeCommands)	Close_cb() (in SetBoxParameters)	coords (in AutoDockTools.Utilities24.write_largest_cluster_ligand)
checkHydrogens() (in LigandMixin)	Close_cb() (in SetMapTypes)	coords (in AutoDockTools.Utilities24.write_lowest_energy_ligand)
checkIsPeptide() (in LigandMixin)	Close_cb() (in SetOtherOptions)	coords (in AutoDockTools.autogpfCommands)
checkIsPeptide() (in Gpf4MacroInit)	Close_cb() (in SetUpCovalentMap)	crds (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)
checkIsPeptide() (in GpfMacroInit)	Close_cb() (in AddAutoDockHost)	createCanvas() (in InteractiveGraphBuilder)
checkit() (in AddAutoDockHost)	Close_cb() (in AutoStarter)	createMenus() (in InteractiveGraphBuilder)
checklb() (in AddAutoDockHost)	Close_cb() (in PyADCalcClosestPairs)	createReverseIndex() (in HistogramRI)
checkLigTypes() (in GridParameters)	Close_cb() (in PyADCalcVDWEnergies)	CRITICAL_DEPENDENCIES (in AutoDockTools)
checkLigTypes() (in GridParameters)	CloseCF_cb() (in ShowAutoDockClusteringStates)	ctr (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)
CheckMacroAtomTypes (in AutoDockTools.autogpfCommands)	closeform3() (in ConformationPlayer)	ctr (in AutoDockTools.Utilities24.pdbq_to_pdbqt)
checkMolCharges() (in AutoDockTools.autotorsCommands)	closeform3() (in PopulationPlayer)	ctr (in AutoDockTools.Utilities24.pdbqs_to_pdbqt)
checkMolLines() (in ADGetDLG)	closeform3() (in StatesPlayerWidget)	ctr (in AutoDockTools.Utilities24.pdbqt_to_pdbq)
checkNameStr() (in AutoDockTools.autoanalyzeCommands)	CloseHIST_cb() (in ShowAutoDockStatesHISTOGRAM)	ctr (in AutoDockTools.Utilities24.pdbqt_to_pdbqs)
checkPrevious() (in AutoStarter)	CloseStats_cb() (in ConformationPlayer)	ctr (in AutoDockTools.Utilities24.prepare_ligand)
checkStatus() (in WebServices)	CloseStats_cb() (in PopulationPlayer)	ctr (in AutoDockTools.Utilities24.prepare_ligand4)
chooseConformation() (in ADMacroLigandChart)	closeX_cb() (in AF_ProcessHingeResidues)	ctr (in AutoDockTools.Utilities24.prepare_receptor)
chooseFlexResMol_cb() (in Gpf4FlexResChooser)	Clust (in AutoDockTools.cluster_ad)	ctr (in AutoDockTools.Utilities24.prepare_receptor4)
chooseLigand_cb() (in Dpf4LigandChooser)	clust0 (in AutoDockTools.Utilities24.compute_rms_between_methods)	custom_counter() (in ConformationPlayer)
chooseLigand_cb() (in DpfLigandChooser)	clust0 (in AutoDockTools.Utilities24.summarize_results)	custom_counter() (in StatesPlayerWidget)
chooseLigand_cb() (in Gpf4LigandChooser)	clust0 (in AutoDockTools.Utilities24.summarize_wcg_docking)	custom_validate() (in ConformationPlayer)
chooseLigand_cb() (in GpfLigandChooser)	cluster (in AutoDockTools)	custom_validate() (in StatesPlayerWidget)
chooseLigand_cb() (in Ators4MoleculeChooser)	Cluster (in AutoDockTools.cluster)	customizeGUI() (in AddAutoDockHost)
chooseLigand_cb() (in AtorsMoleculeChooser)	cluster_ad (in AutoDockTools)	customizeGUI() (in AutoStarter)
chooseMol() (in AutoAutoTors)	Cluster_AD (in AutoDockTools.cluster_ad)

D

d (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	doit() (in ADDeleteDLG)	doit() (in AUTOTORS4Writer)
d (in AutoDockTools.Utilities24.compute_rms_between_methods)	doit() (in ADDockingChooser)	doit() (in AUTOTORSWriter)
d (in AutoDockTools.Utilities24.prepare_flexdocking4)	doit() (in ADEPDBMol)	doit() (in Ators4MoleculeChooser)
d (in AutoDockTools.Utilities24.prepare_flexreceptor4)	doit() (in ADGetAGrid)	doit() (in Ators4Reader)
d (in AutoDockTools.Utilities24.summarize_docking_directory)	doit() (in ADGetDLG)	doit() (in AtorsInit)
d (in AutoDockTools.Utilities24.summarize_results)	doit() (in ADGetDirDLGs)	doit() (in AtorsInitMol)
d (in AutoDockTools.Utilities24.summarize_results4)	doit() (in ADGetOutput)	doit() (in AtorsMoleculeChooser)
d (in AutoDockTools.Utilities24.summarize_wcg_docking)	doit() (in ADMacroLigandChart)	doit() (in AtorsReader)
d (in AutoDockTools.Utilities24.write_all_complexes)	doit() (in ADMakeAllGrids)	doit() (in AtorsRefWriter)
d (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)	doit() (in ADReadMacro)	doit() (in AutoAutoTors)
d (in AutoDockTools.Utilities24.write_largest_cluster_ligand)	doit() (in ADSeeSpots)	doit() (in AutoRoot)
d (in AutoDockTools.Utilities24.write_lowest_energy_ligand)	doit() (in ADSelectDLG)	doit() (in ChangeAromaticCutOff)
data (in AutoDockTools.histogram)	doit() (in ADShowBindingSite)	doit() (in CheckAromatic)
dataList (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)	doit() (in MakeAutoDockCLUSTERING)	doit() (in DefiningRotatableBonds)
debug (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	doit() (in MakeAutoDockSubsetCLUSTERING)	doit() (in MarkRoot)
DefineNewAtomParms (in AutoDockTools.autogpfCommands)	doit() (in ReadAutoDockClusteringStates)	doit() (in ProcessBonds)
DefineNewAtomParmsGUI (in AutoDockTools.autogpfCommands)	doit() (in ReadAutoDockStates)	doit() (in ProcessCharges)
DefiningRotatableBonds (in AutoDockTools.autotorsCommands)	doit() (in ShowAutoDockClusteringStates)	doit() (in RigidMolecule)
DefiningRotatableBondsGUI (in AutoDockTools.autotorsCommands)	doit() (in ShowAutoDockPopulation)	doit() (in RigidMolecule4)
delete() (in InteractiveGraphBuilder)	doit() (in ShowAutoDockStates)	doit() (in SelectRoot)
delete() (in InteractiveGraphObject)	doit() (in ShowAutoDockStatesBaseCmd)	doit() (in SetBondRotatableFlag)
delete_single_nonstd_residues (in AutoDockTools.Utilities24.prepare_receptor)	doit() (in ShowAutoDockStatesByEnergy)	doit() (in SetCarbonNames)
delete_single_nonstd_residues (in AutoDockTools.Utilities24.prepare_receptor4)	doit() (in ShowAutoDockStatesHISTOGRAM)	doit() (in SetTorsionNumber)
delItem_cb() (in AddAutoDockHost)	doit() (in WriteAutoDockClustering)	doit() (in SetTorsionNumberGUICommand)
deselect() (in InteractiveGraphObject)	doit() (in WriteAutoDockStates)	doit() (in StopAutoTors)
destroy() (in AppServicePortSoapBindingSOAP)	doit() (in Dpf4ClusterWriter)	doit() (in StopCheckAromatic)
destroyInput_Dec (in nbcr_sdsc_edu_opal_types)	doit() (in Dpf4FlexResSelector)	doit() (in TogglerootSphere)
destroyOutput_Dec (in nbcr_sdsc_edu_opal_types)	doit() (in Dpf4GALSWriter)	doit() (in PyAD4CalcAD4Energies)
destroyRequest (in AutoDockTools.AppService_services)	doit() (in Dpf4GAWriter)	doit() (in PyAD4CalcHBONDEnergies)
destroyRequestWrapper (in AutoDockTools.AppService_services)	doit() (in Dpf4InitLigand)	doit() (in PyAD4CalcInternalEnergies)
destroyResponse (in AutoDockTools.AppService_services)	doit() (in Dpf4LSWriter)	doit() (in PyADCalcAD3Energies)
destroyResponseWrapper (in AutoDockTools.AppService_services)	doit() (in Dpf4LigPDBQReader)	doit() (in PyADCalcClosestPairs)
detect_bonded_fragments() (in RotatableBondManager)	doit() (in Dpf4LigandChooser)	doit() (in PyADCalcDSOLVEnergies)
detectIsPeptide() (in AutoDockMoleculePreparation)	doit() (in Dpf4MacroChooser)	doit() (in PyADCalcVDWEnergies)
dict (in AutoDockTools.Utilities24.prepare_ligand)	doit() (in Dpf4MacroSelector)	done_cb() (in ClusterDockingChooser)
dict (in AutoDockTools.Utilities24.prepare_ligand4)	doit() (in Dpf4SAWriter)	done_cb() (in ModelDockingChooser)
directory (in AutoDockTools.Utilities24.compute_rms_between_methods)	doit() (in DpfClusterWriter)	done_cb() (in AF_EditHinge)
directory (in AutoDockTools.Utilities24.prepare_gpf4)	doit() (in DpfEditor)	done_cb() (in AF_ProcessHingeResidues)
directory (in AutoDockTools.Utilities24.summarize_docking_directory)	doit() (in DpfGALSWriter)	done_cb() (in AF_ProcessResidues)
directory (in AutoDockTools.Utilities24.summarize_results)	doit() (in DpfGAWriter)	done_cb() (in AF_SetHinge)
directory (in AutoDockTools.Utilities24.summarize_results4)	doit() (in DpfInitLigand)	done_cb() (in DefiningRotatableBonds)
directory (in AutoDockTools.Utilities24.summarize_time)	doit() (in DpfLSWriter)	DoNewType() (in CheckMacroAtomTypes)
directory (in AutoDockTools.Utilities24.summarize_wcg_docking)	doit() (in DpfLigPDBQReader)	doNqeRemoteCommand() (in AutoStarter)
directory (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)	doit() (in DpfLigandChooser)	download() (in WebServices)
directory_pathname (in AutoDockTools.Utilities24.summarize_docking_directory)	doit() (in DpfLoadDefaults)	dpf3_filename (in AutoDockTools.Utilities24.dpf3_to_dpf4)
disallow (in AutoDockTools.Utilities24.prepare_flexdocking4)	doit() (in DpfMacroChooser)	dpf3_to_dpf4 (in AutoDockTools.Utilities24)
disallow (in AutoDockTools.Utilities24.prepare_flexreceptor4)	doit() (in DpfMacroSelector)	Dpf4ClusterWriter (in AutoDockTools.autodpfCommands)
disallowed_pairs (in AutoDockTools.Utilities24.prepare_flexdocking4)	doit() (in DpfSAWriter)	Dpf4ClusterWriterGUI (in AutoDockTools.autodpfCommands)
disallowed_pairs (in AutoDockTools.Utilities24.prepare_flexreceptor4)	doit() (in DpfSetDpo)	Dpf4FlexResSelector (in AutoDockTools.autodpfCommands)
dismiss() (in AF_EditHinge)	doit() (in GA)	Dpf4FlexResSelectorGUI (in AutoDockTools.autodpfCommands)
dismiss() (in AF_ProcessHingeResidues)	doit() (in LS)	Dpf4GALSWriter (in AutoDockTools.autodpfCommands)
dismiss() (in AF_ProcessResidues)	doit() (in SetAutoDock4Parameters)	Dpf4GALSWriterGUI (in AutoDockTools.autodpfCommands)
dismiss() (in AF_SetHinge)	doit() (in SetDockingRunParms)	Dpf4GAWriter (in AutoDockTools.autodpfCommands)
dismiss() (in DefiningRotatableBonds)	doit() (in SimAnneal)	Dpf4GAWriterGUI (in AutoDockTools.autodpfCommands)
dismiss_cb() (in ADSeeSpots)	doit() (in StopAutoDpf)	Dpf4InitLigand (in AutoDockTools.autodpfCommands)
dismiss_cb() (in SelectCenter)	doit() (in AF_EditHinge)	Dpf4InitLigandGUI (in AutoDockTools.autodpfCommands)
dismiss_cb() (in SetCarbonNames)	doit() (in AF_FlexFileWriter)	Dpf4LigandChooser (in AutoDockTools.autodpfCommands)
Dismiss_cb() (in SetTorsionNumberGUICommand)	doit() (in AF_LigandDirectoryWriter)	Dpf4LigandChooserGUI (in AutoDockTools.autodpfCommands)
displayForm() (in DefiningRotatableBonds)	doit() (in AF_MacroChooser)	Dpf4LigPDBQReader (in AutoDockTools.autodpfCommands)
dist() (in AutoDockTools.AutoDockBondClassifier)	doit() (in AF_MacroReader)	Dpf4LigPDBQReaderGUI (in AutoDockTools.autodpfCommands)
dist() (in AutoDockTools.Utilities24.compute_rms_between_methods)	doit() (in AF_ProcessHingeResidues)	Dpf4LSWriter (in AutoDockTools.autodpfCommands)
dist() (in EnergyCalculator)	doit() (in AF_ProcessResidues)	Dpf4LSWriterGUI (in AutoDockTools.autodpfCommands)
dist_LC_LC (in AutoDockTools.Utilities24.compute_rms_between_methods)	doit() (in AF_RigidFileWriter)	Dpf4MacroChooser (in AutoDockTools.autodpfCommands)
dist_LC_LE (in AutoDockTools.Utilities24.compute_rms_between_methods)	doit() (in AF_SelectResidues)	Dpf4MacroChooserGUI (in AutoDockTools.autodpfCommands)
dist_LE_LC (in AutoDockTools.Utilities24.compute_rms_between_methods)	doit() (in AF_SetBondRotatableFlag)	Dpf4MacroSelector (in AutoDockTools.autodpfCommands)
dist_LE_LE (in AutoDockTools.Utilities24.compute_rms_between_methods)	doit() (in AF_SetHinge)	Dpf4MacroSelectorGUI (in AutoDockTools.autodpfCommands)
dlg_list (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	doit() (in AF_StepBack)	Dpf4SAWriter (in AutoDockTools.autodpfCommands)
dlg_list (in AutoDockTools.Utilities24.compute_rms_between_methods)	doit() (in CheckMacroAtomTypes)	Dpf4SAWriterGUI (in AutoDockTools.autodpfCommands)
dlg_list (in AutoDockTools.Utilities24.summarize_results)	doit() (in DefineNewAtomParms)	dpf_filename (in AutoDockTools.Utilities24.prepare_dpf)
dlg_list (in AutoDockTools.Utilities24.summarize_results4)	doit() (in Gpf4FlexResChooser)	dpf_filename (in AutoDockTools.Utilities24.prepare_dpf4)
dlg_list (in AutoDockTools.Utilities24.summarize_time)	doit() (in Gpf4FlexResReader)	dpf_filename (in AutoDockTools.Utilities24.summarize_docking_directory)
dlg_list (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)	doit() (in Gpf4InitLigand)	dpf_ligand (in AutoDockTools.Utilities24.summarize_docking_directory)
dlg_list (in AutoDockTools.Utilities24.write_largest_cluster_ligand)	doit() (in Gpf4LigReader)	dpf_pathname (in AutoDockTools.Utilities24.summarize_docking_directory)
dlg_pathname_list (in AutoDockTools.Utilities24.summarize_docking_directory)	doit() (in Gpf4LigandChooser)	DpfClusterWriter (in AutoDockTools.autodpfCommands)
dlgfilename (in AutoDockTools.Utilities24.write_lowest_energy_ligand)	doit() (in Gpf4MacroChooser)	DpfClusterWriterGUI (in AutoDockTools.autodpfCommands)
DlgParser (in AutoDockTools)	doit() (in Gpf4MacroInit)	DpfEditor (in AutoDockTools.autodpfCommands)
DlgParser (in AutoDockTools.DlgParser)	doit() (in Gpf4MacroReader)	DpfEditorGUI (in AutoDockTools.autodpfCommands)
dm (in AutoDockTools.Utilities24.prepare_dpf)	doit() (in Gpf4ParameterFileSelector)	DpfGALSWriter (in AutoDockTools.autodpfCommands)
dm (in AutoDockTools.Utilities24.prepare_dpf4)	doit() (in Gpf4SetAtomTypes)	DpfGALSWriterGUI (in AutoDockTools.autodpfCommands)
do_stats() (in Cluster)	doit() (in Gpf4SetMapTypes)	DpfGAWriter (in AutoDockTools.autodpfCommands)
do_stats() (in Clustering)	doit() (in Gpf4Writer)	DpfGAWriterGUI (in AutoDockTools.autodpfCommands)
do_update() (in ADKill)	doit() (in GpfAddSol)	DpfInitLigand (in AutoDockTools.autodpfCommands)
doAtomPick_cb() (in SetUpCovalentMap)	doit() (in GpfEditor)	DpfInitLigandGUI (in AutoDockTools.autodpfCommands)
Docking (in AutoDockTools)	doit() (in GpfInitLigand)	DpfLigandChooser (in AutoDockTools.autodpfCommands)
Docking (in AutoDockTools.Docking)	doit() (in GpfLigReader)	DpfLigandChooserGUI (in AutoDockTools.autodpfCommands)
Docking (in AutoDockTools.VisionInterface)	doit() (in GpfLigandChooser)	DpfLigPDBQReader (in AutoDockTools.autodpfCommands)
Docking (in AutoDockTools.VisionInterface.Docking)	doit() (in GpfLoadDefaults)	DpfLigPDBQReaderGUI (in AutoDockTools.autodpfCommands)
docking_filename (in AutoDockTools.Utilities24.write_all_complexes)	doit() (in GpfMacroChooser)	DpfLoadDefaults (in AutoDockTools.autodpfCommands)
docking_name (in AutoDockTools.Utilities24.summarize_docking_directory)	doit() (in GpfMacroInit)	DpfLoadDefaultsGUI (in AutoDockTools.autodpfCommands)
docking_parameter_list (in AutoDockTools.DockingParameters)	doit() (in GpfMacroReader)	DpfLSWriter (in AutoDockTools.autodpfCommands)
docking_parameter_list4 (in AutoDockTools.DockingParameters)	doit() (in GpfMergeNonPolarHs)	DpfLSWriterGUI (in AutoDockTools.autodpfCommands)
docking_parameter_list4_1 (in AutoDockTools.DockingParameters)	doit() (in GpfSetGpo)	DpfMacroChooser (in AutoDockTools.autodpfCommands)
docking_pathname (in AutoDockTools.Utilities24.summarize_docking_directory)	doit() (in GpfWriter)	DpfMacroChooserGUI (in AutoDockTools.autodpfCommands)
DockingLogObject (in AutoDockTools.Docking)	doit() (in SelectCenter)	DpfMacroSelector (in AutoDockTools.autodpfCommands)
DockingParameter4FileMaker (in AutoDockTools.DockingParameters)	doit() (in SetBoxParameters)	DpfMacroSelectorGUI (in AutoDockTools.autodpfCommands)
DockingParameter4FileMaker (in AutoDockTools.Utilities24.prepare_dpf4)	doit() (in SetMapTypes)	DpfSAWriter (in AutoDockTools.autodpfCommands)
DockingParameterFileBrowserNE (in AutoDockTools.VisionInterface.AdtNodes)	doit() (in SetOtherOptions)	DpfSAWriterGUI (in AutoDockTools.autodpfCommands)
DockingParameterFileMaker (in AutoDockTools.DockingParameters)	doit() (in SetUpCovalentMap)	DpfSetDpo (in AutoDockTools.autodpfCommands)
DockingParameterFileMaker (in AutoDockTools.Utilities24.prepare_dpf)	doit() (in ADpilot_Cluster)	dpo (in AutoDockTools.DockingParameters)
DockingParameters (in AutoDockTools)	doit() (in ADpilot_ClusterGUICommand)	dpo (in AutoDockTools.Utilities24.summarize_docking_directory)
DockingParameters (in AutoDockTools.DockingParameters)	doit() (in ADpilot_Template)	DPO4 (in AutoDockTools.Utilities24.dpf3_to_dpf4)
dockings (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	doit() (in ADpilot_TemplateGUICommand)	draw() (in GraphLine)
doIntRemoteCommand() (in AutoStarter)	doit() (in ADProcessManager)	draw() (in GraphObjects)
doit() (in ADChooseMacro)	doit() (in AutoStarter)

E

e (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)	EnergyCalculator (in AutoDockTools.energyCalculator)	EpdbParser (in AutoDockTools)
editAtomsToMove_cb() (in AF_SetHinge)	energyConstants (in AutoDockTools)	EpdbParser (in AutoDockTools.EpdbParser)
editNoneMenu() (in InteractiveGraphObject)	enter() (in InteractiveGraphBuilder)	epsij (in AutoDockTools.energyConstants)
ehist (in AutoDockTools.interactiveHistogramGraph)	enter_cb() (in AutoDockTools.autotorsCommands)	exclude_torsFreeEnergy (in AutoDockTools.Utilities24.compute_AutoDock41_score)
elist (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)	EntropiaParser (in AutoDockTools)	exit() (in InteractiveGraphBuilder)
energy_average_maps (in AutoDockTools.Utilities24)	EntropiaParser (in AutoDockTools.EntropiaParser)
energyCalculator (in AutoDockTools)	entropiaPresent (in AutoDockTools.autostartCommands)

F

face (in AutoDockTools.autogpfCommands)	findAutoMacroCenter() (in SetBoxParameters)	float
FaultType_Def (in nbcr_sdsc_edu_opal_types)	findNearest() (in AutoDockMoleculePreparation)	form (in SetRotatableBonds)
fdp (in AutoDockTools.Utilities24.prepare_flexdocking4)	first (in AutoDockTools.Utilities24.compute_AutoDock41_score)	fptr (in AutoDockTools.Utilities24.compute_rms_between_methods)
fdp (in AutoDockTools.Utilities24.prepare_flexreceptor4)	first (in AutoDockTools.Utilities24.compute_rms_between_methods)	fptr (in AutoDockTools.Utilities24.energy_average_maps)
FE_desol_coeff (in AutoDockTools.energyConstants)	first (in AutoDockTools.Utilities24.summarize_results4)	fptr (in AutoDockTools.Utilities24.pdbq_to_pdbqt)
FE_estat_coeff (in AutoDockTools.energyConstants)	fitToScale() (in GraphObjects)	fptr (in AutoDockTools.Utilities24.pdbqs_to_pdbqt)
FE_hbond_coeff (in AutoDockTools.energyConstants)	fitToScale() (in GraphPoints)	fptr (in AutoDockTools.Utilities24.pdbqt_to_pdbq)
FE_tors_coeff (in AutoDockTools.energyConstants)	fitToScale() (in HistogramNodeSet)	fptr (in AutoDockTools.Utilities24.pdbqt_to_pdbqs)
FE_vdW_coeff (in AutoDockTools.energyConstants)	FlagCheck (in AutoDockTools)	fptr (in AutoDockTools.Utilities24.summarize_results)
field_defn (in EntropiaParser)	FlagsArrayType_Def (in nbcr_sdsc_edu_opal_types)	fptr (in AutoDockTools.Utilities24.summarize_results4)
fields (in AutoDockTools.Utilities24.summarize_docking_directory)	FlagsType_Def (in nbcr_sdsc_edu_opal_types)	fptr (in AutoDockTools.Utilities24.summarize_time)
file (in AutoDockTools.Utilities24.summarize_results4)	fld_fn (in AutoDockTools.Utilities24.energy_average_maps)	fptr (in AutoDockTools.Utilities24.summarize_wcg_docking)
fillForm() (in AddAutoDockHost)	flex_filename (in AutoDockTools.Utilities24.prepare_flexdocking4)
findAutoLigandCenter() (in SetBoxParameters)	flexres_filename (in AutoDockTools.Utilities24.prepare_flexreceptor4)

G

GA (in AutoDockTools.autodpfCommands)	getMacroVal() (in AutoStarter)	GraphObjects (in AutoDockTools.interactiveHistogramGraph)
GAGUI (in AutoDockTools.autodpfCommands)	getModelLines() (in DlgParser)	GraphPoints (in AutoDockTools.interactiveHistogramGraph)
genetic_algorithm_list (in AutoDockTools.DockingParameters)	getMolecule() (in ReadAutoDockStates)	grid_parameter_list (in AutoDockTools.GridParameters)
genetic_algorithm_list4 (in AutoDockTools.DockingParameters)	getMolSet() (in ClusterDockingChooser)	grid_parameter_list (in AutoDockTools.GridParameters_AD4)
genetic_algorithm_list4_1 (in AutoDockTools.DockingParameters)	getMolSet() (in ModelDockingChooser)	grid_parameter_list4 (in AutoDockTools.GridParameters)
genetic_algorithm_local_search_list (in AutoDockTools.DockingParameters)	getNeighbors() (in MarkRoot)	gridOpts (in AutoDockTools.autogpfCommands)
genetic_algorithm_local_search_list4 (in AutoDockTools.DockingParameters)	getNewDpfInfo() (in DlgParser)	GridParameter4FileMaker (in AutoDockTools.GridParameters)
genetic_algorithm_local_search_list4_1 (in AutoDockTools.DockingParameters)	getNewGaussTorCts() (in Dpf4InitLigand)	GridParameterFileBrowserNE (in AutoDockTools.VisionInterface.AdtNodes)
genetic_algorithm_local_search_list4_1_with_parameter_file (in AutoDockTools.DockingParameters)	getNewGaussTorCts() (in DpfInitLigand)	GridParameterFileMaker (in AutoDockTools.GridParameters)
genetic_algorithm_local_search_list4_with_parameter_file (in AutoDockTools.DockingParameters)	getNewHardTorCts() (in Dpf4InitLigand)	GridParameters (in AutoDockTools)
Get_argList() (in JobInputType_Def)	getNewHardTorCts() (in DpfInitLigand)	GridParameters (in AutoDockTools.GridParameters)
Get_baseURL() (in StatusOutputType_Def)	getNonBondTable() (in DlgParser)	GridParameters (in AutoDockTools.GridParameters_AD4)
get_best_energy_info() (in AutoDockTools.Utilities24.summarize_results4)	getObjects() (in AF_ProcessHingeResidues)	GridParameters_AD4 (in AutoDockTools)
Get_binaryLocation() (in AppConfigType_Def)	getObjects() (in AF_ProcessResidues)	guiCallback() (in WebServices)
Get_code() (in StatusOutputType_Def)	getObjects() (in AF_SetHinge)	guiCallback() (in ADChooseMacro)
Get_contents() (in InputFileType_Def)	getObjects() (in DefiningRotatableBonds)	guiCallback() (in ADDeleteDLG)
get_coords() (in Cluster_AD)	getOutputAsBase64ByName() (in AppServicePortSoapBindingSOAP)	guiCallback() (in ADDockingChooser)
Get_defaultArgs() (in AppConfigType_Def)	getOutputAsBase64ByNameInput_Dec (in nbcr_sdsc_edu_opal_types)	guiCallback() (in ADDrawHistogram)
get_dist() (in Cluster_AD)	getOutputAsBase64ByNameOutput_Dec (in nbcr_sdsc_edu_opal_types)	guiCallback() (in ADEPDBMol)
get_distance() (in Clusterer)	getOutputAsBase64ByNameRequest (in AutoDockTools.AppService_services)	guiCallback() (in ADGetAGrid)
get_distance_subset() (in AutoDockTools.autoanalyzeCommands)	getOutputAsBase64ByNameRequestWrapper (in AutoDockTools.AppService_services)	guiCallback() (in ADGetDLG)
get_energy() (in EnergyCalculator)	getOutputAsBase64ByNameResponse (in AutoDockTools.AppService_services)	guiCallback() (in ADGetDirDLGs)
get_energy_breakdown() (in AutoDockTools.Utilities24.summarize_results4)	getOutputAsBase64ByNameResponseWrapper (in AutoDockTools.AppService_services)	guiCallback() (in ADGetOutput)
Get_extension() (in ImplicitParamsType_Def)	getOutputs() (in AppServicePortSoapBindingSOAP)	guiCallback() (in ADMacroLigandChart)
Get_fileName() (in OutputsByNameInputType_Def)	getOutputsInput_Dec (in nbcr_sdsc_edu_opal_types)	guiCallback() (in ADMakeAllGrids)
get_filename() (in AutoDockTools.Utilities24.summarize_results4)	getOutputsOutput_Dec (in nbcr_sdsc_edu_opal_types)	guiCallback() (in ADReadMacro)
Get_flag() (in FlagsArrayType_Def)	getOutputsRequest (in AutoDockTools.AppService_services)	guiCallback() (in ADSeeSpots)
Get_flags() (in ArgumentsType_Def)	getOutputsRequestWrapper (in AutoDockTools.AppService_services)	guiCallback() (in ADSelectDLG)
get_floats() (in XMLParser)	getOutputsResponse (in AutoDockTools.AppService_services)	guiCallback() (in ADShowBindingSite)
Get_id() (in FlagsType_Def)	getOutputsResponseWrapper (in AutoDockTools.AppService_services)	guiCallback() (in MakeAutoDockCLUSTERING)
Get_id() (in ImplicitParamsType_Def)	getPeptideAromatics() (in LigandMixin)	guiCallback() (in MakeAutoDockSubsetCLUSTERING)
Get_id() (in ParamsType_Def)	getPeptideAromatics() (in CheckAromatic)	guiCallback() (in ReadAutoDockStates)
Get_implicitParams() (in ArgumentsType_Def)	getPeptideBondDict() (in LigandMixin)	guiCallback() (in ShowAutoDockStatesBaseCmd)
Get_info() (in AppMetadataType_Def)	getPopulations() (in DlgParser)	guiCallback() (in WriteAutoDockClustering)
Get_inputFile() (in JobInputType_Def)	getProjectVal() (in AutoStarter)	guiCallback() (in WriteAutoDockStates)
get_internal_energy() (in EnergyCalculator)	getReDict() (in DlgParser)	guiCallback() (in Dpf4ClusterWriter)
get_ints() (in XMLParser)	getReDict() (in XMLParser)	guiCallback() (in Dpf4FlexResSelector)
Get_ioType() (in ImplicitParamsType_Def)	getReverseSubtree() (in AF_SetHinge)	guiCallback() (in Dpf4GALSWriter)
Get_ioType() (in ParamsType_Def)	getRMSD() (in Conformation)	guiCallback() (in Dpf4GAWriter)
Get_item() (in getOutputAsBase64ByNameOutput_Dec)	getRMSD_custom() (in Conformation)	guiCallback() (in Dpf4InitLigand)
Get_jobID() (in JobSubOutputType_Def)	getRMSD_subset() (in Conformation)	guiCallback() (in Dpf4LSWriter)
Get_jobID() (in OutputsByNameInputType_Def)	getRMSD_subset() (in AutoDockTools.autoanalyzeCommands)	guiCallback() (in Dpf4LigPDBQReader)
Get_jobOut() (in BlockingOutputType_Def)	getSeedInfo() (in DlgParser)	guiCallback() (in Dpf4LigandChooser)
get_largest_cluster_info() (in AutoDockTools.Utilities24.summarize_results4)	getSet() (in AF_SetHinge)	guiCallback() (in Dpf4MacroChooser)
Get_max() (in ImplicitParamsType_Def)	getShortModelLines() (in DlgParser)	guiCallback() (in Dpf4MacroSelector)
get_max_dist() (in Clusterer)	getSideLengths() (in GridParameter4FileMaker)	guiCallback() (in Dpf4SAWriter)
Get_message() (in FaultType_Def)	getSideLengths() (in GridParameterFileMaker)	guiCallback() (in DpfClusterWriter)
Get_message() (in StatusOutputType_Def)	getSideLengths() (in AutoDockTools.autogpfCommands)	guiCallback() (in DpfEditor)
Get_metadata() (in AppConfigType_Def)	getSSResidues() (in ADShowBindingSite)	guiCallback() (in DpfGALSWriter)
Get_min() (in ImplicitParamsType_Def)	getStatString() (in ConformationPlayer)	guiCallback() (in DpfGAWriter)
get_min_dist() (in Clusterer)	getStatString() (in PopulationPlayer)	guiCallback() (in DpfInitLigand)
Get_name() (in ImplicitParamsType_Def)	gettags() (in InteractiveGraphObject)	guiCallback() (in DpfLSWriter)
Get_name() (in InputFileType_Def)	getTime() (in DlgParser)	guiCallback() (in DpfLigPDBQReader)
Get_name() (in OutputFileType_Def)	getTorCts() (in Dpf4InitLigand)	guiCallback() (in DpfLigandChooser)
Get_numProcs() (in JobInputType_Def)	getTorCts() (in DpfInitLigand)	guiCallback() (in DpfLoadDefaults)
Get_outputFile() (in JobOutputType_Def)	getTorsionOnlyCoords() (in Conformation)	guiCallback() (in DpfMacroChooser)
Get_parallel() (in AppConfigType_Def)	getTraj() (in SimAnneal)	guiCallback() (in DpfMacroSelector)
Get_param() (in ImplicitParamsArrayType_Def)	getTrajState() (in TrajParser)	guiCallback() (in DpfSAWriter)
Get_param() (in ParamsArrayType_Def)	getTransformedCoords() (in AF_SetHinge)	guiCallback() (in GA)
Get_paramType() (in ParamsType_Def)	getTypes() (in DockingParameter4FileMaker)	guiCallback() (in LS)
Get_required() (in ImplicitParamsType_Def)	getTypes() (in GridParameter4FileMaker)	guiCallback() (in SetAutoDock4Parameters)
Get_required() (in ParamsType_Def)	getTypes() (in DockingParameter4FileMaker)	guiCallback() (in SetDockingRunParms)
get_runs() (in XMLParser)	getTypes() (in GpfInitLigand)	guiCallback() (in SimAnneal)
Get_semanticType() (in ImplicitParamsType_Def)	gettypes() (in LibraryGpfWriter)	guiCallback() (in StopAutoDpf)
Get_semanticType() (in ParamsType_Def)	getUserSeed1() (in SetDockingRunParms)	guiCallback() (in AF_EditHinge)
Get_separator() (in ParamsArrayType_Def)	getUserSeed2() (in SetDockingRunParms)	guiCallback() (in AF_FlexFileWriter)
get_state() (in AF_SetHinge)	getVertices() (in ADSeeSpots)	guiCallback() (in AF_LigandDirectoryWriter)
Get_status() (in BlockingOutputType_Def)	getWARNINGS() (in DlgParser)	guiCallback() (in AF_MacroChooser)
Get_status() (in JobSubOutputType_Def)	go() (in ClusterDockingChooser)	guiCallback() (in AF_MacroReader)
Get_stdErr() (in JobOutputType_Def)	go() (in ModelDockingChooser)	guiCallback() (in AF_ProcessHingeResidues)
Get_stdOut() (in JobOutputType_Def)	go_cb() (in AutoAutoTors)	guiCallback() (in AF_ProcessResidues)
get_subset_internal_energy() (in EnergyCalculator)	gpf3_filename (in AutoDockTools.Utilities24.gpf3_to_gpf4)	guiCallback() (in AF_RigidFileWriter)
Get_tag() (in FlagsType_Def)	gpf3_to_gpf4 (in AutoDockTools.Utilities24)	guiCallback() (in AF_SelectResidues)
Get_tag() (in ParamsType_Def)	gpf4_filename (in AutoDockTools.Utilities24.gpf4_to_gpf3)	guiCallback() (in AF_SetHinge)
Get_taggedParams() (in ArgumentsType_Def)	gpf4_to_gpf3 (in AutoDockTools.Utilities24)	guiCallback() (in AF_StepBack)
Get_textDesc() (in FlagsType_Def)	Gpf4FlexResChooser (in AutoDockTools.autogpfCommands)	guiCallback() (in CheckMacroAtomTypes)
Get_textDesc() (in ImplicitParamsType_Def)	Gpf4FlexResChooserGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in DefineNewAtomParms)
Get_textDesc() (in ParamsType_Def)	Gpf4FlexResReader (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4FlexResChooser)
Get_types() (in AppMetadataType_Def)	Gpf4FlexResReaderGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4FlexResReader)
Get_untaggedParams() (in ArgumentsType_Def)	Gpf4InitLigand (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4LigReader)
Get_url() (in OutputFileType_Def)	Gpf4LigandChooser (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4LigandChooser)
Get_usage() (in AppMetadataType_Def)	Gpf4LigandChooserGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4MacroChooser)
Get_value() (in ParamsType_Def)	Gpf4LigReader (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4MacroReader)
getAllHingeAtoms() (in AF_SetHinge)	Gpf4LigReaderGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4ParameterFileSelector)
getAppConfig() (in AppServicePortSoapBindingSOAP)	Gpf4MacroChooser (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4SetAtomTypes)
getAppConfigOutput_Dec (in nbcr_sdsc_edu_opal_types)	Gpf4MacroChooserGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4SetMapTypes)
getAppConfigRequest (in AutoDockTools.AppService_services)	Gpf4MacroInit (in AutoDockTools.autogpfCommands)	guiCallback() (in Gpf4Writer)
getAppConfigRequestWrapper (in AutoDockTools.AppService_services)	Gpf4MacroReader (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfAddSol)
getAppConfigResponse (in AutoDockTools.AppService_services)	Gpf4MacroReaderGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfEditor)
getAppConfigResponseWrapper (in AutoDockTools.AppService_services)	Gpf4ParameterFileSelector (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfLigReader)
getAppMetadata() (in AppServicePortSoapBindingSOAP)	Gpf4ParameterFileSelectorGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfLigandChooser)
getAppMetadataOutput_Dec (in nbcr_sdsc_edu_opal_types)	Gpf4SetAtomTypes (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfLoadDefaults)
getAppMetadataRequest (in AutoDockTools.AppService_services)	Gpf4SetAtomTypesGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfMacroChooser)
getAppMetadataRequestWrapper (in AutoDockTools.AppService_services)	Gpf4SetMapTypes (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfMacroReader)
getAppMetadataResponse (in AutoDockTools.AppService_services)	Gpf4SetMapTypesGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfMergeNonPolarHs)
getAppMetadataResponseWrapper (in AutoDockTools.AppService_services)	Gpf4Writer (in AutoDockTools.autogpfCommands)	guiCallback() (in GpfWriter)
getAppServicePortType() (in AppServiceInterface)	Gpf4WriterGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in SelectCenter)
getAppServicePortType() (in AppServiceLocator)	gpf_filename (in AutoDockTools.Utilities24.prepare_gpf)	guiCallback() (in SetBoxParameters)
getAppServicePortTypeAddress() (in AppServiceLocator)	gpf_filename (in AutoDockTools.Utilities24.prepare_gpf4)	guiCallback() (in SetMapTypes)
getButton() (in ADDrawHistogram)	gpf_filename (in AutoDockTools.Utilities24.summarize_docking_directory)	guiCallback() (in SetOtherOptions)
getCenterMapPt() (in DlgParser)	gpf_pathname (in AutoDockTools.Utilities24.summarize_docking_directory)	guiCallback() (in SetUpCovalentMap)
getClusterInfo() (in DlgParser)	GpfAddSol (in AutoDockTools.autogpfCommands)	guiCallback() (in ADpilot_ClusterGUICommand)
getClusterRecord() (in DlgParser)	GpfAddSolGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in ADpilot_TemplateGUICommand)
getCmd() (in AutoDockStarter)	GpfEditor (in AutoDockTools.autogpfCommands)	guiCallback() (in ADProcessManager)
getCmd() (in AutoStarter)	GpfEditorGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in AddAutoDockHost)
getCmdParams() (in AutoDockStarter)	GpfInitLigand (in AutoDockTools.autogpfCommands)	guiCallback() (in AutoDockStarter)
getCoords() (in Conformation)	GpfLigandChooser (in AutoDockTools.autogpfCommands)	guiCallback() (in AutoStarter)
getCoords_subset() (in Conformation)	GpfLigandChooserGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in AUTOTORS4Writer)
getCoords_subset() (in AutoDockTools.autoanalyzeCommands)	GpfLigReader (in AutoDockTools.autogpfCommands)	guiCallback() (in AUTOTORSWriter)
getDielConst() (in SetOtherOptions)	GpfLigReaderGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in Ators4MoleculeChooser)
getDihe() (in Dpf4InitLigand)	GpfLoadDefaults (in AutoDockTools.autogpfCommands)	guiCallback() (in Ators4Reader)
getDihe() (in DpfInitLigand)	GpfLoadDefaultsGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in AtorsMoleculeChooser)
getDlgStates() (in DlgParser)	gpfm (in AutoDockTools.Utilities24.prepare_gpf)	guiCallback() (in AtorsReader)
getDocking() (in ADDrawHistogram)	gpfm (in AutoDockTools.Utilities24.prepare_gpf4)	guiCallback() (in AtorsRefWriter)
getEnergyText() (in ADDrawHistogram)	GpfMacroChooser (in AutoDockTools.autogpfCommands)	guiCallback() (in AutoAutoTors)
getEntropiaUIObject() (in AutoStarter)	GpfMacroChooserGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in AutoRoot)
getFlags() (in AutoDockStarter)	GpfMacroInit (in AutoDockTools.autogpfCommands)	guiCallback() (in ChangeAromaticCutOff)
getFlags() (in AutoStarter)	GpfMacroReader (in AutoDockTools.autogpfCommands)	guiCallback() (in DefiningRotatableBonds)
getHost() (in AutoStarter)	GpfMacroReaderGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in MarkRoot)
getHostVal() (in AutoStarter)	GpfMergeNonPolarHs (in AutoDockTools.autogpfCommands)	guiCallback() (in RigidMolecule)
getIfd() (in ADSeeSpots)	GpfSetGpo (in AutoDockTools.autogpfCommands)	guiCallback() (in RigidMolecule4)
getInitialConfs() (in DlgParser)	GpfWriter (in AutoDockTools.autogpfCommands)	guiCallback() (in SelectRoot)
getInputs() (in AutoDockStarter)	GpfWriterGUI (in AutoDockTools.autogpfCommands)	guiCallback() (in SetCarbonNames)
getItem() (in AddAutoDockHost)	gpo (in AutoDockTools.GridParameters_AD4)	guiCallback() (in SetTorsionNumberGUICommand)
getLigandAtomCount() (in DlgParser)	gpo (in AutoDockTools.Utilities24.summarize_docking_directory)	guiCallback() (in StopAutoTors)
getLigandBondDict() (in LigandMixin)	GPO3 (in AutoDockTools.Utilities24.gpf4_to_gpf3)	guiCallback() (in TogglerootSphere)
getligands() (in LibraryDpfWriter)	GPO4 (in AutoDockTools.Utilities24.gpf3_to_gpf4)	guiCallback() (in PyADCalcClosestPairs)
getMacro() (in AutoStarter)	GraphLine (in AutoDockTools.interactiveHistogramGraph)	guiCallback() (in PyADCalcVDWEnergies)

H

h (in AutoDockTools.Objects)	hideASelector() (in PyADCalcVDWEnergies)	hideStepSizeOpts() (in SetDockingRunParms)
h (in AutoDockTools)	hideDisplay() (in PyADCalcClosestPairs)	histNB (in AutoDockTools.interactiveHistogramGraph)
hasAmide (in SetRotatableBonds)	hideDSelector() (in PyADCalcClosestPairs)	histogram (in AutoDockTools)
hasGuan (in SetRotatableBonds)	hideDSelector() (in PyADCalcVDWEnergies)	Histogram (in AutoDockTools.histogram)
hasPeptide (in SetRotatableBonds)	hideEnergyOpts() (in SetDockingRunParms)	HistogramNode (in AutoDockTools.interactiveHistogramGraph)
hasSelected (in SetRotatableBonds)	hideInfo() (in ADDrawHistogram)	HistogramNodeSet (in AutoDockTools.interactiveHistogramGraph)
hbondBuilder (in AutoDockTools.Utilities24.summarize_results)	hideInfo() (in ADMacroLigandChart)	HistogramRI (in AutoDockTools.histogram)
hbondBuilder (in AutoDockTools.Utilities24.summarize_wcg_docking)	hideLibOpts() (in SetDockingRunParms)	hostDict (in AutoDockTools.Objects)
help (in AutoDockTools.Utilities24.summarize_time)	hideOutputOpts() (in SetDockingRunParms)	hostDict (in AutoDockTools)
hide_xyz() (in AF_SetHinge)	hidePalette_cb() (in ADSeeSpots)	hostMacros (in AutoDockTools.adthosts)
hideASelector() (in PyADCalcClosestPairs)	hideShowHide() (in AutoDockTools.autoanalyzeCommands)	hRI (in AutoDockTools.histogram)

I

i (in AutoDockTools.autoanalyzeCommands)	initLPO4() (in AutoDockTools.autotorsCommands)	InputFileType_Def (in nbcr_sdsc_edu_opal_types)
implemented (in AutoDockTools.DockingParameters)	initModule() (in AutoDockTools.WebServices)	instantiate() (in HistogramNode)
ImplicitParamsArrayType_Def (in nbcr_sdsc_edu_opal_types)	initModule() (in AutoDockTools.autoanalyzeCommands)	instantiate() (in InteractiveGraphObject)
ImplicitParamsType_Def (in nbcr_sdsc_edu_opal_types)	initModule() (in AutoDockTools.autodpfCommands)	int
importAdtLib() (in AutoDockTools.VisionInterface.AdtNodes)	initModule() (in AutoDockTools.autoflexCommands)	InteractiveGraphBuilder (in AutoDockTools.interactiveHistogramGraph)
inactivate_all_torsions (in AutoDockTools.Utilities24.prepare_ligand)	initModule() (in AutoDockTools.autogpfCommands)	InteractiveGraphObject (in AutoDockTools.interactiveHistogramGraph)
inactivate_all_torsions (in AutoDockTools.Utilities24.prepare_ligand4)	initModule() (in AutoDockTools.autopilotCommands)	interactiveHistogramGraph (in AutoDockTools)
info() (in ADDrawHistogram)	initModule() (in AutoDockTools.autostartCommands)	InteractiveHistogramGraph (in AutoDockTools.interactiveHistogramGraph)
initForm() (in WebServices)	initModule() (in AutoDockTools.autotorsCommands)	IOType_Def (in nbcr_sdsc_edu_opal_types)
initLPO() (in AutoDockTools.autotorsCommands)	initModule() (in AutoDockTools.pyAutoDockCommands)

J

JobInputType_Def (in nbcr_sdsc_edu_opal_types)	JobOutputType_Def (in nbcr_sdsc_edu_opal_types)	JobSubOutputType_Def (in nbcr_sdsc_edu_opal_types)

K

key0 (in AutoDockTools.Utilities24.write_lowest_energy_ligand)	keywords (in EpdbParser)	keywords (in XMLParser)
keywords (in DlgParser)	keywords (in ResultParser)	kill() (in ADKill)
keywords (in EntropiaParser)	keywords (in TrajParser)

L

l (in AutoDockTools.Utilities24.prepare_flexdocking4)	ligand_filename (in AutoDockTools.Utilities24.gpf4_to_gpf3)	list_filename (in AutoDockTools.Utilities24.prepare_gpf4)
largest (in AutoDockTools.Utilities24.compute_rms_between_methods)	ligand_filename (in AutoDockTools.Utilities24.prepare_dpf)	literal (in destroyInput_Dec)
largest (in AutoDockTools.Utilities24.write_largest_cluster_ligand)	ligand_filename (in AutoDockTools.Utilities24.prepare_dpf4)	literal (in destroyOutput_Dec)
launchJob() (in AppServicePortSoapBindingSOAP)	ligand_filename (in AutoDockTools.Utilities24.prepare_flexdocking4)	literal (in getAppConfigOutput_Dec)
launchJobBlocking() (in AppServicePortSoapBindingSOAP)	ligand_filename (in AutoDockTools.Utilities24.prepare_gpf)	literal (in getAppMetadataOutput_Dec)
launchJobBlockingInput_Dec (in nbcr_sdsc_edu_opal_types)	ligand_filename (in AutoDockTools.Utilities24.prepare_gpf4)	literal (in getOutputAsBase64ByNameInput_Dec)
launchJobBlockingOutput_Dec (in nbcr_sdsc_edu_opal_types)	ligand_filename (in AutoDockTools.Utilities24.prepare_ligand)	literal (in getOutputAsBase64ByNameOutput_Dec)
launchJobBlockingRequest (in AutoDockTools.AppService_services)	ligand_filename (in AutoDockTools.Utilities24.prepare_ligand4)	literal (in getOutputsInput_Dec)
launchJobBlockingRequestWrapper (in AutoDockTools.AppService_services)	ligand_filename (in AutoDockTools.Utilities24.prepare_ligand_dict)	literal (in getOutputsOutput_Dec)
launchJobBlockingResponse (in AutoDockTools.AppService_services)	ligand_filename (in AutoDockTools.Utilities24.summarize_docking_directory)	literal (in launchJobBlockingInput_Dec)
launchJobBlockingResponseWrapper (in AutoDockTools.AppService_services)	ligand_pathname (in AutoDockTools.Utilities24.summarize_docking_directory)	literal (in launchJobBlockingOutput_Dec)
launchJobInput_Dec (in nbcr_sdsc_edu_opal_types)	Ligand_Writer (in AutoDockTools.VisionInterface.AdtNodes)	literal (in launchJobInput_Dec)
launchJobOutput_Dec (in nbcr_sdsc_edu_opal_types)	Ligand_Writer_AD4 (in AutoDockTools.VisionInterface.AdtNodes)	literal (in launchJobOutput_Dec)
launchJobRequest (in AutoDockTools.AppService_services)	LigandDictionaryMaker (in AutoDockTools.Utilities24.prepare_ligand_dict)	literal (in opalFaultOutput_Dec)
launchJobRequestWrapper (in AutoDockTools.AppService_services)	ligandfilename (in AutoDockTools.Utilities24.compute_AutoDock41_score)	literal (in queryStatusInput_Dec)
launchJobResponse (in AutoDockTools.AppService_services)	LigandMixin (in AutoDockTools)	literal (in queryStatusOutput_Dec)
launchJobResponseWrapper (in AutoDockTools.AppService_services)	LigandMixin (in AutoDockTools.LigandMixin)	ll (in AutoDockTools.atomTypeTools)
LC_coords (in AutoDockTools.Utilities24.compute_rms_between_methods)	LigandPreparation (in AutoDockTools.MoleculePreparation)	loadFile() (in InteractiveGraphBuilder)
ldm (in AutoDockTools.Utilities24.prepare_ligand_dict)	LigandWriter (in AutoDockTools.MoleculePreparation)	loadHostFile() (in AutoDockHosts)
LE_coords (in AutoDockTools.Utilities24.compute_rms_between_methods)	ligAts (in AutoDockTools.Utilities24.summarize_wcg_docking)	local_search_list (in AutoDockTools.DockingParameters)
lib_parameter_file_writer (in AutoDockTools)	ligMol (in AutoDockTools.Utilities24.summarize_wcg_docking)	local_search_list4 (in AutoDockTools.DockingParameters)
LibraryDpfWriter (in AutoDockTools.lib_parameter_file_writer)	limit_torsions() (in LigandPreparation)	local_search_list4_1 (in AutoDockTools.DockingParameters)
LibraryGpfWriter (in AutoDockTools.lib_parameter_file_writer)	limit_torsions() (in RotatableBondManager)	LonepairMerger (in AutoDockTools.atomTypeTools)
lig_non_std (in AutoDockTools.Utilities24.compute_AutoDock41_score)	limitTorsions() (in LigandMixin)	LPO (in AutoDockTools.Utilities24.prepare_ligand)
ligand (in AutoDockTools.Utilities24.compute_AutoDock41_score)	lines (in AutoDockTools.Utilities24.energy_average_maps)	LPO (in AutoDockTools.Utilities24.prepare_ligand4)
ligand_dict_filename (in AutoDockTools.Utilities24.prepare_ligand_dict)	lines (in AutoDockTools.Utilities24.write_largest_cluster_ligand)	LS (in AutoDockTools.autodpfCommands)
ligand_filename (in AutoDockTools.Utilities24.dpf3_to_dpf4)	lines (in AutoDockTools.Utilities24.write_lowest_energy_ligand)	LSGUI (in AutoDockTools.autodpfCommands)
ligand_filename (in AutoDockTools.Utilities24.gpf3_to_gpf4)	list_filename (in AutoDockTools.Utilities24.prepare_gpf)

M

m (in AutoDockTools.MoleculePreparation)	markSph (in AutoDockTools.autotorsCommands)	mol (in AutoDockTools.Utilities24.prepare_ligand4)
m (in AutoDockTools.atomTypeTools)	match() (in DlgParser)	mol (in AutoDockTools.Utilities24.prepare_receptor)
macroStem (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	match() (in XMLParser)	mol (in AutoDockTools.Utilities24.prepare_receptor4)
make_clustering() (in Clusterer)	materials (in AutoDockTools.autogpfCommands)	mol (in AutoDockTools.Utilities24.repair_ligand4)
make_clusters() (in Cluster_AD)	maxBound() (in AutoDockTools.interactiveHistogramGraph)	mol (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)
make_covalentmap_string() (in GridParameters)	MAXTORS (in AutoDockTools.autotorsCommands)	MoleculePreparation (in AutoDockTools)
make_covalentmap_string() (in GridParameters)	maxval (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	mols (in AutoDockTools.Utilities24.pdbq_to_pdbqt)
make_hierarchical_clustering() (in Clusterer)	menuText (in AutoDockTools.autoanalyzeCommands)	mols (in AutoDockTools.Utilities24.pdbqs_to_pdbqt)
make_intnbp_r_eps_string() (in DockingParameters)	menuText (in AutoDockTools.autodpfCommands)	mols (in AutoDockTools.Utilities24.pdbqt_to_pdb)
make_intnbp_r_eps_string() (in GridParameters)	menuText (in AutoDockTools.autoflexCommands)	mols (in AutoDockTools.Utilities24.pdbqt_to_pdbq)
make_intnbp_r_eps_string() (in GridParameters)	menuText (in AutoDockTools.autogpfCommands)	mols (in AutoDockTools.Utilities24.pdbqt_to_pdbqs)
make_map_string() (in DockingParameters)	menuText (in AutoDockTools.autopilotCommands)	mols (in AutoDockTools.Utilities24.prepare_ligand)
make_map_string() (in GridParameters)	menuText (in AutoDockTools.autostartCommands)	mols (in AutoDockTools.Utilities24.prepare_ligand4)
make_map_string() (in GridParameters)	menuText (in AutoDockTools.autotorsCommands)	mols (in AutoDockTools.Utilities24.prepare_receptor)
make_param_string() (in DockingParameters)	MergeLonePairs (in AutoDockTools.VisionInterface.AdtNodes)	mols (in AutoDockTools.Utilities24.prepare_receptor4)
make_param_string() (in GridParameters)	mergeLPS() (in LonepairMerger)	mouse1DownCanvas() (in InteractiveGraphBuilder)
make_param_string() (in GridParameters)	MergeNonPolarHydrogens (in AutoDockTools.VisionInterface.AdtNodes)	mouse2DownCanvas() (in InteractiveGraphBuilder)
make_sol_par_string() (in GridParameters)	mergeNPHS() (in LigandMixin)	MouseDown() (in ADDrawHistogram)
MakeAutoDockCLUSTERING (in AutoDockTools.autoanalyzeCommands)	mergeNPHS() (in NonpolarHydrogenMerger)	MouseUp() (in ADDrawHistogram)
MakeAutoDockCLUSTERINGGUI (in AutoDockTools.autoanalyzeCommands)	messages (in AutoDockTools.autogpfCommands)	mRequiredSynonyms (in Docking)
MakeAutoDockSubsetCLUSTERING (in AutoDockTools.autoanalyzeCommands)	minBound() (in AutoDockTools.interactiveHistogramGraph)	mRequiredTypes (in Docking)
MakeAutoDockSubsetCLUSTERINGGUI (in AutoDockTools.autoanalyzeCommands)	minval (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	ms (in AutoDockTools.Utilities24.compute_AutoDock41_score)
makeEditMenu() (in InteractiveGraphBuilder)	MixIn() (in AutoDockTools.LigandMixin)	ms (in AutoDockTools.Utilities24.summarize_results)
makeFileMenu() (in InteractiveGraphBuilder)	mode (in AutoDockTools.Utilities24.compute_AutoDock41_score)	ms (in AutoDockTools.Utilities24.summarize_wcg_docking)
makeIfdEntry() (in ADMacroLigandChart)	mode (in AutoDockTools.Utilities24.prepare_ligand)	myCallback() (in Add_SolvationParameters)
makeIfdLabelButton() (in ADMacroLigandChart)	mode (in AutoDockTools.Utilities24.prepare_ligand4)	myCallback() (in AdtPrepareDpf3)
makeJF() (in AutoStarter)	mode (in AutoDockTools.Utilities24.prepare_receptor)	myCallback() (in AdtPrepareDpf4)
makeJobFile() (in AutoDockStarter)	mode (in AutoDockTools.Utilities24.prepare_receptor4)	myCallback() (in AdtPrepareGpf3)
makeJobFile() (in AutoStarter)	mode (in AutoDockTools.Utilities24.summarize_results)	myCallback() (in AdtPrepareGpf4)
makeModel() (in DlgParser)	mode (in AutoDockTools.Utilities24.summarize_results4)	myCallback() (in Assign_AD4Types)
makeModels() (in DlgParser)	mode (in AutoDockTools.Utilities24.summarize_wcg_docking)	myCallback() (in Ligand_Writer)
MakeRef_cb() (in ConformationPlayer)	ModelDockingChooser (in AutoDockTools.autoanalyzeCommands)	myCallback() (in Ligand_Writer_AD4)
MakeRef_cb() (in StatesPlayerWidget)	modlib (in AutoDockTools)	myCallback() (in ManageAromaticCarbons)
ManageAromaticCarbons (in AutoDockTools.VisionInterface.AdtNodes)	modlist (in AutoDockTools.modlib)	myCallback() (in ManageRotatableBonds)
ManageRotatableBonds (in AutoDockTools.VisionInterface.AdtNodes)	mol (in AutoDockTools.Utilities24.pdbq_to_pdbqt)	myCallback() (in MergeLonePairs)
map_stem (in AutoDockTools.Utilities24.energy_average_maps)	mol (in AutoDockTools.Utilities24.pdbqs_to_pdbqt)	myCallback() (in MergeNonPolarHydrogens)
MAPS (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	mol (in AutoDockTools.Utilities24.pdbqt_to_pdb)	myCallback() (in RemoveWaters)
maps (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	mol (in AutoDockTools.Utilities24.pdbqt_to_pdbq)	myxview() (in InteractiveGraphBuilder)
MarkRoot (in AutoDockTools.autotorsCommands)	mol (in AutoDockTools.Utilities24.pdbqt_to_pdbqs)	myyview() (in InteractiveGraphBuilder)
MarkRootGUI (in AutoDockTools.autotorsCommands)	mol (in AutoDockTools.Utilities24.prepare_ligand)

N

N (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	new_write_map_nbp() (in GridParameters)	num_clusters (in AutoDockTools.Utilities24.summarize_results4)
nameA() (in AF_ProcessResidues)	nextFrame() (in ConformationPlayer)	num_hbonds (in AutoDockTools.Utilities24.summarize_results)
nameAromatics() (in LigandMixin)	nodeList (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)	num_hbonds (in AutoDockTools.Utilities24.summarize_wcg_docking)
nbcr_sdsc_edu_opal_types (in AutoDockTools.AppService_services_types)	nodeList (in AutoDockTools.interactiveHistogramGraph)	num_pts (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)
nbenergy() (in EnergyCalculator)	non_std_types (in AutoDockTools.Utilities24.compute_AutoDock41_score)	Numeric
new_dpo (in AutoDockTools.DockingParameters)	NONCRITICAL_DEPENDENCIES (in AutoDockTools)	nxpts (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)
new_fn (in AutoDockTools.Utilities24.energy_average_maps)	NonpolarHydrogenMerger (in AutoDockTools.atomTypeTools)	nypts (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)
new_gpo (in AutoDockTools.GridParameters_AD4)	norm_maps (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)	nzpts (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)
new_read() (in GridParameters)	normalize() (in Histogram)
new_write() (in GridParameters)	npts (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)

O

Objects (in AutoDockTools)	onAddCmdToViewer() (in Gpf4FlexResReader)	onRemoveObjectFromViewer() (in ADReadMacro)
oh (in AutoDockTools.Utilities24.summarize_docking_directory)	onAddCmdToViewer() (in Gpf4InitLigand)	onRemoveObjectFromViewer() (in ADShowBindingSite)
OK_cb() (in MakeAutoDockCLUSTERING)	onAddCmdToViewer() (in Gpf4LigReader)	onRemoveObjectFromViewer() (in MakeAutoDockSubsetCLUSTERING)
OK_cb() (in MakeAutoDockSubsetCLUSTERING)	onAddCmdToViewer() (in Gpf4LigandChooser)	onRemoveObjectFromViewer() (in ReadAutoDockStates)
ol (in AutoDockTools.Utilities24.summarize_docking_directory)	onAddCmdToViewer() (in Gpf4MacroChooser)	onRemoveObjectFromViewer() (in ShowAutoDockClusteringStates)
onAddCmdToViewer() (in ADDeleteDLG)	onAddCmdToViewer() (in Gpf4MacroInit)	onRemoveObjectFromViewer() (in ShowAutoDockStatesBaseCmd)
onAddCmdToViewer() (in ADDockingChooser)	onAddCmdToViewer() (in Gpf4MacroReader)	onRemoveObjectFromViewer() (in ShowAutoDockStatesHISTOGRAM)
onAddCmdToViewer() (in ADDrawHistogram)	onAddCmdToViewer() (in Gpf4ParameterFileSelector)	onRemoveObjectFromViewer() (in WriteAutoDockClustering)
onAddCmdToViewer() (in ADEPDBMol)	onAddCmdToViewer() (in Gpf4SetMapTypes)	onRemoveObjectFromViewer() (in Dpf4InitLigand)
onAddCmdToViewer() (in ADGetDLG)	onAddCmdToViewer() (in Gpf4Writer)	onRemoveObjectFromViewer() (in DpfInitLigand)
onAddCmdToViewer() (in ADMacroLigandChart)	onAddCmdToViewer() (in GpfAddSol)	onRemoveObjectFromViewer() (in AF_MacroChooser)
onAddCmdToViewer() (in ADMakeAllGrids)	onAddCmdToViewer() (in GpfEditor)	onRemoveObjectFromViewer() (in AF_MacroReader)
onAddCmdToViewer() (in ADReadMacro)	onAddCmdToViewer() (in GpfInitLigand)	onRemoveObjectFromViewer() (in Gpf4MacroInit)
onAddCmdToViewer() (in ADSeeSpots)	onAddCmdToViewer() (in GpfLigReader)	onRemoveObjectFromViewer() (in GpfMacroInit)
onAddCmdToViewer() (in ADSelectDLG)	onAddCmdToViewer() (in GpfLigandChooser)	onRemoveObjectFromViewer() (in AutoAutoTors)
onAddCmdToViewer() (in ADShowBindingSite)	onAddCmdToViewer() (in GpfLoadDefaults)	onRemoveObjectFromViewer() (in DefiningRotatableBonds)
onAddCmdToViewer() (in ShowAutoDockStatesBaseCmd)	onAddCmdToViewer() (in GpfMacroChooser)	onRemoveObjectFromViewer() (in SetTorsionNumberGUICommand)
onAddCmdToViewer() (in WriteAutoDockClustering)	onAddCmdToViewer() (in GpfMacroInit)	onRemoveObjectFromViewer() (in TogglerootSphere)
onAddCmdToViewer() (in WriteAutoDockStates)	onAddCmdToViewer() (in GpfMacroReader)	onRemoveObjectFromViewer() (in PyADCalcClosestPairs)
onAddCmdToViewer() (in Dpf4ClusterWriter)	onAddCmdToViewer() (in GpfMergeNonPolarHs)	onRemoveObjFromViewer() (in Dpf4MacroSelector)
onAddCmdToViewer() (in Dpf4FlexResSelector)	onAddCmdToViewer() (in GpfSetGpo)	onRemoveObjFromViewer() (in DpfMacroChooser)
onAddCmdToViewer() (in Dpf4GALSWriter)	onAddCmdToViewer() (in GpfWriter)	opalFaultOutput_Dec (in nbcr_sdsc_edu_opal_types)
onAddCmdToViewer() (in Dpf4GAWriter)	onAddCmdToViewer() (in SelectCenter)	openOtherMM() (in ADShowBindingSite)
onAddCmdToViewer() (in Dpf4InitLigand)	onAddCmdToViewer() (in SetBoxParameters)	optr (in AutoDockTools.Utilities24.compute_AutoDock41_score)
onAddCmdToViewer() (in Dpf4LSWriter)	onAddCmdToViewer() (in SetMapTypes)	optr (in AutoDockTools.Utilities24.energy_average_maps)
onAddCmdToViewer() (in Dpf4LigPDBQReader)	onAddCmdToViewer() (in SetOtherOptions)	ostr (in AutoDockTools.Utilities24.compute_AutoDock41_score)
onAddCmdToViewer() (in Dpf4LigandChooser)	onAddCmdToViewer() (in SetUpCovalentMap)	ostr (in AutoDockTools.Utilities24.compute_rms_between_methods)
onAddCmdToViewer() (in Dpf4MacroChooser)	onAddCmdToViewer() (in ADpilot_Cluster)	ostr (in AutoDockTools.Utilities24.summarize_results)
onAddCmdToViewer() (in Dpf4MacroSelector)	onAddCmdToViewer() (in ADpilot_ClusterGUICommand)	ostr (in AutoDockTools.Utilities24.summarize_results4)
onAddCmdToViewer() (in Dpf4SAWriter)	onAddCmdToViewer() (in ADpilot_Template)	ostr (in AutoDockTools.Utilities24.summarize_time)
onAddCmdToViewer() (in DpfClusterWriter)	onAddCmdToViewer() (in ADpilot_TemplateGUICommand)	ostr (in AutoDockTools.Utilities24.summarize_wcg_docking)
onAddCmdToViewer() (in DpfEditor)	onAddCmdToViewer() (in ADProcessManager)	output_filename (in AutoDockTools.Utilities24.summarize_docking_directory)
onAddCmdToViewer() (in DpfGALSWriter)	onAddCmdToViewer() (in AutoStarter)	output_filepath (in AutoDockTools.Utilities24.summarize_docking_directory)
onAddCmdToViewer() (in DpfGAWriter)	onAddCmdToViewer() (in AUTOTORS4Writer)	output_fileptr (in AutoDockTools.Utilities24.summarize_docking_directory)
onAddCmdToViewer() (in DpfInitLigand)	onAddCmdToViewer() (in AUTOTORSWriter)	output_gpf_filename (in AutoDockTools.Utilities24.prepare_gpf)
onAddCmdToViewer() (in DpfLSWriter)	onAddCmdToViewer() (in Ators4MoleculeChooser)	output_gpf_filename (in AutoDockTools.Utilities24.prepare_gpf4)
onAddCmdToViewer() (in DpfLigPDBQReader)	onAddCmdToViewer() (in Ators4Reader)	output_stem (in AutoDockTools.Utilities24.write_all_complexes)
onAddCmdToViewer() (in DpfLigandChooser)	onAddCmdToViewer() (in AtorsMoleculeChooser)	outputfilename (in AutoDockTools.Utilities24.compute_AutoDock41_score)
onAddCmdToViewer() (in DpfLoadDefaults)	onAddCmdToViewer() (in AtorsReader)	outputfilename (in AutoDockTools.Utilities24.compute_consensus_maps_from_dlgs)
onAddCmdToViewer() (in DpfMacroChooser)	onAddCmdToViewer() (in AtorsRefWriter)	outputfilename (in AutoDockTools.Utilities24.compute_rms_between_methods)
onAddCmdToViewer() (in DpfMacroSelector)	onAddCmdToViewer() (in AutoAutoTors)	outputfilename (in AutoDockTools.Utilities24.dpf3_to_dpf4)
onAddCmdToViewer() (in DpfSAWriter)	onAddCmdToViewer() (in ChangeAromaticCutOff)	outputfilename (in AutoDockTools.Utilities24.gpf3_to_gpf4)
onAddCmdToViewer() (in DpfSetDpo)	onAddCmdToViewer() (in CheckAromatic)	outputfilename (in AutoDockTools.Utilities24.gpf4_to_gpf3)
onAddCmdToViewer() (in AF_EditHinge)	onAddCmdToViewer() (in MarkRoot)	outputfilename (in AutoDockTools.Utilities24.prepare_ligand)
onAddCmdToViewer() (in AF_FlexFileWriter)	onAddCmdToViewer() (in SelectRoot)	outputfilename (in AutoDockTools.Utilities24.prepare_ligand4)
onAddCmdToViewer() (in AF_LigandDirectoryWriter)	onAddCmdToViewer() (in SetCarbonNames)	outputfilename (in AutoDockTools.Utilities24.prepare_receptor)
onAddCmdToViewer() (in AF_MacroReader)	onAddCmdToViewer() (in SetRotatableBonds)	outputfilename (in AutoDockTools.Utilities24.prepare_receptor4)
onAddCmdToViewer() (in AF_ProcessHingeResidues)	onAddCmdToViewer() (in SetTorsionNumberGUICommand)	outputfilename (in AutoDockTools.Utilities24.repair_ligand4)
onAddCmdToViewer() (in AF_ProcessResidues)	onAddCmdToViewer() (in PyADCalcAD3Energies)	outputfilename (in AutoDockTools.Utilities24.summarize_results)
onAddCmdToViewer() (in AF_RigidFileWriter)	onAddCmdToViewer() (in PyADCalcClosestPairs)	outputfilename (in AutoDockTools.Utilities24.summarize_results4)
onAddCmdToViewer() (in AF_SelectResidues)	onAddCmdToViewer() (in PyADCalcVDWEnergies)	outputfilename (in AutoDockTools.Utilities24.summarize_time)
onAddCmdToViewer() (in AF_SetBondRotatableFlag)	onPick() (in ClusterDockingChooser)	outputfilename (in AutoDockTools.Utilities24.summarize_wcg_docking)
onAddCmdToViewer() (in AF_SetHinge)	onPick() (in ModelDockingChooser)	outputfilename (in AutoDockTools.Utilities24.write_clustering_histogram_postscript)
onAddCmdToViewer() (in AF_StepBack)	onPick() (in AF_MacroChooser)	outputfilename (in AutoDockTools.Utilities24.write_largest_cluster_ligand)
onAddCmdToViewer() (in CheckMacroAtomTypes)	onPick() (in Ators4MoleculeChooser)	outputfilename (in AutoDockTools.Utilities24.write_lowest_energy_ligand)
onAddCmdToViewer() (in DefineNewAtomParms)	onPick() (in AtorsMoleculeChooser)	OutputFileType_Def (in nbcr_sdsc_edu_opal_types)
onAddCmdToViewer() (in Gpf4FlexResChooser)	onRemoveObjectFromViewer() (in ADGetDLG)	OutputsByNameInputType_Def (in nbcr_sdsc_edu_opal_types)

P

p (in AutoDockTools.Utilities24.summarize_time)	Play_cb() (in StatesPlayerWidget)	print_macro_residue_contacts() (in ADShowBindingSite)
p (in AutoDockTools.Utilities24.summarize_wcg_docking)	PlayRev_cb() (in StatesPlayerWidget)