Index

A

Aborted OESystem::OEConsoleProgressTracer OESystem::OETracerBase AbsPath OEPlatform::OEFile Acquire OEPlatform::OECondition OEPlatform::OEMutex OEPlatform::OESpinlock OEPlatform::OETryMutex AdaptGrad OEMolPotential::OEInterAdaptor OEMolPotential::OEQuatAdaptor OEMolPotential::OESubsetAdaptor OEMolPotential::OETorAdaptor OEMolPotential::OETorQuatAdaptor AdaptHessian OEMolPotential::OESubsetAdaptor AdaptHostCoords OEFF::OEComplexFF OEMolPotential::OEInterMolFunc1 AdaptVar OEOpt::OEAdaptor Add OEChem::OEAtomBondSet OEChem::OEIsMember OEChem::OEIsMemberPtr OEChem::OEMolPropertyList OEChem::OEVectorBindings AddAlias OESystem::OEParameter AddAtom OEBio::OEInteractionHintFragment OEChem::OEAtomBondSet OEChem::OEConfBase OEChem::OEGroupBase AddAtoms OEChem::OEAtomBondSet AddBaseData OESystem::OEBase AddBond OEChem::OEAtomBase OEChem::OEAtomBondSet OEChem::OEConfBase OEChem::OEGroupBase AddBonds OEChem::OEAtomBondSet AddChild OESystem::OEAnnotation AddCofactorCode OESpruce::OEDesignUnitSplitOptions AddColorer OEShape::OEColorForceField AddColorGaussian OEShape::OEShapeQuery AddConstMol OEMedChem::OEMCSFragDatabase AddConstraint OEChem::OECliqueSearch OEChem::OEMCSSearch OEChem::OESubSearch AddCurveSegment OEDepict::OE2DPath AddCutoff OEShape::OEROCSOptions AddData OESystem::OEBase AddDefault OESystem::OETypedParameter AddDetail OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter AddExcipientCode OESpruce::OEDesignUnitSplitOptions AddFeature OEBio::OEReceptorCustomConstraints OEDocking::OECustomConstraints AddFlexibleResidue OESz::OESzybkiProteinOptions AddFP OEGraphSim::OEFPDatabase AddFrag OEConfGen::OEMakeFragLib AddFragLib OEConfGen::OEBuilderBase OEConfGen::OEOmega AddGaussian OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase AddHeterogenMetadata OESpruce::OEStructureMetadata AddHistory OESystem::OEHeader AddIllegalRange OESystem::OEParameter AddIllegalValue OESystem::OEParameter AddIndexedMol OEMedChem::OECreateMMPIndexStatus AddInteraction OEShape::OEColorForceField AddInterface OESystem::OEInterface AddKeyword OESpruce::OEStructureMetadata AddKeywords OESpruce::OEStructureMetadata AddLabel OEGrapheme::OEColorGradientDisplayOptions AddLegalEntry OESystem::OEMultiParameter AddLegalRange OESystem::OEParameter AddLegalValue OESystem::OEParameter AddLigandName OEBio::OEMolComplexCategorizer AddLineSegment OEDepict::OE2DPath AddLipidCode OESpruce::OEDesignUnitSplitOptions AddMarkedValue OEGrapheme::OEColorGradientDisplayOptions AddMarkedValues OEGrapheme::OEColorGradientDisplayOptions AddMatchedPair OEMedChem::OEMatchedPairTransform AddMol OEFastROCS::OEShapeDatabase OEMedChem::OEMCSFragDatabase OEMedChem::OEMatchedPairAnalyzer AddMolecule OEBio::OEInteractionHintContainer OEGrapheme::OERamachandranPlot OEShape::OEROCS AddMolFunc OEMolPotential::OEGenericFF OEMolPotential::OEGenericFF2 AddMutation OESpruce::OEDesignUnitMutationOptions AddNewSphere OEBio::OEReceptorConstraintFeature AddNormalizationRule OEMolProp::OEFilter AddOption OESystem::OEOptions AddPair OEChem::OEMatch AddParameter OESystem::OEInterface OESystem::OEOptions AddParameterSuffix OESystem::OEOptions AddProteinConstraint OEBio::OEReceptor

AddRamachandran OEGrapheme::OERamachandranPlot AddReceptor OEDocking::OEPosit AddRings OEChem::OE2DRingDictionary AddRole OESystem::OERoleSet AddSample OEGraphSim::OEFPHistogram OEGraphSim::OEFPVariogram AddScore OEShape::OEBestOverlayResults OEShape::OEROCSResult AddSDData OEMedChem::OEMatchedPair AddSequenceMetadata OESpruce::OEStructureMetadata AddShapeGaussian OEShape::OEShapeQuery AddSiteResidue OESpruce::OESuperpositionOptions AddSmarts OEBio::OEReceptorConstraintFeature OEDocking::OEFeature AddSphere OEDocking::OEFeature AddStartingMaterial OEChem::OELibraryGen AddStartPoint OEDepict::OE2DPath AddStop OESystem::OEColorGradientBase addstream OEPlatform::oemultiostream AddStringDefault OESystem::OEConstParameter OESystem::OEParameter AddStringValue OESystem::OEParameter AddSVGClass OEDepict::OESVGGroup AddTautomer OESpruce::OEHeterogenMetadata AddTautomers OESpruce::OEHeterogenMetadata AddToDB OEBio::OEResidueCategoryData AddTorsionLibrary OEConfGen::OETorLib AddTorsionRule OEConfGen::OETorLib AddType OEShape::OEColorForceField AddUnindexedMol OEMedChem::OECreateMMPIndexStatus AddValue OESystem::OETypedParameter AIER Alignment AllInDB OEBio::OEResidueCategoryData Alternate Locations AltLoc AltConf OEAltLocationFactory anisou.java Example Code AnnotatePose OEDocking::OEDock OEDocking::OEScore append OEPlatform::oeofstream appendringdict.java Example Code ApplyCharges OEProton::OEDesignUnitCharges aromatic ring system identification asisstartsexample.java Example Code, [1] AsRegularGrid OESystem::OESkewGrid assigncharges.java Example Code assigncharges.txt Example Code Assignment operator OEMolPotential::OEBendPotential OEMolPotential::OECoulombPotential OEMolPotential::OEFFParams OEMolPotential::OEFFPotential OEMolPotential::OEInterCoulombPotential OEMolPotential::OEInterNonBondPotBase OEMolPotential::OEInterNonBondPotential OEMolPotential::OEInterVdwPotential OEMolPotential::OEInteractParams OEMolPotential::OENonBondIntcsOptions OEMolPotential::OENonBondPotBase OEMolPotential::OENonBondPotential OEMolPotential::OEOutOfPlanePotential OEMolPotential::OEStretchPotential OEMolPotential::OETorsionPotential OEMolPotential::OEVdwPotential atom aromaticity atom chirality atom connection atom degree atom heavy degree atom heavy valence atom name atom parent atom properties atom radius atom ring membership atom stereo atom type name atom valence atomic hybridization atomic number, [1] atomic symbol AtomMatch OEChem::OESubSearch

B

backbone.java Example Code bemismurckoperception.java Example Code besthit.java Example Code BestOverlay OEShape::OEMultiRefOverlay OEShape::OEOverlay bestshapeoverlay.java Example Code bestshapeoverlaymulticonfquery.java Example Code besttverskyshapeoverlay.java Example Code Beta Sheet bfactor2img.java Example Code bfactor2img.txt Example Code Bind OEPB::OEBind Biopolymer Residue BLOSUM62 bond aromaticity bond begin atom bond begin atom index

bond chirality bond end atom bond end atom index bond index bond order bond parent bond properties bond ring membership bond stereo, [1] bond type name boundentropy.java Example Code Broadcast OEPlatform::OECondition Bug-fix release Build OEConfGen::OEConformerBuilder OEConfGen::OEFragBuilder OEConfGen::OEMacrocycleBuilder OEConfGen::OEMacrocycleOmega OEConfGen::OEMolBuilder OEConfGen::OEOmega BuildExpressions OEChem::OEQMol OEChem::OEQMolBase building toolkit projects, [1], [2]

C

CacheScoringSetup OEDocking::OEDock OEDocking::OEScore CalcAM1 OEMolAM1::OEAM1 OEMolAM1::OEOptimizedAM1 CalcAtomPotentials OEPB::OEZap calcet.java Example Code CalcForces OEPB::OEZap CalcPotentialGrid OEPB::OEZap CalcSolvationEnergy OEPB::OEZap CalculateRMSD OEChem::OEConfRMSD Cancel OEChem::OESubSearchResult canonical isomeric SMILES, [1] canonical SMILES, [1] cansmi.java Example Code catmols.java Example Code CheckAtomTypes OESzmap::OESzmapEngine CheckCharges OEProton::OEChargeEngineBase chemblsolubility.java Example Code chiral atom chiral bond CIP Classification Clear OEBio::OEDesignUnit OEBio::OEIridiumData OEBio::OEReceptor OEBio::OEReceptorCustomConstraints OEBio::OESequenceAlignment OEBio::OEStructureQuality OEChem::OEAtomBase OEChem::OEAtomBondSet OEChem::OEBondBase OEChem::OECSVHeader OEChem::OEGroupBase OEChem::OEMatch OEChem::OEMatchBase OEChem::OEMolBase OEChem::OEMolDatabase OEChem::OEMolPropertyList OEChem::OETrans OEDepict::OEAlignmentResult OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame OEDocking::OECustomConstraints OEMolPotential::OEInteractParams OEMolPotential::OEMolFunc OEShape::OEBestOverlayResults OEShape::OEColorForceField OEShape::OEShapeQuery OESpicoli::OESurface OESystem::OEBase OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase OESystem::OEGrid OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OEInterface OESystem::OEMultiGrid OESystem::OEOptions OESystem::OEScalarGrid OESystem::OESkewGrid OESz::OESzybkiResults OESzmap::OESzmapResults clear OEPlatform::oeisstream OEPlatform::oeistdstream OEPlatform::oeiwrapperstream OEPlatform::oemultiostream OEPlatform::oeosstream OEPlatform::oeostdstream OEPlatform::oeowrapperstream ClearAtoms OEChem::OEAtomBondSet ClearAtomsAndBonds OEChem::OEAtomBondSet ClearBase OEChem::OEMCMolBase OEChem::OEMol OEChem::OEMolBase ClearBits OESystem::OEBitVector ClearBonds OEChem::OEAtomBondSet ClearBoxRange OEGrapheme::OEColorGradientDisplayOptions ClearCofactorCodes OESpruce::OEDesignUnitSplitOptions ClearColorForceField OEShape::OEBestOverlay ClearColorGaussians OEShape::OEShapeQuery ClearConstraints OEChem::OECliqueSearch OEChem::OEMCSSearch OEChem::OESubSearch ClearCoords OEChem::OEConfBase OEChem::OEMolBase ClearCSVHeader OEChem::oemolstreambase ClearCustomConstraints OEBio::OEReceptor ClearCutoff OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions ClearCutoffs OEShape::OEROCSOptions ClearDBCategory OEBio::OEResidueCategoryData ClearDefaults OESystem::OEParameter ClearExcipientCodes OESpruce::OEDesignUnitSplitOptions ClearFixAtoms OESz::OESzybki ClearFlexibleResidues OESz::OESzybkiProteinOptions ClearFocusTarget OEPB::OEZap ClearFragLibs OEConfGen::OEBuilderBase OEConfGen::OEOmega ClearHarmonicConstraints OESz::OESzybki ClearHeterogenMetadata OESpruce::OEStructureMetadata ClearIndexableFragmentRange OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMatchedPairAnalyzerOptions ClearIndexedMols OEMedChem::OEMCSFragDatabase ClearInteractions OEShape::OEColorForceField ClearKeywords OESpruce::OEStructureMetadata ClearLabels OEGrapheme::OEColorGradientDisplayOptions ClearLigandConstraints OESpruce::OESuperpositionOptions ClearLigandSubSearch OEBio::OEMolComplexCategorizer ClearLipidCodes OESpruce::OEDesignUnitSplitOptions ClearMarkedValues OEGrapheme::OEColorGradientDisplayOptions ClearMCMol OEChem::OEMCMolBase OEChem::OEMol ClearMolBase OEChem::OEMCMolBase OEChem::OEMol ClearMolecule OEShape::OEShapeQuery ClearMolecules OEShape::OEROCS ClearMutations OESpruce::OEDesignUnitMutationOptions ClearNormalizationRules OEMolProp::OEFilter ClearPredicates OEMolPotential::OEMolFunc ClearProteinConstraint OEBio::OEReceptor ClearProteinConstraints OEBio::OEReceptor ClearQuerySurfaceArcFxn OEGrapheme::OEColorOverlapDisplayOptions OEGrapheme::OEShapeOverlapDisplayOptions ClearReceptor OEBio::OEDesignUnit ClearReceptors OEDocking::OEPosit ClearRoles OESystem::OERoleSet

ClearSDData OEMedChem::OEMatchedPair ClearSequenceMetadata OESpruce::OEStructureMetadata ClearShapeGaussians OEShape::OEShapeQuery ClearShapeGrid OEShape::OEShapeQuery ClearSiteResidues OESpruce::OESuperpositionOptions ClearSmarts OEBio::OEReceptorConstraintFeature OEDocking::OEFeature ClearSpheres OEBio::OEReceptorConstraintFeature OEDocking::OEFeature ClearStartingMaterial OEChem::OELibraryGen ClearStartPoints OEShape::OECartesianStarts ClearStarts OEShape::OEQuatStarts ClearSurfaceArcFxn OEGrapheme::OEShapeQueryDisplayOptions ClearTautomers OESpruce::OEHeterogenMetadata ClearTorsionConstraint OESz::OESzybki ClearTorsionLibrary OEConfGen::OETorLib ClearTracer OEFastROCS::OEShapeDatabaseOptions ClearUserStarts OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay ClearValues OESystem::OEParameter ClearVertexClique OESpicoli::OESurface cliquealign.java Example Code Close OEPlatform::OEDirectoryScan close OEChem::oemolistream OEChem::oemolithread OEChem::oemolostream OEChem::oemolothread OEChem::oemolstreambase OEPlatform::oeistream OEPlatform::oeostream ClusterHasBadClash OEBio::OEPlaceHydrogensDetails CMake, [1], [2], [3] coloroptimizationexample.java Example Code coloroverlap.java Example Code ColorScore OEShape::OEColorOverlap colorscore.java Example Code CombineMols OEChem::OEAbsCanonicalConfTest OEChem::OEAbsoluteConfTest OEChem::OEConfTestBase OEChem::OEDefaultConfTest OEChem::OEIsomericConfTest OEChem::OEOmegaConfTest Command Line command line options parsing CompareMols OEChem::OEAbsCanonicalConfTest OEChem::OEAbsoluteConfTest OEChem::OEConfTestBase OEChem::OEDefaultConfTest OEChem::OEIsomericConfTest OEChem::OEOmegaConfTest compiler complex2img.java Example Code complex2img.txt Example Code Compress OEChem::OEMolBase OEChem::OETrans configure, [1] configure.bat, [1] connected components identification ConstraintsMet OESpruce::OEStructuralSuperposition Constructor OEBio::OEReceptor OEBio::OEReceptorConstraintFeature OEDocking::OEDock OEDocking::OEDockOptions OEDocking::OEHybrid OEDocking::OEMakeReceptorOptions OEDocking::OEPoseOptimizer OEDocking::OEPoseOptimizerOptions OEDocking::OEPosit OEDocking::OEPositOptions OEDocking::OEScore OEGraphSim::OESimSearchResult OEMath::OESphere OESz::OEFixedProteinLigandOptimizer OESz::OEFlexProteinLigandOptimizer OESz::OEProteinFlexOptions OESz::OEProteinLigandOptOptions Constructors OEBio::OEAltGroup OEBio::OEAltLocation OEBio::OEAltLocationFactory OEBio::OEAltLocationState OEBio::OEAtomMatchResidue OEBio::OEAtomMatchResidueID OEBio::OECationPiInteractionHint OEBio::OEChelatorInteractionHint OEBio::OEClashInteractionHint OEBio::OEContactInteractionHint OEBio::OECovalentInteractionHint OEBio::OECrystalSymmetryParams OEBio::OEDesignUnit OEBio::OEHBondInteractionHint OEBio::OEHalogenBondInteractionHint OEBio::OEHasAlternateLocation OEBio::OEHasInteractionHint OEBio::OEHasInteractionHintType OEBio::OEHasPDBAtomIndex OEBio::OEHasResidueInteractionHint OEBio::OEHasSecondaryStructure OEBio::OEHierChain OEBio::OEHierFragment OEBio::OEHierResidue OEBio::OEHierView OEBio::OEInteractionHint OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintContainer OEBio::OEInteractionHintFragment OEBio::OEInteractionHintTypeBase OEBio::OEIridiumData OEBio::OEIsBackboneAtom OEBio::OEIsCTerminalAtom OEBio::OEIsCationPiInteractionHint OEBio::OEIsChelatorInteractionHint OEBio::OEIsClashInteractionHint OEBio::OEIsContactInteractionHint OEBio::OEIsCovalentInteractionHint OEBio::OEIsDisulfideBond OEBio::OEIsHBondInteractionHint OEBio::OEIsHalogenBondInteractionHint OEBio::OEIsHetAtom OEBio::OEIsInterInteractionHint OEBio::OEIsIntermolecularChelatorInteractionHint OEBio::OEIsIntermolecularHBondInteractionHint OEBio::OEIsIntraInteractionHint OEBio::OEIsIntramolecularChelatorInteractionHint OEBio::OEIsIntramolecularHBondInteractionHint OEBio::OEIsNTerminalAtom OEBio::OEIsNonIdealHBondInteractionHint OEBio::OEIsSaltBridgeInteractionHint OEBio::OEIsStackingInteractionHint OEBio::OEIsUnpairedLigandInteractionHint OEBio::OEIsUnpairedProteinInteractionHint OEBio::OEIsWater OEBio::OELigandInteractionHintComponent OEBio::OEMolComplexCategorizer OEBio::OEMolComplexFilter OEBio::OEPerceiveInteractionOptions OEBio::OEPlaceHydrogensDetails OEBio::OEPlaceHydrogensMoverNote OEBio::OEPlaceHydrogensOptions OEBio::OEProteinInteractionHintComponent OEBio::OERamachandranAnalysis OEBio::OEReceptorCustomConstraints OEBio::OEResidueCategoryData OEBio::OESaltBridgeInteractionHint OEBio::OESequenceAlignment OEBio::OESplitMolComplexOptions OEBio::OEStackingInteractionHint OEBio::OEStructureQuality OEChem::OE2DRingDictionary OEChem::OE2DRingDictionaryCreatorOptions OEChem::OEAbsoluteConfTest OEChem::OEAnisoUij OEChem::OEAtomBondSet OEChem::OEAtomIsInResidue OEChem::OECSVHeader OEChem::OECliqueSearch OEChem::OEConfRMSD OEChem::OEConfRMSDOptions OEChem::OEConstCoords OEChem::OECoordArray OEChem::OECreateSubSearchDatabaseOptions OEChem::OEEuler OEChem::OEExprBase OEChem::OEExtractRingTemplateOptions OEChem::OEFileStringParameter OEChem::OEFuzzy OEChem::OEGetNbrAtom OEChem::OEGraphMol OEChem::OEHasAlphaBetaUnsat OEChem::OEHasAtomInGroup OEChem::OEHasAtomName OEChem::OEHasAtomStereoSpecified OEChem::OEHasAtomicNum OEChem::OEHasBondInGroup OEChem::OEHasBondStereoSpecified OEChem::OEHasChainID OEChem::OEHasFormalCharge OEChem::OEHasFragmentNumber OEChem::OEHasGroupType OEChem::OEHasHvyDegree OEChem::OEHasIdx OEChem::OEHasMapIdx OEChem::OEHasOrder OEChem::OEHasResidueNumber OEChem::OEHydrogenCounter OEChem::OEIdxSelected OEChem::OEInChIOptions OEChem::OEInSamePart OEChem::OEIsAtomHybridization OEChem::OEIsMDLStereoGroup OEChem::OEIsMember OEChem::OEIsMemberPtr OEChem::OEIsProductGroup OEChem::OEIsRGroup OEChem::OEIsReactantGroup OEChem::OEIsRotor OEChem::OEIsRxnComponentGroup OEChem::OEIsomericConfTest OEChem::OELibraryGen OEChem::OELingoSim OEChem::OEMCSMaxAtomsCompleteCycles OEChem::OEMCSMaxBondsCompleteCycles OEChem::OEMCSSearch OEChem::OEMMFFTypeResult OEChem::OEMatch OEChem::OEMatchFunc OEChem::OEMatchPair OEChem::OEMol OEChem::OEMolDBException OEChem::OEMolDatabase OEChem::OEMolDatabaseSaveOptions OEChem::OEMolGDPropertyFxn OEChem::OEMolParameter OEChem::OEMolPropertyList OEChem::OEMolReaderParameter OEChem::OEMolSDPropertyFxn OEChem::OEMolTaggedPropertyFxn OEChem::OEMolWriterParameter OEChem::OEMutableCoords OEChem::OENbrs OEChem::OENearestNbrs OEChem::OENthAtom OEChem::OEOmegaConfTest OEChem::OEOutFileStringParameter OEChem::OEParseSmilesOptions OEChem::OEPartPredT OEChem::OEPredicateParameter OEChem::OEQMol OEChem::OEQMolBase OEChem::OEQuaternion OEChem::OERefInputAppOptions OEChem::OEResidue OEChem::OERotMatrix OEChem::OESDDataPair OEChem::OESimilarByRMSD OEChem::OESimpleAppOptions OEChem::OESubSearch OEChem::OESubSearchDatabase OEChem::OESubSearchQuery OEChem::OESubSearchResult OEChem::OESubSearchScreen OEChem::OETorsion OEChem::OETrans OEChem::OETranslation OEChem::OEUnAtomPredParameter OEChem::OEUnBondPredParameter OEChem::OEUnaryToBinaryAnd OEChem::OEUnaryToBinaryOr OEChem::OEUniMolecularRxn OEChem::OEVectorBindings OEChem::oemolistream OEChem::oemolithread OEChem::oemolostream OEChem::oemolothread OEConfGen::OEConfFixOptions OEConfGen::OEConfSlicer OEConfGen::OEConformerBuilder OEConfGen::OEFlipperOptions OEConfGen::OEFragBuilder OEConfGen::OEFragBuilderOptions OEConfGen::OEFragOptions OEConfGen::OEMacrocycleBuilder OEConfGen::OEMacrocycleBuilderOptions OEConfGen::OEMacrocycleOmega OEConfGen::OEMacrocycleOmegaOptions OEConfGen::OEMakeFragLib OEConfGen::OEMolBuilder OEConfGen::OEMolBuilderOptions OEConfGen::OEOmega OEConfGen::OEOmegaOptions OEConfGen::OERingFragOptions OEConfGen::OESliceEnsembleOptions OEConfGen::OETorDriveOptions OEConfGen::OETorDriver OEConfGen::OETorLib OEConstr::OEHarmonicPotential OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay OEDepict::OE2DMolDisplay OEDepict::OE2DMolDisplayOptions OEDepict::OE2DPath OEDepict::OE2DPathPoint OEDepict::OE2DPoint OEDepict::OEAlignmentOptions OEDepict::OEAlignmentResult OEDepict::OEAtomSVGAtomIdxMarkup OEDepict::OEAtomSVGNoMarkup OEDepict::OEAtomSVGResidueMarkup OEDepict::OEBondSVGBondIdxMarkup OEDepict::OEBondSVGNoMarkup OEDepict::OEDisplayAtomIdx OEDepict::OEDisplayAtomMapIdx OEDepict::OEDisplayBondIdx OEDepict::OEDisplayNoAtomProp OEDepict::OEDisplayNoBondProp OEDepict::OEFont OEDepict::OEHighlightBase OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByColor OEDepict::OEHighlightByLasso OEDepict::OEHighlightByStick OEDepict::OEHighlightLabel OEDepict::OEHighlightOverlayBase OEDepict::OEHighlightOverlayByBallAndStick OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFileBase OEDepict::OEImageFileCreatorBase OEDepict::OEImageFrame OEDepict::OEImageGrid OEDepict::OEImageTable OEDepict::OEImageTableOptions OEDepict::OEJavaImageBase OEDepict::OELegendLayout OEDepict::OELegendLayoutOptions OEDepict::OEMultiPageImageFile OEDepict::OENearestAtom OEDepict::OENearestBond OEDepict::OEPen OEDepict::OEPrepareDepictionOptions OEDepict::OEReport OEDepict::OEReportOptions OEDepict::OESVGClass OEDepict::OESVGGroup OEDocking::OEBox OEDocking::OECustomConstraints OEDocking::OEPositResults OEDocking::OESinglePoseResult OEFF::OEComplexEnergies OEFF::OEComplexFF OEFF::OEComplexFFParameter OEFF::OEFF14SBParsley OEFF::OEFF14SBParsleyComplex OEFF::OEFF14SBParsleyParams OEFF::OEFF14SBSmirnoff OEFF::OEFF14SBSmirnoffComplex OEFF::OEFF14SBSmirnoffParams OEFF::OEForceFieldParameter OEFF::OEMMFFAmberComplex OEFF::OEMMFFComplex OEFF::OEMMFFIEFF OEFF::OEMMFFIEFFOptions OEFF::OEMMFFSheffield OEFF::OEMMFFSheffieldOptions OEFF::OESmirnoffComplex OEFastROCS::OEDBTracer OEFastROCS::OEFastROCSHistogram OEFastROCS::OEShapeDatabase OEFastROCS::OEShapeDatabaseOptions OEFastROCS::OEShapeDatabaseScore OEGraphSim::OECreateFastFPDatabaseOptions OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions OEGraphSim::OEFPHistogram OEGraphSim::OEFPPattern OEGraphSim::OEFPTypeBase OEGraphSim::OEFPTypeParams OEGraphSim::OEFPVariogram OEGraphSim::OEFastFPDatabase OEGraphSim::OEFastFPDatabaseParams OEGraphSim::OEFingerPrint OEGraphSim::OESimFuncBase OEGraphSim::OESimScore OEGraphSim::OESimScorePair OEGraphSim::OETanimotoSim OEGraphSim::OETverskySim OEGrapheme::OE2DActiveSiteDisplay OEGrapheme::OE2DActiveSiteDisplayOptions OEGrapheme::OE2DActiveSiteLegendDisplayOptions OEGrapheme::OE2DPropMap OEGrapheme::OEAlignedDepictionFrom3DOptions OEGrapheme::OEAlphaRainbowArcFxn OEGrapheme::OEAtomGlyphBase OEGrapheme::OEAtomGlyphCircle OEGrapheme::OEBondGlyphArrow OEGrapheme::OEBondGlyphBase OEGrapheme::OEBondGlyphCircle OEGrapheme::OEBondGlyphCross OEGrapheme::OEBondGlyphCurvedArrow OEGrapheme::OEBondGlyphScissors OEGrapheme::OEBondGlyphStitch OEGrapheme::OEBondGlyphZigZag OEGrapheme::OEBrickRoadArcFxn OEGrapheme::OECastleArcFxn OEGrapheme::OECogArcFxn OEGrapheme::OEColorForceFieldDisplay OEGrapheme::OEColorForceFieldLegendDisplayOptions OEGrapheme::OEColorGradientDisplayOptions OEGrapheme::OEColorGradientLabel OEGrapheme::OEColorOverlapDisplayOptions OEGrapheme::OEComplexSurfaceArcFxnBase OEGrapheme::OEDefaultArcFxn OEGrapheme::OEDefaultBuriedArcFxn OEGrapheme::OEDefaultCavityArcFxn OEGrapheme::OEDefaultSolventArcFxn OEGrapheme::OEDefaultVoidArcFxn OEGrapheme::OEDepictionFrom3DOptions OEGrapheme::OEEyelashArcFxn OEGrapheme::OEFlowerArcFxn OEGrapheme::OENearestResidue OEGrapheme::OENecklaceArcFxn OEGrapheme::OEOliveBranchArcFxn OEGrapheme::OEPearlsArcFxn OEGrapheme::OEPeptideDisplayOptions OEGrapheme::OEPlotMarker OEGrapheme::OERaceTrackArcFxn OEGrapheme::OERailroadTrackArcFxn OEGrapheme::OERamachandranPlot OEGrapheme::OEResidueSVGNoMarkup OEGrapheme::OEResidueSVGStandardMarkup OEGrapheme::OESawArcFxn OEGrapheme::OEShapeOverlapDisplay OEGrapheme::OEShapeOverlapDisplayOptions OEGrapheme::OEShapeQueryDisplay OEGrapheme::OEShapeQueryDisplayOptions OEGrapheme::OESimpsonArcFxn OEGrapheme::OEStitchArcFxn OEGrapheme::OESunArcFxn OEGrapheme::OESurfaceArc OEGrapheme::OEWreathArcFxn OEMath::OEBox OEMedChem::OEBemisMurckoOptions OEMedChem::OECreateMMPIndexOptions OEMedChem::OECreateMMPIndexStatus OEMedChem::OEMCSFragDatabase OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMCSMolSimScore OEMedChem::OEMCSSimFuncBase OEMedChem::OEMCSTanimotoSim OEMedChem::OEMCSTverskySim OEMedChem::OEMatchedPair OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMatchedPairTransform OEMedChem::OEMatchedPairTransformExtractOptions OEMolAM1::OEAM1 OEMolAM1::OEAM1Options OEMolAM1::OEAM1Results OEMolAM1::OEOptimizedAM1 OEMolMMFF::OEMMFF OEMolMMFF::OEMMFF94sParams OEMolMMFF::OEMMFFOutOfPlane OEMolMMFF::OEMMFFParams OEMolMMFF::OEMMFFStretchBend OEMolPotential::OEBendParams OEMolPotential::OEBendPotential OEMolPotential::OECoulombPotential OEMolPotential::OEFFParams OEMolPotential::OEFFPotential OEMolPotential::OEGenericFF OEMolPotential::OEGenericFF2 OEMolPotential::OEInterAdaptor OEMolPotential::OEInterCoulombPotential OEMolPotential::OEInterNonBondPotBase OEMolPotential::OEInterNonBondPotential OEMolPotential::OEInterVdwPotential OEMolPotential::OEInteractParams OEMolPotential::OEInteraction OEMolPotential::OENonBondIntcsOptions OEMolPotential::OENonBondPotBase OEMolPotential::OENonBondPotential OEMolPotential::OENumericMolFunc2 OEMolPotential::OEOutOfPlaneParams OEMolPotential::OEOutOfPlanePotential OEMolPotential::OEQuatAdaptor OEMolPotential::OEScaledMolFunc OEMolPotential::OEStretchParams OEMolPotential::OEStretchPotential OEMolPotential::OESubsetAdaptor OEMolPotential::OETorAdaptor OEMolPotential::OETorQuatAdaptor OEMolPotential::OETorsionParams OEMolPotential::OETorsionPotential OEMolPotential::OEVdwParams OEMolPotential::OEVdwPotential OEMolProp::OEFilter OEMolProp::OEXLogPResult OEMolSmirnoff::OEParsley OEMolSmirnoff::OEParsleyParams OEMolSmirnoff::OESmirnoff OEMolSmirnoff::OESmirnoffParams OEOpt::OEBFGSOpt OEOpt::OECGLineMinimize OEOpt::OEConjGradOpt OEOpt::OEDFPOpt OEOpt::OEFComponent OEOpt::OEFletcherReevesOpt OEOpt::OEHestenesStiefelOpt OEOpt::OEMaxStepLineMinimize OEOpt::OENRLineSearch OEOpt::OENewtonOpt OEOpt::OEQNLineMinimize OEOpt::OERibierePolakOpt OEOpt::OESteepestDescentOpt OEPB::OEArea OEPB::OEBind OEPB::OEBindResults OEPB::OEET OEPB::OESimpleBindResults OEPB::OEZap OEPlatform::OECondition OEPlatform::OEDirectoryScan OEPlatform::OEFile OEPlatform::OEHalfFloat OEPlatform::OELockCondition OEPlatform::OEMutex OEPlatform::OESpinlock OEPlatform::OEThread OEPlatform::OEThreadLocal OEPlatform::OETryMutex OEPlatform::oeifstream OEPlatform::oeigzstream OEPlatform::oeiofstream OEPlatform::oeisstream OEPlatform::oeistdstream OEPlatform::oeistream OEPlatform::oeiwrapperstream OEPlatform::oemultiostream OEPlatform::oeofstream OEPlatform::oeogzstream OEPlatform::oeosstream OEPlatform::oeostdstream OEPlatform::oeostream OEPlatform::oeowrapperstream OEPlatform::oestream OEProton::OEAM1BCCCharges OEProton::OEAM1BCCELF10Charges OEProton::OEAM1Charges OEProton::OEAmberFF94Charges OEProton::OEChargeEngineNoOp OEProton::OEChargeParameter OEProton::OEClearCharges OEProton::OECombineChargeEngines OEProton::OEDesignUnitCharges OEProton::OEELF OEProton::OEELFCharges OEProton::OEELFOptions OEProton::OEFormalChargeOptions OEProton::OEFormalToPartialCharges OEProton::OEGasteigerCharges OEProton::OEInitialCharges OEProton::OEMMFF94Charges OEProton::OESpreadMetalCharges OEProton::OETautomerMolFunction OEProton::OETautomerOptions OEProton::OETyperMolFunction OEShape::OEAnalyticColorFunc OEShape::OEAnalyticOptions OEShape::OEAnalyticShapeFunc OEShape::OEAsIsStarts OEShape::OEAtAtomStarts OEShape::OEBestOverlay OEShape::OEBestOverlayResults OEShape::OEBestOverlayScore OEShape::OECartesianStarts OEShape::OEColorForceField OEShape::OEColorOptions OEShape::OEColorOverlap OEShape::OEColorResults OEShape::OEColorTanimotoCutoff OEShape::OEExactColorFunc OEShape::OEExactShapeFunc OEShape::OEFitColorTverskyCutoff OEShape::OEFitTverskyComboCutoff OEShape::OEFitTverskyCutoff OEShape::OEGridColorFunc OEShape::OEGridShapeFunc OEShape::OEHermite OEShape::OEHermiteOptions OEShape::OEHermiteShapeFunc OEShape::OEHighestTverskyCombo OEShape::OEInertialStarts OEShape::OEIsColorAtomPred OEShape::OEMultiRefOverlay OEShape::OEOverlap OEShape::OEOverlapCutoff OEShape::OEOverlapFunc OEShape::OEOverlapPrep OEShape::OEOverlapResults OEShape::OEOverlay OEShape::OEOverlayOptions OEShape::OEQuatStarts OEShape::OEROCS OEShape::OEROCSOptions OEShape::OEROCSResult OEShape::OERandomStarts OEShape::OERefColorTverskyCutoff OEShape::OERefTverskyComboCutoff OEShape::OERefTverskyCutoff OEShape::OEShapeGridOptions OEShape::OEShapeOptions OEShape::OEShapeQuery OEShape::OEShapeQueryPublic OEShape::OESubrocsStarts OEShape::OETanimotoComboCutoff OEShape::OETanimotoCutoff OESheff::OESheffield OESheff::OESheffieldOptions OESpicoli::OESurface OESpruce::OEBioUnitExtractionOptions OESpruce::OECapBuilderOptions OESpruce::OEDesignUnitBuildOptions OESpruce::OEDesignUnitEnumerateSitesOptions OESpruce::OEDesignUnitMutationOptions OESpruce::OEDesignUnitPrepOptions OESpruce::OEDesignUnitSplitOptions OESpruce::OEHeterogenMetadata OESpruce::OEIsModeledAtom OESpruce::OELoopBuilderOptions OESpruce::OEMakeDesignUnitOptions OESpruce::OEPocket OESpruce::OEPocketOptions OESpruce::OEProtonateDesignUnitOptions OESpruce::OESecondaryStructureSuperposition OESpruce::OESequenceMetadata OESpruce::OESidechainBuilderOptions OESpruce::OEStructuralSuperposition OESpruce::OEStructureMetadata OESpruce::OESuperpositionOptions OESystem::OEAnd OESystem::OEAnnotation OESystem::OEBInitializer OESystem::OEBase OESystem::OEBaseData OESystem::OEBaseDataT OESystem::OEBinaryAnd OESystem::OEBinaryIOHandler OESystem::OEBinaryNot OESystem::OEBinaryOr OESystem::OEBitVector OESystem::OEBoolParameter OESystem::OEBoundedBuffer OESystem::OEColor OESystem::OEColorGradientBase OESystem::OEColorStop OESystem::OEConcatIter OESystem::OEConsoleProgressTracer OESystem::OEConstParameter OESystem::OEContainer OESystem::OECycleTimer OESystem::OEDots OESystem::OEDoubleParameter OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase OESystem::OEExponentColorGradient OESystem::OEExponentialColorGradient OESystem::OEFloatParameter OESystem::OEGaussian OESystem::OEGaussianContainer OESystem::OEGrid OESystem::OEHasRole OESystem::OEHeader OESystem::OEIntParameter OESystem::OEInterface OESystem::OEIter OESystem::OEIterBase OESystem::OELinearColorGradient OESystem::OELogarithmicColorGradient OESystem::OEMultiGrid OESystem::OEMultiParameter OESystem::OENot OESystem::OEOr OESystem::OEOwnedPtr OESystem::OEPredIter OESystem::OEProtectedBuffer OESystem::OERandom OESystem::OERole OESystem::OERoles OESystem::OEScalarGrid OESystem::OESharedPtr OESystem::OESkewGrid OESystem::OEStopwatch OESystem::OEStringParameter OESystem::OEThreadedDots OESystem::OEUIntParameter OESystem::OEUnboundedBuffer OESystem::OEUnownedPtr OESystem::OEWallTimer OESystem::oeprogressstream OESz::OEFreeFormConf OESz::OEFreeFormConfAdvanced OESz::OEFreeFormConfOptions OESz::OEFreeFormConfResults OESz::OEFreeFormSolvOptions OESz::OEFreeFormSolvResults OESz::OEProteinLigandOptResults OESz::OERestrictionEnergyResult OESz::OESingleConfResult OESz::OESzybki OESz::OESzybkiEnsembleResults OESz::OESzybkiGeneralOptions OESz::OESzybkiOptOptions OESz::OESzybkiOptions OESz::OESzybkiProteinOptions OESz::OESzybkiResults OESz::OESzybkiSolventOptions OESz::OETorsionScanOptions OESz::OETorsionScanResult OESzmap::OESzmapEngine OESzmap::OESzmapEngineOptions OESzmap::OESzmapResults convert.java Example Code Copy OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEPredIter CoreToMoleculeCount OEMedChem::OEMCSFragDatabase CoreToMolecules OEMedChem::OEMCSFragDatabase Cosine similarity measure Count OEChem::OEMolBase OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase CountBits OESystem::OEBitVector CountRangeBits OESystem::OEBitVector CPK CreateComplexCopy OEGrapheme::OEComplexSurfaceArcFxnBase CreateCopy OEBio::OEAtomMatchResidue OEBio::OECationPiInteractionHint OEBio::OEChelatorInteractionHint OEBio::OEClashInteractionHint OEBio::OEContactInteractionHint OEBio::OECovalentInteractionHint OEBio::OEDesignUnit OEBio::OEHBondInteractionHint OEBio::OEHalogenBondInteractionHint OEBio::OEHasAlternateLocation OEBio::OEHasInteractionHint OEBio::OEHasInteractionHintType OEBio::OEHasPDBAtomIndex OEBio::OEHasResidueInteractionHint OEBio::OEHasSecondaryStructure OEBio::OEInteractionHint OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintFragment OEBio::OEInteractionHintTypeBase OEBio::OEIsBackboneAtom OEBio::OEIsCTerminalAtom OEBio::OEIsCationPiInteractionHint OEBio::OEIsChelatorInteractionHint OEBio::OEIsClashInteractionHint OEBio::OEIsContactInteractionHint OEBio::OEIsCovalentInteractionHint OEBio::OEIsDisulfideBond OEBio::OEIsHBondInteractionHint OEBio::OEIsHalogenBondInteractionHint OEBio::OEIsHetAtom OEBio::OEIsInterInteractionHint OEBio::OEIsIntermolecularChelatorInteractionHint OEBio::OEIsIntermolecularHBondInteractionHint OEBio::OEIsIntraInteractionHint OEBio::OEIsIntramolecularChelatorInteractionHint OEBio::OEIsIntramolecularHBondInteractionHint OEBio::OEIsNTerminalAtom OEBio::OEIsNonIdealHBondInteractionHint OEBio::OEIsNucleicAcidBase OEBio::OEIsNucleicAcidPhosphate OEBio::OEIsNucleicAcidSugar OEBio::OEIsSaltBridgeInteractionHint OEBio::OEIsStackingInteractionHint OEBio::OEIsUnpairedLigandInteractionHint OEBio::OEIsUnpairedProteinInteractionHint OEBio::OEIsWater OEBio::OELigandInteractionHintComponent OEBio::OEMolComplexCategorizer OEBio::OEMolComplexCategorizerBase OEBio::OEMolComplexFilter OEBio::OEProteinInteractionHintComponent OEBio::OEReceptorConstraintFeature OEBio::OESaltBridgeInteractionHint OEBio::OEStackingInteractionHint OEChem::OEAbsCanonicalConfTest OEChem::OEAbsoluteConfTest OEChem::OEAtomBondSet OEChem::OEAtomIsInAgent OEChem::OEAtomIsInChain OEChem::OEAtomIsInProduct OEChem::OEAtomIsInReactant OEChem::OEAtomIsInResidue OEChem::OEAtomIsInRing OEChem::OEBondIsInChain OEChem::OEBondIsInRing OEChem::OEConfTestBase OEChem::OEDefaultConfTest OEChem::OEEuler OEChem::OEExprBase OEChem::OEGetNbrAtom OEChem::OEHasAlphaBetaUnsat OEChem::OEHasAnisou OEChem::OEHasAtomInGroup OEChem::OEHasAtomName OEChem::OEHasAtomStereoSpecified OEChem::OEHasAtomicNum OEChem::OEHasBondInGroup OEChem::OEHasBondStereoSpecified OEChem::OEHasChainID OEChem::OEHasFormalCharge OEChem::OEHasFragmentNumber OEChem::OEHasGroupType OEChem::OEHasHvyDegree OEChem::OEHasIdx OEChem::OEHasMapIdx OEChem::OEHasOrder OEChem::OEHasResidueNumber OEChem::OEIdxSelected OEChem::OEInSamePart OEChem::OEIsAromaticAtom OEChem::OEIsAromaticBond OEChem::OEIsAtomHybridization OEChem::OEIsBridgeHead OEChem::OEIsCAlpha OEChem::OEIsCarbon OEChem::OEIsChiralAtom OEChem::OEIsChiralBond OEChem::OEIsHalide OEChem::OEIsHalogen OEChem::OEIsHeavy OEChem::OEIsHetero OEChem::OEIsHydrogen OEChem::OEIsInvertibleNitrogen OEChem::OEIsMDLStereoGroup OEChem::OEIsMember OEChem::OEIsMemberPtr OEChem::OEIsMetal OEChem::OEIsNitrogen OEChem::OEIsNonRingAtomDoubleBondedToRing OEChem::OEIsOxygen OEChem::OEIsPhosphorus OEChem::OEIsPolar OEChem::OEIsPolarHydrogen OEChem::OEIsProductGroup OEChem::OEIsRGroup OEChem::OEIsReactantGroup OEChem::OEIsRotor OEChem::OEIsRxnComponentGroup OEChem::OEIsSulfur OEChem::OEIsTermHeavyAtom OEChem::OEIsValidAtomValence OEChem::OEIsValidMDLAtomValence OEChem::OEIsomericConfTest OEChem::OEMCSFunc OEChem::OEMCSMaxAtoms OEChem::OEMCSMaxAtomsCompleteCycles OEChem::OEMCSMaxBonds OEChem::OEMCSMaxBondsCompleteCycles OEChem::OEMatch OEChem::OEMatchBase OEChem::OEMatchFunc OEChem::OEMolBase OEChem::OEMolDatabase OEChem::OEMolPropertyFxn OEChem::OEMolPropertyList OEChem::OENthAtom OEChem::OEOmegaConfTest OEChem::OEPartPredT OEChem::OEQMolBase OEChem::OEQuaternion OEChem::OERotMatrix OEChem::OESimilarByRMSD OEChem::OETransBase OEChem::OETranslation OEChem::OEUnaryToBinaryAnd OEChem::OEUnaryToBinaryOr OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay OEDepict::OE2DMolDisplay OEDepict::OEAlignmentResult OEDepict::OEAtomSVGAtomIdxMarkup OEDepict::OEAtomSVGMarkupBase OEDepict::OEAtomSVGNoMarkup OEDepict::OEAtomSVGResidueMarkup OEDepict::OEBondSVGBondIdxMarkup OEDepict::OEBondSVGMarkupBase OEDepict::OEBondSVGNoMarkup OEDepict::OEDisplayAtomIdx OEDepict::OEDisplayAtomMapIdx OEDepict::OEDisplayAtomPropBase OEDepict::OEDisplayBondIdx OEDepict::OEDisplayBondPropBase OEDepict::OEDisplayNoAtomProp OEDepict::OEDisplayNoBondProp OEDepict::OEHighlightBase OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByColor OEDepict::OEHighlightByLasso OEDepict::OEHighlightByStick OEDepict::OEImageFileCreatorBase OEDocking::OEAlignReceptorFunction OEDocking::OEFeature OEGraphSim::OESimFuncBase OEGraphSim::OETanimotoSim OEGraphSim::OETverskySim OEGrapheme::OEAlphaRainbowArcFxn OEGrapheme::OEAtomGlyphBase OEGrapheme::OEAtomGlyphCircle OEGrapheme::OEBondGlyphArrow OEGrapheme::OEBondGlyphBase OEGrapheme::OEBondGlyphCircle OEGrapheme::OEBondGlyphCross OEGrapheme::OEBondGlyphCurvedArrow OEGrapheme::OEBondGlyphScissors OEGrapheme::OEBondGlyphStitch OEGrapheme::OEBondGlyphZigZag OEGrapheme::OEBrickRoadArcFxn OEGrapheme::OECastleArcFxn OEGrapheme::OECogArcFxn OEGrapheme::OEComplexSurfaceArcFxnBase OEGrapheme::OEDefaultArcFxn OEGrapheme::OEDefaultBuriedArcFxn OEGrapheme::OEDefaultCavityArcFxn OEGrapheme::OEDefaultSolventArcFxn OEGrapheme::OEDefaultVoidArcFxn OEGrapheme::OEEyelashArcFxn OEGrapheme::OEFlowerArcFxn OEGrapheme::OENecklaceArcFxn OEGrapheme::OENullArcFxn OEGrapheme::OEOliveBranchArcFxn OEGrapheme::OEPearlsArcFxn OEGrapheme::OERaceTrackArcFxn OEGrapheme::OERailroadTrackArcFxn OEGrapheme::OEResidueSVGMarkupBase OEGrapheme::OEResidueSVGNoMarkup OEGrapheme::OEResidueSVGStandardMarkup OEGrapheme::OESawArcFxn OEGrapheme::OESimpsonArcFxn OEGrapheme::OEStitchArcFxn OEGrapheme::OESunArcFxn OEGrapheme::OESurfaceArcFxnBase OEGrapheme::OEWreathArcFxn OEMedChem::OEBemisMurckoOptions OEMedChem::OEMCSSimFuncBase OEMedChem::OEMCSTanimotoSim OEMedChem::OEMCSTverskySim OEMedChem::OEMatchedPair OEMedChem::OEMatchedPairTransform OEMolPotential::OEFFParams OEMolPotential::OENonBondIntcsOptions OEOpt::OELineMinimize OEProton::OEChargeEngineBase OEProton::OEDesignUnitCharges OEProton::OESpreadMetalCharges OEProton::OETautomerMolFunction OEProton::OETyperMolFunction OEShape::OEHighestColorTanimoto OEShape::OEHighestComboScore OEShape::OEHighestFitColorTversky OEShape::OEHighestFitTversky OEShape::OEHighestFitTverskyCombo OEShape::OEHighestOverlap OEShape::OEHighestRefColorTversky OEShape::OEHighestRefTversky OEShape::OEHighestRefTverskyCombo OEShape::OEHighestScaledColor OEShape::OEHighestTanimoto OEShape::OEHighestTanimotoCombo OEShape::OEHighestTverskyCombo OEShape::OEIsColorAtomPred OEShape::OEOverlayScoreCutoff OEShape::OEStarts OESpicoli::OESurface OESpruce::OEIsModeledAtom OESystem::OEAnd OESystem::OEAnnotation OESystem::OEBase OESystem::OEBaseData OESystem::OEBaseDataT OESystem::OEBinaryAnd OESystem::OEBinaryFalse OESystem::OEBinaryFunction OESystem::OEBinaryIOHandler OESystem::OEBinaryNot OESystem::OEBinaryOr OESystem::OEBinaryPredicate OESystem::OEBinaryTrue OESystem::OEColor OESystem::OEContainer OESystem::OEErrorHandlerImplBase OESystem::OEFixedGrid OESystem::OEFixedMultiGrid OESystem::OEGaussian OESystem::OEGaussianContainer OESystem::OEGrid OESystem::OEGridBase OESystem::OEHasRole OESystem::OEIsFalse OESystem::OEIsTrue OESystem::OEMultiGrid OESystem::OENot OESystem::OEOr OESystem::OEParameter OESystem::OERoles OESystem::OEScalarGrid OESystem::OESkewGrid OESystem::OEUnaryFunction OESystem::OEUnaryPredicate CreateGrid OEShape::OEHermite CreateImage OEDepict::OEImageFileCreatorBase createmcsfragdatabase.java Example Code createmmpindex.java Example Code createmmpindexthreaded.java Example Code CreatePredicateCopy OESystem::OEBinaryPredicate OESystem::OEUnaryPredicate createquery.java Example Code createringdict.java Example Code Crystal Symmetry Crystallographic Space Group Crystallographic Unit Cell CSV, [1] csv2sdf.java Example Code customcolorffprep.java Example Code cyclic membership

D

Daylight Daylight SMILES Debug OESystem::OEErrorHandler Delete OEChem::OEConfBase OEChem::OEMolDatabase DeleteAtom OEChem::OEGroupBase OEChem::OEMolBase DeleteBond OEChem::OEGroupBase OEChem::OEMolBase DeleteColorGaussian OEShape::OEShapeQuery DeleteConf OEChem::OEMCMolBase DeleteConfs OEChem::OEMCMolBase DeleteData OESystem::OEBase DeleteFeature OEBio::OEReceptorCustomConstraints OEDocking::OECustomConstraints DeleteGaussian OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase DeleteGaussians OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase DeleteGroup OEChem::OEMolBase DeleteInteraction OEBio::OEInteractionHintContainer DeleteInteractions OEBio::OEInteractionHintContainer DeleteInterface OESystem::OEInterface DeleteOptions OESystem::OEOptions DeleteParameter OESystem::OEInterface OESystem::OEOptions DeleteRole OESystem::OERoleSet DeleteShapeGaussian OEShape::OEShapeQuery DeleteSmarts OEBio::OEReceptorConstraintFeature OEDocking::OEFeature DeleteSphere OEBio::OEReceptorConstraintFeature OEDocking::OEFeature DeleteStop OESystem::OEColorGradientBase denseomega.java Example Code depict.java Example Code

depict.txt Example Code Describe OEBio::OEPlaceHydrogensDetails OEBio::OEPlaceHydrogensMoverNote Destructor OEDocking::OEBoxBase OEDocking::OEFeature OEDocking::OESphereBase DetermineCategory OEBio::OEIridiumData Dice similarity measure Dihedral DirContents OEPlatform::OEFile DirPath OEPlatform::OEFile Dock OEDocking::OEPosit dockmolecules.java Example Code DockMultiConformerMolecule OEDocking::OEDock OEDocking::OEPosit dots.java Example Code downloading DrawArc OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawCircle OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawCubicBezier OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawLine OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawPath OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawPie OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawPoint OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawPolygon OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawQuadraticBezier OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawRectangle OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame DrawText OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame OEDepict::OEImageTable DrawTriangle OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame

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Elapsed OESystem::OECycleTimer OESystem::OEStopwatch OESystem::OEWallTimer ElementToGridIdx OESystem::OEGridBase OESystem::OESkewGrid ElementToSpatialCoord OESystem::OEGridBase OESystem::OESkewGrid Empty OESystem::OEBoundedBuffer OESystem::OEUnboundedBuffer Energy OESz::OEFixedProteinLigandOptimizer OESz::OEFlexProteinLigandOptimizer environment variable OE_DIR, [1], [2], [3] OE_LICENSE, [1], [2], [3], [4] eof OEChem::oemolistream OEPlatform::oestream Error OESystem::OEErrorHandler EstimateEnergies OESz::OEFreeFormConfAdvanced EstimateFreeEnergies OESz::OEFreeFormConf EstimateRestrictionEnergy OESz::OEFreeFormConfAdvanced Euclidean similarity measure

Example Code anisou.java appendringdict.java asisstartsexample.java, [1] assigncharges.java assigncharges.txt backbone.java bemismurckoperception.java besthit.java bestshapeoverlay.java bestshapeoverlaymulticonfquery.java besttverskyshapeoverlay.java bfactor2img.java bfactor2img.txt boundentropy.java calcet.java cansmi.java catmols.java chemblsolubility.java cliquealign.java coloroptimizationexample.java coloroverlap.java colorscore.java complex2img.java complex2img.txt convert.java createmcsfragdatabase.java createmmpindex.java createmmpindexthreaded.java createquery.java createringdict.java csv2sdf.java customcolorffprep.java denseomega.java depict.java depict.txt dockmolecules.java dots.java excludedvolume.java excludedvolume.txt extractringtemplates.java extractscaffold.java findsimilarconfs.java flexibleprotein.java flexresidues.java freeformconf.java freeformconfadvanced.java freeformconfadvrstr.java freeformconfrstr.java freeformsolv.java generate2d.java getreasonabletautomers.java gettitles.java hermiteexpansion.java hermitetanimoto.java implicitmillsdeannoringsexample.java inertialatheavyatomstartsexample.java, [1] libgen.java ligandentropy.java ligandflexproteinnewton.java ligandmultipleoptions.java macrocycle.java makefastfp.java makefastfp.txt makefraglib.java makereceptor.java match2img.java match2img.txt matchedpairtransform.java matchedpairtransformlist.java matchedpairtransformprobe.java mcs3dalign.java mcsalign2d.java mcsalign2d.txt mcsfragdatabase.java mdlquery2img.java mdlquery2img.txt mdlreaction2img.java mdlreaction2img.txt minpath.java mol2img.java mol2img.txt mol2nam_example.java mol2nam_example.txt molchunk.java molcount.java molextract.java molfilter.java molgrep.java molpropcsv.java molpropsddata.java molproptable.java mols2img.java mols2img.txt mols2pdf.java mols2pdf.txt molstats.java nam2mol_example.java nam2mol_example.txt neutralionization.java nxnshape.java oecheminfo.java oemedcheminfo.java overlapcolor.java overlapquery.java overlayallres.java overlaybestres.java overlaystruct.java parts2mols.java posemolecules.java posemolsmultireceptor.java printatomnames.java printinteractions.java proteinligandpb.java proteinmultipleoptions.java proteinprep.java proteinprep.txt quietfilter.java randomizeatoms.java randomsample.java receptoroutercontourvolume.java rescore.java rescoreposes.java reshist.java ringdict2pdf.java ringdict2pdf.txt ringsubset.java rmsd.java rocsmodeexample.java rotorcount.java sdf2csv.java sdfilter.java sdfmodprops.java sdfrename.java searchfastfp.java searchfastfp.txt searchfp.java searchfp.txt setoutercontourvolume.java setreasonablechargestate.java shapedatabasechunker.java shapedatabaseprep.java shapedistancematrix.java shapeoverlap2pdf.java shapeoverlap2pdf.txt shapeprops.java simpleconformer.java simplefastrocssearch.java simplenewton.java simpleomega.java simpleoverlap.java simpleprepscript.java simpleprotein.java, [1] simplesmirnoff.java simplevacuum.java singleconformer.java singleconformermacrocycle.java sizefilter.java smartsalign.java smartsalign2d.java smartsalign2d.txt solutionentropy.java specificmolprop.java sphereexclusionclustering.java splitmolcomplex.java splitmolcomplex.txt splitmolcomplexfrags.java splitmolcomplexfrags.txt splitmolcomplexlowlevel.java splitmolcomplexlowlevel.txt stereoandtorsion.java stripsalts.java szmapbestorientations.java szmapenergies.java toggleinnercontour.java tophits.java tophitsconf.java tophitsquery.java torsiondrive.java translate_example.java translate_example.txt unimolrxn.java uniqinchi.java uniqmol.java usercolor.java userinertialstartsexample.java, [1] viewmdlsearch.java viewmdlsearch.txt wibergbondorders.java zapatoms1.java zapbind.java zapfocussing.java zapforces.java zapgrid1.java zapgrid2.java zapgrid3.java zapsolv1.java zaptransfer.java ExceedsMaxRotors OEConfGen::OETorDriveOptions excludedvolume.java Example Code excludedvolume.txt Example Code Exists OEPlatform::OEFile explicit atom degree explicit hydrogen count explicit valence Extend OEMath::OEBox Extract OEChem::OEEuler OEChem::OEQuaternion OEChem::OERotMatrix OEChem::OETrans OEChem::OETransBase OEChem::OETranslation extractringtemplates.java Example Code extractscaffold.java Example Code

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Factory OESystem::OEInterface Fatal OESystem::OEErrorHandler fd OEPlatform::oeifstream OEPlatform::oeofstream Feature release file formats FileName OEPlatform::OEFile FindDupParameters OESystem::OEOptions FindSimilarConfs OESz::OEFreeFormConf findsimilarconfs.java Example Code fingerprint FirstBit OESystem::OEBitVector FixAtoms OESz::OESzybki flexibleprotein.java Example Code flexresidues.java Example Code

flush OEChem::oemolostream OEPlatform::oeostream formal charge, [1] FoundInDB OEBio::OEResidueCategoryData freeformconf.java Example Code freeformconfadvanced.java Example Code freeformconfadvrstr.java Example Code freeformconfrstr.java Example Code freeformsolv.java Example Code FromHexString OESystem::OEBitVector FromIndex OEMedChem::OEMatchedPair FromSmiles OEMedChem::OEMatchedPair Full OESystem::OEBoundedBuffer OESystem::OEUnboundedBuffer Functor

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g++ Gasteiger charge gcc generate2d.java Example Code GenerateConfs OEConfGen::OETorDriver GenerateMissingFrags OEConfGen::OEMakeFragLib Get OEChem::OEMolPropertyFxn OEChem::OEVectorBindings OEMolPotential::OEInteractParams OESystem::OEBoundedBuffer OESystem::OEInterface OESystem::OEOwnedPtr OESystem::OEProtectedBuffer OESystem::OESharedPtr OESystem::OEUnboundedBuffer OESystem::OEUnownedPtr get OEPlatform::oeistream Get_dc OEConstr::OEHarmonicPotential Get_kc OEConstr::OEHarmonicPotential GetA OEBio::OECrystalSymmetryParams OESheff::OESheffieldOptions OESystem::OEColor GetActive OEChem::OEMCMolBase GetAddCarbonSkeleton OEChem::OE2DRingDictionaryCreatorOptions GetAddCarbonSkeletonWithBondStereo OEChem::OE2DRingDictionaryCreatorOptions GetAddDepictionHydrogens OEDepict::OEAlignmentOptions OEDepict::OEPrepareDepictionOptions GetAddInteractionHints OESpruce::OEDesignUnitEnumerateSitesOptions GetAddMetadata OEBio::OEPlaceHydrogensOptions GetAddRGroup OEBio::OESplitMolComplexOptions GetAddStyle OESpruce::OEDesignUnitEnumerateSitesOptions GetAdjustHCount OEBio::OESplitMolComplexOptions GetAliases OESystem::OEParameter GetAlignment OEDepict::OEFont GetAllColor OEShape::OEColorOverlap GetAllowBuildDisulfideBridges OESpruce::OELoopBuilderOptions GetAllowedClashType OEDocking::OEPositOptions GetAllowTruncate OESpruce::OECapBuilderOptions GetAllScores OEGraphSim::OEFastFPDatabase GetAlpha OEBio::OECrystalSymmetryParams OEGraphSim::OETverskySim OEMedChem::OEMCSTverskySim GetAltAtoms OEBio::OEAltLocationFactory GetAltConfs OEBio::OEIridiumData GetAlternateLocation OEChem::OEResidue GetAlternateLocation() OEBio::OEAtomMatchResidueID GetAlternateLocationHandling OESpruce::OEDesignUnitSplitOptions GetAltsMustBeCompatible OEBio::OEPlaceHydrogensOptions GetAminoAcidScale OEGrapheme::OEPeptideDisplayOptions GetAnalyticCoulombicBindingEnergy OEPB::OEBindResults GetAnalyticOptions OEShape::OEAnalyticColorFunc OEShape::OEAnalyticShapeFunc GetAngle OEBio::OEPlaceHydrogensMoverNote OESz::OETorsionScanResult GetAngles OEChem::OEEuler GetAntiAliasing OEDepict::OEJavaImageBase GetApplyWarts OEProton::OETautomerOptions GetArea OEMath::OEBox OEMath::OESphere OEPB::OEArea GetArg OEPlatform::OEThread GetAromaticStyle OEDepict::OE2DMolDisplayOptions GetAsDensity OEBio::OEIridiumData GetAssignBondiRadii OEShape::OEOverlapPrep GetAssignColor OEShape::OEOverlapPrep GetAssignMapIdx OEChem::OELibraryGen GetAssignPartialChargesAndRadii OESpruce::OEDesignUnitPrepOptions GetAssumptions OEBio::OESplitMolComplexOptions GetAtom OEBio::OEHierChain OEBio::OEHierFragment OEBio::OEHierResidue OEBio::OEHierView OEBio::OEInteractionHintFragment OEBio::OEReceptorProteinConstraint OEChem::OEMolBase OEDepict::OEAtomDisplayBase OEDepict::OENearestAtom OEDocking::OEProteinConstraint GetAtom1 OEMolPotential::OEVdwParams GetAtom2 OEMolPotential::OEVdwParams GetAtomColor OEDepict::OE2DMolDisplayOptions GetAtomColorStyle OEDepict::OE2DMolDisplayOptions GetAtomDisplay OEDepict::OE2DMolDisplay OEGrapheme::OESurfaceArc GetAtomDisplays OEDepict::OE2DMolDisplay GetAtomExpr OEConfGen::OEConfFixOptions GetAtomExternalHighlight OEDepict::OEHighlightByColor GetAtomExternalHighlightRatio OEDepict::OEHighlightByStick GetAtomicBondOrder OEMolAM1::OEAM1Results GetAtomicNum OEChem::OEAtomBase GetAtomicPotentials OESz::OEFreeFormSolvResults GetAtomicRadiiType OESz::OEFreeFormSolvOptions OESz::OESzybkiSolventOptions GetAtomIndex1 OEMolPotential::OEBendParams OEMolPotential::OEOutOfPlaneParams OEMolPotential::OEStretchParams OEMolPotential::OETorsionParams OEMolPotential::OEVdwParams GetAtomIndex2 OEMolPotential::OEBendParams OEMolPotential::OEOutOfPlaneParams OEMolPotential::OEStretchParams OEMolPotential::OETorsionParams OEMolPotential::OEVdwParams GetAtomIndex3 OEMolPotential::OEBendParams OEMolPotential::OEOutOfPlaneParams OEMolPotential::OETorsionParams GetAtomIndex4 OEMolPotential::OEOutOfPlaneParams OEMolPotential::OETorsionParams GetAtomLabelFont OEDepict::OE2DMolDisplayOptions GetAtomLabelFontScale OEDepict::OE2DMolDisplayOptions GetAtomLabelMonochrome OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByLasso OEDepict::OEHighlightByStick OEDepict::OEHighlightOverlayByBallAndStick GetAtomList OEChem::OEMolBase GetAtomMapSize OEBio::OEAltLocationFactory GetAtomPredicate OEConfGen::OEFlipperOptions GetAtomPropertyFunctor OEDepict::OE2DMolDisplayOptions GetAtomPropLabelFont OEDepict::OE2DMolDisplayOptions GetAtomPropLabelFontScale OEDepict::OE2DMolDisplayOptions GetAtoms OEBio::OEHierResidue OEBio::OEHierView OEBio::OEInteractionHintFragment OEChem::OEAtomBase OEChem::OEAtomBondSet OEChem::OEGroupBase OEChem::OEMatch OEChem::OEMatchBase OEChem::OEMolBase OEDepict::OEAlignmentResult OEMolPotential::OEInteraction OESpicoli::OESurface OESpruce::OEPocket GetAtomsElement OESpicoli::OESurface GetAtomStereoStyle OEDepict::OE2DMolDisplayOptions GetAtomSVGMarkupFunctor OEDepict::OE2DMolDisplayOptions GetAtomTypeIndex OEMolPotential::OEFFParams GetAtomTypeName OEMolPotential::OEFFParams GetAtomTypes OEGraphSim::OEFPTypeParams GetAtomVisibilityFunctor OEDepict::OE2DMolDisplayOptions GetAttachmentPoints OEMedChem::OEMatchedPairTransformExtractOptions GetAuthor OESpruce::OEStructureMetadata GetAxial OEChem::OEAtomBase GetB OEBio::OECrystalSymmetryParams OESheff::OESheffieldOptions OESystem::OEColor GetBackboneClashRejectThreshold OESpruce::OELoopBuilderOptions GetBackboneMatch OEBio::OESequenceAlignment GetBackColor OEDepict::OEPen GetBackgroundColor OEDepict::OE2DMolDisplayOptions GetBadClashOverlapDistance OEBio::OEPlaceHydrogensOptions GetBallRadiusScale OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightOverlayByBallAndStick GetBaseWriteFxns OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase GetBendParams OEMolPotential::OEFFParams GetBeta OEBio::OECrystalSymmetryParams OEGraphSim::OETverskySim OEMedChem::OEMCSTverskySim GetBFactor OEChem::OEResidue GetBgn OEChem::OEBondBase OEChem::OENbrs GetBgnAngle OEGrapheme::OESurfaceArc GetBgnFragment OEBio::OEInteractionHint GetBgnIdx OEChem::OEBondBase GetBgnPen OEDepict::OE2DBondDisplay GetBigStep OESystem::OEDots GetBinaryIOHandler OEChem::oemolstreambase GetBinBoundaries OEGraphSim::OEFPHistogram GetBinCenters OEGraphSim::OEFPHistogram GetBindingEnergy OEPB::OESimpleBindResults GetBinIdx OEGraphSim::OEFPHistogram GetBinWidth OEGraphSim::OEFPHistogram GetBioUnitExtractionOptions OESpruce::OEMakeDesignUnitOptions GetBit OEGraphSim::OEFPPattern GetBodies OEDepict::OEReport GetBody OEDepict::OEReport GetBodyCell OEDepict::OEImageTable GetBodyCells OEDepict::OEImageTable GetBond OEChem::OEAtomBase OEChem::OEMolBase OEDepict::OEBondDisplayBase OEDepict::OENearestBond GetBondColorStyle OEDepict::OE2DMolDisplayOptions GetBondDisplay OEDepict::OE2DMolDisplay GetBondDisplays OEDepict::OE2DMolDisplay GetBondExpr OEConfGen::OEConfFixOptions GetBondLineAtomLabelGapScale OEDepict::OE2DMolDisplayOptions GetBondLineGapScale OEDepict::OE2DMolDisplayOptions GetBondList OEChem::OEMolBase GetBondMapSize OEBio::OEAltLocationFactory GetBondOrder OEMolAM1::OEAM1Results GetBondOrders OEMolAM1::OEAM1Results GetBondPredicate OEConfGen::OEFlipperOptions GetBondPropertyFunctor OEDepict::OE2DMolDisplayOptions GetBondPropLabelFont OEDepict::OE2DMolDisplayOptions GetBondPropLabelFontScale OEDepict::OE2DMolDisplayOptions GetBonds OEChem::OEAtomBase OEChem::OEAtomBondSet OEChem::OEGroupBase OEChem::OEMatch OEChem::OEMatchBase OEChem::OEMolBase OEDepict::OEAlignmentResult GetBondStereoStyle OEDepict::OE2DMolDisplayOptions GetBondSVGMarkupFunctor OEDepict::OE2DMolDisplayOptions GetBondTypes OEGraphSim::OEFPTypeParams GetBondWidthScaling OEDepict::OE2DMolDisplayOptions GetBoolData OESystem::OEBase GetBoundarySpacing OEPB::OEZap GetBoundingBoxPen OEDepict::OEHighlightLabel GetBoundLigandArea OEPB::OESimpleBindResults GetBoundLigandAreaEnergy OEPB::OESimpleBindResults GetBoundLigandCoulombEnergy OEPB::OEBindResults GetBoundLigandZapEnergy OEPB::OESimpleBindResults GetBoundProteinArea OEPB::OESimpleBindResults GetBoundProteinAreaEnergy OEPB::OESimpleBindResults GetBoundProteinCoulombEnergy OEPB::OEBindResults GetBoundProteinZapEnergy OEPB::OESimpleBindResults GetBoxExtension OEDocking::OEMakeReceptorOptions GetBoxMol OEDocking::OEMakeReceptorOptions GetBoxRangeMax OEGrapheme::OEColorGradientDisplayOptions GetBoxRangeMin OEGrapheme::OEColorGradientDisplayOptions GetBoxRangePen OEGrapheme::OEColorGradientDisplayOptions GetBrief OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter getbuffer OEPlatform::oeisstream GetBuildLoops OESpruce::OEDesignUnitBuildOptions GetBuildOptions OESpruce::OEDesignUnitPrepOptions GetBuildSidechains OESpruce::OEDesignUnitBuildOptions GetBundleCofactors OEBio::OEMolComplexCategorizer OEBio::OEMolComplexCategorizerBase GetBurialFactor OESpruce::OEPocketOptions GetBuriedArea OEPB::OESimpleBindResults GetBuriedAreaEnergy OEPB::OESimpleBindResults GetButtonFont OEDepict::OELegendLayoutOptions GetButtonHeightScale OEDepict::OELegendLayoutOptions GetButtonPen OEDepict::OELegendLayoutOptions GetButtonWidthScale OEDepict::OELegendLayoutOptions GetBypassPredicate OEBio::OEPlaceHydrogensOptions getbyte OEChem::oemolistream OEPlatform::oeistream getByteArray OEChem::oemolostream GetC OEBio::OECrystalSymmetryParams GetCalculatedGeometries OEBio::OEInteractionHint GetCalculatedGeometry OEBio::OEInteractionHint GetCalculateFrozenTerms OESz::OESzybkiOptOptions GetCalculateGradients OESz::OESzybkiGeneralOptions GetCAlphaMatch OEBio::OESequenceAlignment GetCanon OEChem::OEParseSmilesOptions GetCanonOrder OEConfGen::OEMolBuilderOptions OEMolProp::OEFilter GetCapBuilderOptions OESpruce::OEDesignUnitBuildOptions GetCapCTermini OESpruce::OEDesignUnitBuildOptions GetCapNTermini OESpruce::OEDesignUnitBuildOptions GetCarbonHybridization OEProton::OETautomerOptions GetCarbonRadius OEShape::OEBestOverlay OEShape::OEOverlap OEShape::OEShapeOptions GetCategorizer OEBio::OESplitMolComplexOptions GetCategory OEBio::OEIridiumData GetCavitySolventParameter OESz::OESzybkiSolventOptions GetCell OEDepict::OEImageGrid OEDepict::OEImageTable OEDepict::OEReport GetCellBorderPen OEDepict::OEImageTableOptions GetCellColor OEDepict::OEImageTableOptions GetCellFont OEDepict::OEImageTableOptions GetCellGap OEDepict::OEImageGrid OEDepict::OEReportOptions GetCellHeight OEDepict::OEImageGrid OEDepict::OEReport OEDepict::OEReportOptions GetCells OEDepict::OEImageGrid OEDepict::OEImageTable OEDepict::OEReport GetCellWidth OEDepict::OEImageGrid OEDepict::OEReport OEDepict::OEReportOptions GetCenter OEGrapheme::OESurfaceArc OESystem::OEGaussian OESystem::OEGaussianBase GetChainID OEBio::OEAtomMatchResidueID OEBio::OEHierChain OEBio::OESequenceAlignment OEChem::OEResidue OESpruce::OESequenceMetadata GetChains OEBio::OEHierView GetCharge OEDepict::OE2DAtomDisplay GetChargeAliquot OEProton::OESpreadMetalCharges GetChargeEngine OESpruce::OEDesignUnitPrepOptions GetCharges OEMolAM1::OEAM1Results GetChargeType OESz::OEFreeFormSolvOptions OESz::OESzybkiEnsembleResults GetChelatorType OEBio::OEChelatorInteractionHint GetChi1 OEBio::OERotamer GetChi2 OEBio::OERotamer GetChi3 OEBio::OERotamer GetChi4 OEBio::OERotamer GetChildren OESystem::OEAnnotation GetChiral OEChem::OEInChIOptions GetClassName OEDepict::OEAtomSVGAtomIdxMarkup OEDepict::OEAtomSVGMarkupBase OEDepict::OEAtomSVGNoMarkup OEDepict::OEAtomSVGResidueMarkup OEDepict::OEBondSVGBondIdxMarkup OEDepict::OEBondSVGMarkupBase OEDepict::OEBondSVGNoMarkup OEGrapheme::OEResidueSVGMarkupBase OEGrapheme::OEResidueSVGNoMarkup OEGrapheme::OEResidueSVGStandardMarkup GetClearBackground OEGrapheme::OEColorOverlapDisplayOptions OEGrapheme::OEShapeOverlapDisplayOptions OEGrapheme::OEShapeQueryDisplayOptions GetClearCoordinates OEChem::OELibraryGen OEChem::OEUniMolecularRxn OEProton::OETautomerOptions GetClearCoords OEDepict::OEAlignmentOptions OEDepict::OEPrepareDepictionOptions OEGrapheme::OEAlignedDepictionFrom3DOptions GetClusterScore OEBio::OEPlaceHydrogensDetails GetCoefficients OEShape::OEHermite GetCofactorCodes OESpruce::OEDesignUnitSplitOptions GetCollapseNonSiteAlts OESpruce::OEDesignUnitEnumerateSitesOptions GetCollectProteinByChain OEBio::OESplitMolComplexOptions GetColor OEDepict::OEFont OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByColor OEDepict::OEHighlightByLasso OEDepict::OEHighlightByStick OEGrapheme::OEColorForceFieldDisplay OESpicoli::OESurface OESystem::OEAnnotation OESystem::OEColorStop OESystem::OEGaussian OESystem::OEGaussianBase GetColorAt OESystem::OEColorGradientBase GetColorAtomStyle OEGrapheme::OEShapeQueryDisplayOptions GetColorElement OESpicoli::OESurface GetColorForceField OEShape::OEColorOptions OEShape::OEOverlapPrep OEShape::OEShapeQueryBase OEShape::OEShapeQueryPublic GetColorForceFieldType OEFastROCS::OEShapeDatabase GetColorFunc OEShape::OEOverlapFunc GetColorGaussians OEShape::OEShapeQueryBase GetColorGridSpacing OEFastROCS::OEShapeDatabase GetColorOptimization OEFastROCS::OEShapeDatabaseOptions GetColorOptions OEShape::OEColorFunc GetColors OEDepict::OEHighlightOverlayBase OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase GetColorScore OEFastROCS::OEShapeDatabaseScore OEShape::OEOverlapResults GetColorStopLabelFont OEGrapheme::OEColorGradientDisplayOptions GetColorStopLabelFontScale OEGrapheme::OEColorGradientDisplayOptions GetColorStopPrecision OEGrapheme::OEColorGradientDisplayOptions GetColorStopVisibility OEGrapheme::OEColorGradientDisplayOptions GetColorStyle OEDepict::OELegendLayoutOptions GetColorTanimoto OEFastROCS::OEShapeDatabaseScore OEShape::OEOverlapResults GetColorTversky OEFastROCS::OEShapeDatabaseScore OEShape::OEOverlapResults GetColorTypes OEGrapheme::OEColorForceFieldDisplay GetColumnName OEChem::OECSVHeader GetColumnNames OEChem::OECSVHeader GetCombinedFilter OEBio::OESplitMolComplexOptions GetCommandLine OESystem::OEHeader GetComment OESystem::OEHeader GetCommentEnergy OEConfGen::OETorDriveOptions GetComplexArea OEPB::OESimpleBindResults GetComplexAreaEnergy OEPB::OESimpleBindResults GetComplexCoulombEnergy OEPB::OEBindResults GetComplexZapEnergy OEPB::OESimpleBindResults GetComponent OEBio::OEDesignUnit OESzmap::OESzmapResults GetComponentID OEBio::OEDesignUnit GetComponentNames OEDocking::OEDock OEDocking::OEScore GetComponents OEBio::OEDesignUnit OEMolPotential::OEGenericFF OEMolPotential::OEGenericFF2 GetComponentsWithin OEBio::OEDesignUnit GetComponentTag OEBio::OEDesignUnit GetComponentType OEBio::OEInteractionHintFragment GetConf OEChem::OEMCMolBase OEPB::OESimpleBindResults GetConfFixOptions OEConfGen::OEOmegaOptions GetConfFreeEnergyFromEnsemble OESz::OESzybkiResults GetConfGenRMS OESz::OEFreeFormSolvOptions GetConfIdx OEFastROCS::OEShapeDatabaseScore OESz::OESingleConfResult OESz::OESzybkiResults GetConfigurationalEntropy OESz::OESzybkiEnsembleResults GetConfList OEChem::OEMCMolBase OEChem::OEMol GetConfResult OESz::OEFreeFormConfResults GetConfs OEChem::OEMCMolBase GetConfsPerHit OEShape::OEROCSOptions GetConfTest OEChem::oemolistream GetConnectBufferDistance OESpruce::OELoopBuilderOptions GetConsiderAtomLabelBoundingBox OEDepict::OEHighlightByLasso GetContactDistance OEMolPotential::OEFFParams GetContext OEMedChem::OEMatchedPairTransformExtractOptions OESzmap::OESzmapEngine GetCoords OEChem::OEConfBase OEChem::OEMolBase OEDepict::OE2DAtomDisplay OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase OESzmap::OESzmapResults GetCoordsPtr OEChem::OEConfBase GetCoordsToInertialFrame OEGrapheme::OEDepictionFrom3DOptions GetCorrSolventOptions OESz::OEFreeFormConfOptions GetCoulombCutoff OEMolPotential::OENonBondIntcsOptions GetCoulombEnergy OEPB::OEBindResults GetCoulombParams OEMolPotential::OEFFParams GetCount OEProton::OETautomerMolFunction GetCounts OEFastROCS::OEDBTracer OEGraphSim::OEFPHistogram OESystem::OEDots GetCPUTime OESz::OESzybkiResults GetCropLength OESpruce::OELoopBuilderOptions GetCSVHeader OEChem::oemolstreambase GetCurrentAtoms OEBio::OEAltLocationFactory GetCurrentLocations OEBio::OEAltLocationFactory GetCurvature OESpicoli::OESurface GetCurvatureElement OESpicoli::OESurface GetCustomConstraints OEBio::OEReceptor GetCutoff OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions GetCutoffGT OEFastROCS::OEShapeDatabaseOptions GetCutoffLT OEFastROCS::OEShapeDatabaseOptions GetData OESystem::OEBase OESystem::OEBaseDataT OESystem::OEBitVector GetDatabaseType OEChem::OESubSearchDatabase OEFastROCS::OEShapeDatabase GetDataIter OESystem::OEBase GetDataTags OEMedChem::OEMatchedPair GetDataType OEBio::OEDesignUnit OEBio::OEInteractionHint OEBio::OEInteractionHintFragment OEChem::OEMolDatabase OEDepict::OE2DMolDisplay OEDepict::OEAtomDisplayBase OEDepict::OEBondDisplayBase OEDepict::OEMolDisplayBase OESpicoli::OESurface OESystem::OEAnnotation OESystem::OEBase OESystem::OEBaseData OESystem::OEBaseDataT OESystem::OEBinaryIOHandler OESystem::OEContainer OESystem::OEFixedGrid OESystem::OEFixedMultiGrid OESystem::OEGaussian OESystem::OEGaussianBase OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase OESystem::OEGrid OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OEMultiGrid OESystem::OEScalarGrid OESystem::OESkewGrid GetDate OESystem::OEHeader GetDefault OEChem::OEPredicateParameter OESystem::OEMultiParameter OESystem::OETypedParameter GetDefaultBondPen OEDepict::OE2DMolDisplayOptions GetDefaultReadFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase GetDefaults OESystem::OETypedParameter GetDefaultsVector OESystem::OEPODParameter GetDefaultWriteFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase GetDegree OEChem::OEAtomBase GetDeleteClashingSolvent OESpruce::OECapBuilderOptions OESpruce::OESidechainBuilderOptions GetDelta OESz::OETorsionScanOptions GetDeltaG OESz::OESingleConfResult GetDensity OEGraphSim::OEFPHistogram GetDepictOrientation OEDepict::OEPrepareDepictionOptions OEGrapheme::OEShapeQueryDisplayOptions GetDepth OEGrapheme::OEComplexSurfaceArcFxnBase GetDerivativeType OEShape::OEShapeGridOptions GetDescendingOrder OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions GetDesignUnit OEDocking::OESinglePoseResult GetDesolvationEnergy OEPB::OEBindResults GetDetail OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter GetDetails OEBio::OEInteractionHint GetDielectric OEFF::OEMMFFSheffieldOptions OEPB::OEET GetDielectricConst OEConfGen::OEMacrocycleBuilderOptions GetDielectricDerivative OESheff::OESheffield GetDielectricModel OEPB::OEZap GetDim OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetDimension OEChem::OEMolBase GetDirection OEMedChem::OEMatchedPairTransformExtractOptions GetDisplayedLigand OEGrapheme::OE2DActiveSiteDisplay GetDisplayedResidues OEGrapheme::OE2DActiveSiteDisplay GetDisplayPos OEDepict::OE2DBondDisplay GetDisplayPosition OEDepict::OENearestAtom OEDepict::OENearestBond OEGrapheme::OENearestResidue GetDisplayType OEDepict::OE2DBondDisplay GetDist OEChem::OENbrs OEDepict::OENearestAtom OEDepict::OENearestBond OEGrapheme::OENearestResidue OESpruce::OESuperpositionOptions GetDist2 OEChem::OENbrs GetDistance OESpicoli::OESurface GetDistanceElement OESpicoli::OESurface GetDoubleData OESystem::OEBase GetDPI OEBio::OEIridiumData GetDuplicateRemoval OESpruce::OEDesignUnitEnumerateSitesOptions GetElectrostaticSolvationFreeEnergy OESz::OEFreeFormSolvResults GetElfLimit OEProton::OEELFOptions GetEnabled OEBio::OEReceptorConstraintFeature OEBio::OEReceptorProteinConstraint OEDocking::OEFeature OEDocking::OEProteinConstraint GetEnd OEChem::OEBondBase OEChem::OENbrs OEDepict::OE2DPath GetEndAngle OEGrapheme::OESurfaceArc GetEndFragment OEBio::OEInteractionHint GetEndIdx OEChem::OEBondBase GetEndPen OEDepict::OE2DBondDisplay GetEndResidueInsertCode OESpruce::OESequenceMetadata GetEndResidueNumber OESpruce::OESequenceMetadata GetEnergy OEChem::OEMolBase OEMolAM1::OEAM1Results OESz::OETorsionScanResult GetEnergyRange OEConfGen::OESliceEnsembleOptions GetEnergyTerm OESz::OESzybkiResults GetEnergyWindow OEConfGen::OEFragOptions OEConfGen::OEMacrocycleOmegaOptions OEConfGen::OEOmegaOptions OEConfGen::OESliceEnsembleOptions GetEnsembleLigPartialSolvEntropy OESz::OESzybkiEnsembleResults GetEnsembleLigSolvEntropy OESz::OESzybkiEnsembleResults GetEnsembleProtDesolvEntropy OESz::OESzybkiEnsembleResults GetEnsembleValue OESzmap::OESzmapResults GetEntries OEBio::OEResidueCategoryData GetEntropicEnergy OESz::OESzybkiEnsembleResults GetEntropy OESz::OESzybki GetEntropy(const OEChem::OEMCMolBase&, unsigned int, unsigned int) OESz::OESzybki GetEnumBridgehead OEConfGen::OEFlipperOptions GetEnumerateCofactorSites OESpruce::OEDesignUnitEnumerateSitesOptions GetEnumerateSitesOptions OESpruce::OEDesignUnitPrepOptions GetEnumEZ OEConfGen::OEFlipperOptions GetEnumNitrogen OEConfGen::OEFlipperOptions OEConfGen::OEMolBuilderOptions GetEnumRing OEConfGen::OEMolBuilderOptions GetEnumRS OEConfGen::OEFlipperOptions GetEnumSpecifiedStereo OEConfGen::OEFlipperOptions GetEquilibriumAngle OEMolPotential::OEFFParams GetEquilibriumBondLength OEMolPotential::OEFFParams GetError OEPB::OEZap GetExactVdWProteinLigand OESz::OESzybkiProteinOptions GetExcipientCodes OESpruce::OEDesignUnitSplitOptions GetExcipients OEBio::OEIridiumData GetExcludeSelf OEDocking::OEPositOptions GetExpectValidMol OEProton::OEChargeEngineBase GetExperimentDate OESpruce::OEStructureMetadata GetExperimentType OESpruce::OEStructureMetadata GetExplicitAtomLabelAngle OEDepict::OE2DMolDisplayOptions GetExplicitDegree OEChem::OEAtomBase GetExplicitHCount OEChem::OEAtomBase GetExplicitHydrogens OEChem::OELibraryGen GetExplicitValence OEChem::OEAtomBase GetExponent OEFF::OEMMFFSheffieldOptions OESystem::OEExponentColorGradient GetExpr OEChem::OEQBase GetExpType OEShape::OEAnalyticOptions GetExtChainID OEChem::OEResidue GetExtend OEBio::OESequenceAlignment GetExtendedSaltBridgeDistance OEBio::OEPerceiveInteractionOptions GetExtension OEDepict::OEImageFileBase OEDepict::OEImageFileCreatorBase GetFaceNormal OESpicoli::OESurface GetFaceNormals OESpicoli::OESurface GetFaceNormalsElement OESpicoli::OESurface GetFailed OEChem::OEMMFFTypeResult GetFamily OEDepict::OEFont GetFastROCSMode OEFastROCS::OEShapeDatabaseOptions GetFComponents OEOpt::OEFunc0 GetFeatureName OEBio::OEReceptorConstraintFeature OEDocking::OEFeature GetFeatures OEBio::OEReceptorCustomConstraints OEDocking::OECustomConstraints GetFeatureSpheres OEBio::OEReceptorConstraintFeature GetFileName OEChem::oemolstreambase GetFill OEDepict::OEPen GetFilterType OEMolProp::OEFilter GetFinalEnergies OESz::OEProteinLigandOptResults GetFinalRMSGradient OESz::OESzybkiResults GetFinalTotalPotential OESz::OESzybkiResults GetFingerPrint OEGraphSim::OEFastFPDatabase GetFingerPrints OEGraphSim::OEFPDatabase GetFitChains OESpruce::OESecondaryStructureSuperposition OESpruce::OEStructuralSuperposition GetFitColorTversky OEShape::OEOverlapResults GetFitConfIdx OEShape::OEBestOverlayScore GetFitHermiteOptions OEShape::OEHermiteShapeFunc GetFitSelfColor OEShape::OEOverlapResults GetFitSelfOverlap OEShape::OEOverlapResults GetFitTversky OEShape::OEColorResults OEShape::OEOverlapResults GetFitTverskyCombo OEShape::OEOverlapResults GetFixDeleteH OEConfGen::OEConfFixOptions GetFixedCoords OEDepict::OEAlignmentOptions GetFixedHLayer OEChem::OEInChIOptions GetFixMaxMatch OEConfGen::OEConfFixOptions GetFixMol OEConfGen::OEConfFixOptions GetFixPattern OESz::OESzybki GetFixPredicate OEConfGen::OEConfFixOptions OESz::OESzybki GetFixRMS OEConfGen::OEConfFixOptions GetFixSmarts OEConfGen::OEConfFixOptions GetFixSubSearch OEConfGen::OEConfFixOptions GetFixUniqueMatch OEConfGen::OEConfFixOptions GetFlagTableFailures OEMolProp::OEFilter GetFlavor OEChem::OEMolDatabase OEChem::OEMolDatabaseSaveOptions OEChem::oemolstreambase GetFlexRange OEDocking::OEPoseOptimizerOptions OESz::OEProteinFlexOptions GetFlipBias OEBio::OEPlaceHydrogensDetails OEBio::OEPlaceHydrogensOptions GetFlipBiasScale OEBio::OEPlaceHydrogensOptions GetFlippedBestClusterScore OEBio::OEPlaceHydrogensMoverNote GetFlipPredicate OEBio::OEPlaceHydrogensOptions GetFloatData OESystem::OEBase GetFocusTarget OEPB::OEZap GetFont OEDepict::OEHighlightLabel GetFontScale OEDepict::OEHighlightLabel GetFooter OEDepict::OEReport GetFooterHeight OEDepict::OEReport OEDepict::OEReportOptions GetFooters OEDepict::OEReport GetFooterWidth OEDepict::OEReport OEDepict::OEReportOptions GetForceField OEConfGen::OEFragBuilderOptions OEConfGen::OETorDriveOptions OEConfGen::OETorDriver OEDocking::OEPoseOptimizerOptions OESz::OEProteinLigandOptOptions OESz::OESzybkiGeneralOptions GetForceFieldType OEFF::OEMMFFSheffieldOptions OESz::OESzybkiGeneralOptions OESz::OETorsionScanOptions GetForeColor OEDepict::OEPen GetFormalCharge OEChem::OEAtomBase GetFormat OEChem::OEMolDatabase OEChem::OEMolDatabaseSaveOptions OEChem::oemolstreambase GetFPType OEGraphSim::OECreateFastFPDatabaseOptions OEGraphSim::OEFPTypeBase OEGraphSim::OEFPTypeParams GetFPTypeBase OEGraphSim::OEFPDatabase OEGraphSim::OEFastFPDatabase OEGraphSim::OEFastFPDatabaseParams OEGraphSim::OEFingerPrint GetFPTypeString OEGraphSim::OEFPTypeBase GetFPVersion OEGraphSim::OEFPTypeBase GetFPVersionString OEGraphSim::OEFPTypeBase GetFragBuilderOptions OEConfGen::OEMolBuilderOptions GetFragGen OEConfGen::OEFragOptions GetFragKeep OEConfGen::OEFragOptions GetFragment OEBio::OEInteractionHint GetFragmentationLimit OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMatchedPairAnalyzerOptions GetFragmentNumber OEBio::OEAtomMatchResidueID OEBio::OEHierFragment OEChem::OEResidue GetFragments OEBio::OEHierChain OEBio::OEHierView GetFromCT OEConfGen::OEMolBuilderOptions GetFromSDData OEMedChem::OEMatchedPair GetFullConformationSearch OEDocking::OEPositOptions GetG OESystem::OEColor GetGamma OEBio::OECrystalSymmetryParams GetGap OEBio::OESequenceAlignment GetGaussians OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase GetGeneralOptions OESz::OESzybkiOptions GetGenerateTautomers OESpruce::OEProtonateDesignUnitOptions GetGlobalOffset OEDepict::OEImageBase GetGlobalStrain OESz::OERestrictionEnergyResult GetGradients OESz::OESzybkiResults GetGradTolerance OESz::OEProteinLigandOptOptions OESz::OESzybkiOptOptions GetGraphics OEDepict::OEJavaImageBase GetGridBuffer OEPB::OEET GetGridOptions OEShape::OEGridColorFunc OEShape::OEGridShapeFunc GetGridSpacing OEPB::OEET OEPB::OEZap OEShape::OEOverlap OEShape::OEShapeGridOptions GetGroup OEBio::OEAltLocationFactory OEChem::OEMolBase GetGroupCount OEBio::OEAltGroup OEBio::OEAltLocationFactory GetGroupDefinition OEChem::OEGroupBase GetGroupID OEBio::OEAltGroup OEBio::OEAltLocation GetGroupId OEDepict::OEAtomSVGAtomIdxMarkup OEDepict::OEAtomSVGMarkupBase OEDepict::OEAtomSVGNoMarkup OEDepict::OEAtomSVGResidueMarkup OEDepict::OEBondSVGBondIdxMarkup OEDepict::OEBondSVGMarkupBase OEDepict::OEBondSVGNoMarkup OEGrapheme::OEResidueSVGMarkupBase OEGrapheme::OEResidueSVGNoMarkup OEGrapheme::OEResidueSVGStandardMarkup GetGroupList OEChem::OEMolBase GetGroups OEBio::OEAltLocationFactory OEChem::OEMolBase GetGroupType OEChem::OEGroupBase Getgz OEChem::oemolstreambase GetHandlerImpl OESystem::OEErrorHandler GetHarmonicConstraints OESz::OESzybki GetHasClash OEDocking::OESinglePoseResult GetHasDefault OESystem::OEParameter GetHasMTZ OEBio::OEIridiumData GetHasValue OESystem::OEParameter GetHBondType OEBio::OEHBondInteractionHint GetHCount OEDepict::OE2DAtomDisplay GetHeader OEDepict::OEReport GetHeaderCell OEDepict::OEImageTable GetHeaderCells OEDepict::OEImageTable GetHeaderColor OEDepict::OEImageTableOptions GetHeaderFont OEDepict::OEImageTableOptions GetHeaderHeight OEDepict::OEReport OEDepict::OEReportOptions GetHeaders OEDepict::OEReport GetHeaderWidth OEDepict::OEReport OEDepict::OEReportOptions GetHeight OEDepict::OE2DMolDisplay OEDepict::OE2DMolDisplayOptions OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame OEGrapheme::OE2DActiveSiteDisplay GetHessianDimension OEOpt::OEBFGSOpt GetHeterogenMetadata OESpruce::OEStructureMetadata GetHetGroupNbrDist OESpruce::OEProtonateDesignUnitOptions GetHighScoresAreBetter OEDocking::OEDock OEDocking::OEPosit OEDocking::OEScore GetHistogram OEFastROCS::OEDBTracer OEFastROCS::OEFastROCSHistogram OEGraphSim::OEFastFPDatabase GetHistory OESystem::OEHeader GetHostComponents OEFF::OEComplexEnergies GetHostEnergy OEFF::OEComplexEnergies GetHPosition OEDepict::OE2DAtomDisplay GetHvyDegree OEChem::OEAtomBase GetHvyValence OEChem::OEAtomBase GetHyb OEChem::OEAtomBase GetHybridizationLevel OEProton::OETautomerOptions GetHydrogens OEChem::OEInChIOptions GetHydrogenStyle OEDepict::OE2DMolDisplayOptions GetHydrophobicSolvationFreeEnergy OESz::OEFreeFormSolvResults GetHyperlink OEDepict::OEFont GetId OEDepict::OESVGGroup GetID OESpruce::OEHeterogenMetadata GetIDs OEBio::OEDesignUnit GetIdx OEChem::OEAtomBase OEChem::OEBondBase OEChem::OEConfBase OEChem::OEMolDatabase OEGraphSim::OESimScore OEMedChem::OEMCSMolSimScore GetIdxA OEGraphSim::OESimScorePair GetIdxB OEGraphSim::OESimScorePair GetIdxFileName OEChem::OEMolDatabaseSaveOptions GetIdxs OEChem::OEMolDatabase GetIEFFCluster OESz::OESzybkiGeneralOptions GetIEFFTerms OEFF::OEMMFFIEFFOptions GetIgnoreHydrogens OEChem::OEConfRMSDOptions GetIgnoreNitrogenStereo OEDocking::OEPositOptions GetIgnoreTerminalHeavy OEChem::OEConfRMSDOptions GetIllegalRanges OESystem::OEParameter GetIllegalValues OESystem::OEParameter GetImplicitHCount OEChem::OEAtomBase GetIncludeInput OEConfGen::OEOmegaOptions GetIndexableFragmentRangeMax OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMatchedPairAnalyzerOptions GetIndexableFragmentRangeMin OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMatchedPairAnalyzerOptions GetInFile OEChem::OERefInputAppOptions OEChem::OESimpleAppOptions GetInitialEnergies OESz::OEProteinLigandOptResults GetInitialOrientation OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay GetInitialRMSGradient OESz::OESzybkiResults GetInitialTotalPotential OESz::OESzybkiResults GetInnerContour OEDepict::OEHighlightByCogwheel GetInnerContourLevel OEBio::OEReceptor GetInnerDielectric OEPB::OEET OEPB::OEZap GetInnerMask OEPB::OEET GetInsertCode OEBio::OEAtomMatchResidueID OEChem::OEResidue GetIntData OESystem::OEBase GetInteractions OEBio::OEInteractionHintContainer OEMolPotential::OEMolFunc GetInteractionType OEBio::OEInteractionHint GetInteractive OEGrapheme::OEPeptideDisplayOptions GetInteractiveStyle OEDepict::OELegendLayoutOptions GetInterComponents OEFF::OEComplexEnergies GetInterEnergy OEFF::OEComplexEnergies OESz::OESzybkiResults GetInterface OESystem::OEHeader OESystem::OEInterface GetInterfaces OESystem::OEInterface GetIntermolecularVdWCutoff OESz::OESzybkiProteinOptions GetIntramolecularLigandEnergy OESz::OESzybkiResults GetIntramolecularVdWCutoff OESz::OESzybkiGeneralOptions GetIntType OEChem::OEAtomBase OEChem::OEBondBase GetInvalidScore OEDocking::OEPosit GetInverse OEChem::OEEuler OEChem::OEQuaternion OEChem::OERotMatrix OEChem::OETrans OEChem::OETransBase OEChem::OETranslation GetInverseHessian OEOpt::OEBFGSOpt GetIonicState OESz::OEFreeFormConfOptions OESz::OEFreeFormSolvOptions GetIridiumData OEBio::OEStructureQuality OESpruce::OEStructureMetadata GetIrrationalRFree OEBio::OEIridiumData GetIsList OESystem::OEParameter GetIsotope OEChem::OEAtomBase GetIsotopes OEMedChem::OEMatchedPairTransformExtractOptions GetIStream OEChem::oemolithread GetIterations OEPB::OEZap GetIterCycleSize OEConfGen::OEMacrocycleOmegaOptions GetIterLimit OEOpt::OEOptimizer0 OEOpt::OEOptimizer1 OEOpt::OEOptimizer2 GetJoin OEPB::OEET GetKeepHessian OEOpt::OEBFGSOpt GetKeepTitle OEChem::OECreateSubSearchDatabaseOptions GetKekule OEProton::OETautomerOptions GetKeyless OESystem::OEParameter GetKeywords OESpruce::OEStructureMetadata GetLabel OEBio::OEPlaceHydrogensMoverNote OEDepict::OE2DAtomDisplay OEGrapheme::OEColorGradientLabel GetLabelFont OEDepict::OE2DAtomDisplay GetLabels OEGrapheme::OEColorGradientDisplayOptions GetLabelStyle OEGrapheme::OEPeptideDisplayOptions GetLambdaX OEShape::OEHermiteOptions GetLambdaY OEShape::OEHermiteOptions GetLambdaZ OEShape::OEHermiteOptions GetLassoScale OEDepict::OEHighlightByLasso GetLayer OEDepict::OE2DMolDisplay GetLayoutStyle OEDepict::OELegendLayoutOptions GetLegalRanges OESystem::OEParameter GetLegalValues OESystem::OEParameter GetLegendArea OEDepict::OELegendLayout GetLegendBoxPen OEDepict::OELegendLayoutOptions GetLegendFont OEGrapheme::OE2DPropMap GetLegendFontScale OEGrapheme::OE2DPropMap GetLegendLocation OEGrapheme::OE2DPropMap GetLevel OEProton::OETautomerOptions OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase GetLigand OEBio::OEDesignUnit GetLigandCharge OESz::OEProteinLigandOptOptions GetLigandComponents OEFF::OEComplexEnergies GetLigandConstraints OESpruce::OESuperpositionOptions GetLigandDensity OEBio::OEIridiumData GetLigandDesolvationEnergy OEPB::OEBindResults GetLigandEnergy OEFF::OEComplexEnergies GetLigandFilter OEBio::OESplitMolComplexOptions GetLigandRMSD OESz::OEProteinLigandOptResults GetLigandRMSDHeavy OESz::OESzybkiGeneralOptions GetLigandSubSearch OEBio::OEMolComplexCategorizer GetLimit OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabaseOptions OEProton::OEELFCharges getline OEChem::oemolistream OEPlatform::oeistream GetLineCap OEDepict::OEPen GetLineJoin OEDepict::OEPen GetLineStipple OEDepict::OEPen GetLineWidth OEDepict::OEPen GetLineWidthScale OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByColor OEDepict::OEHighlightByLasso GetLipidCodes OESpruce::OEDesignUnitSplitOptions GetList OEMolPotential::OEInteractParams OESystem::OEInterface GetLnQrot OESz::OESzybkiResults GetLnQrotational OESz::OESingleConfResult GetLnQvib OESz::OESzybkiResults GetLnQvibrational OESz::OESingleConfResult GetLocalDensity OESpruce::OEPocket GetLocalStrain OESz::OERestrictionEnergyResult GetLocation OEBio::OEAltLocationFactory GetLocationCodes OEBio::OEAltLocationFactory GetLocationCount OEBio::OEAltGroup OEBio::OEAltLocation GetLocationID OEBio::OEAltLocation GetLocations OEBio::OEAltGroup GetLoopBuilderOptions OESpruce::OEDesignUnitBuildOptions GetLoopClashRejectThreshold OESpruce::OELoopBuilderOptions GetLoopDBFilename OESpruce::OELoopBuilderOptions GetLowestdGConfIdx OESz::OEFreeFormConfResults GetLowestRelEneConfIdx OESz::OEFreeFormConfResults GetMacrocycleBuilderOptions OEConfGen::OEMacrocycleOmegaOptions GetMacroCycOptions OEConfGen::OEFragBuilderOptions GetMakePackingResidues OESpruce::OEDesignUnitSplitOptions GetMapIdx OEChem::OEAtomBase GetMargin OEDepict::OE2DMolDisplayOptions OEDepict::OEImageGrid OEDepict::OEImageTableOptions OEDepict::OELegendLayoutOptions GetMarkedValuePen OEGrapheme::OEColorGradientDisplayOptions GetMarkedValuePrecision OEGrapheme::OEColorGradientDisplayOptions GetMarkedValues OEGrapheme::OEColorGradientDisplayOptions GetMaskCutoff OESzmap::OESzmapEngineOptions GetMass OEDepict::OE2DAtomDisplay GetMatchedPairContext OEMedChem::OEMatchedPairTransform GetMatchedPairData OEMedChem::OEMatchedPairTransformExtractOptions GetMatchedPairs OEMedChem::OEMatchedPairTransform OEMedChem::OEMatchedPairTransformExtractOptions GetMatchIndices OEChem::OESubSearchDatabase OEChem::OESubSearchResult GetMatchTitles OEChem::OESubSearchDatabase GetMax OEGraphSim::OEFPHistogram GetMaxAcceptorAngle OEBio::OEPerceiveInteractionOptions GetMaxAllowedAtomPairClashes OEDepict::OEAlignmentOptions GetMaxAtomFilter OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMatchedPairAnalyzerOptions GetMaxAtomIdx OEChem::OEMolBase GetMaxAtomPairDistance OEBio::OEPerceiveInteractionOptions GetMaxAtoms OESpruce::OEBioUnitExtractionOptions GetMaxBindingSiteDist OEBio::OESplitMolComplexOptions GetMaxBondIdx OEChem::OEMolBase GetMaxBondRotations OEDepict::OEAlignmentOptions OEGrapheme::OEAlignedDepictionFrom3DOptions OEGrapheme::OEDepictionFrom3DOptions GetMaxCationPiAngle OEBio::OEPerceiveInteractionOptions GetMaxCationPiDistance OEBio::OEPerceiveInteractionOptions GetMaxCenters OEConfGen::OEFlipperOptions GetMaxChargeAidedHBondDistance OEBio::OEPerceiveInteractionOptions GetMaxColor OESystem::OEColorGradientBase GetMaxConfGen OESz::OEFreeFormSolvOptions GetMaxConfIdx OEChem::OEMCMolBase GetMaxConfRange OEConfGen::OESliceEnsembleOptions

GetMaxConfs OEConfGen::OEMacrocycleOmegaOptions OEConfGen::OEOmegaOptions OEConfGen::OESliceEnsembleOptions OEFastROCS::OEShapeDatabaseOptions GetMaxContactFraction OEBio::OEPerceiveInteractionOptions GetMaxCoreMolecule OEMedChem::OEMCSFragDatabase GetMaxCoreMoleculeCount OEMedChem::OEMCSFragDatabase GetMaxCount OEProton::OEFormalChargeOptions GetMaxCovalentFraction OEBio::OEPerceiveInteractionOptions GetMaxDisplacement OESz::OESzybkiResults GetMaxDistance OEGraphSim::OEFPTypeParams GetMaxDonorAngle OEBio::OEPerceiveInteractionOptions GetMaxFragLimit OEMedChem::OEMCSFragDatabaseOptions GetMaxHalogenAngle OEBio::OEPerceiveInteractionOptions GetMaxHalogenBondDistance OEBio::OEPerceiveInteractionOptions GetMaxHBondDistance OEBio::OEPerceiveInteractionOptions GetMaxHeavyAtom OEBio::OELigandInteractionHintComponent GetMaxHits OEShape::OEROCSOptions GetMaxIter OEConfGen::OEMacrocycleOmegaOptions OESz::OEProteinLigandOptOptions OESz::OESzybkiOptOptions GetMaxLigAtoms OEBio::OEMolComplexCategorizer OESpruce::OEDesignUnitSplitOptions GetMaxLigResidues OEBio::OEMolComplexCategorizer OESpruce::OEDesignUnitSplitOptions GetMaxMatches OEChem::OECliqueSearch OEChem::OEConfRMSDOptions OEChem::OEMCSSearch OEChem::OESubSearch OEChem::OESubSearchQuery GetMaxMetalBondDistance OEBio::OEPerceiveInteractionOptions GetMaxMMPLimit OEMedChem::OEMatchedPairTransformExtractOptions GetMaxMolIdx OEChem::OEMolDatabase OEMedChem::OEMCSFragDatabase OEMedChem::OEMatchedPairAnalyzer GetMaxNbrDist OEProton::OESpreadMetalCharges GetMaxNonIdealAcceptorAngle OEBio::OEPerceiveInteractionOptions GetMaxNonIdealDonorAngle OEBio::OEPerceiveInteractionOptions GetMaxNonIdealHBondDistance OEBio::OEPerceiveInteractionOptions GetMaxNumDevices OEFastROCS::OEShapeDatabase GetMaxOptIterations OEFastROCS::OEShapeDatabase GetMaxOptSteps OEShape::OEOverlayOptions GetMaxOverlays OEFastROCS::OEShapeDatabaseOptions GetMaxParts OESpruce::OEBioUnitExtractionOptions GetMaxPatternMatches OEDepict::OEAlignmentOptions GetMaxPeptideResidues OEBio::OEMolComplexCategorizer GetMaxPiStackAngle OEBio::OEPerceiveInteractionOptions GetMaxPiStackDistance OEBio::OEPerceiveInteractionOptions GetMaxProteinAtoms OEBio::OEMolComplexCategorizer GetMaxRandomTranslation OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay OEShape::OERandomStarts GetMaxRecord OEMedChem::OECreateMMPIndexOptions GetMaxRotors OEConfGen::OETorDriveOptions GetMaxSaltBridgeDistance OEBio::OEPerceiveInteractionOptions GetMaxScfIter OEMolAM1::OEAM1Options GetMaxSearchTime OEConfGen::OETorDriveOptions OEProton::OETautomerOptions GetMaxSeqIdx OEBio::OESequenceAlignment GetMaxSubstateCutoff OEBio::OEPlaceHydrogensOptions GetMaxSubstituentLimit OEMedChem::OEMatchedPairTransformExtractOptions GetMaxSubstituentLimitSkip OEMedChem::OEMatchedPairTransformExtractOptions GetMaxSurfaceArea OESpruce::OEPocketOptions GetMaxSurfaceWaterDist OEBio::OESplitMolComplexOptions GetMaxSystemAtoms OESpruce::OEDesignUnitSplitOptions GetMaxTautomericAtoms OEProton::OETautomerOptions GetMaxTautomersGenerated OEProton::OETautomerOptions GetMaxTautomersToReturn OEProton::OETautomerOptions GetMaxTerminalHeavy OEConfGen::OESliceEnsembleOptions GetMaxTStackAngle OEBio::OEPerceiveInteractionOptions GetMaxTStackDistance OEBio::OEPerceiveInteractionOptions GetMaxUnpairedAngle OEBio::OEPerceiveInteractionOptions GetMaxUnpairedDistance OEBio::OEPerceiveInteractionOptions GetMaxValue OEGrapheme::OE2DPropMap OESystem::OEColorGradientBase GetMaxZoneSize OEProton::OETautomerOptions GetMCMol OEChem::OEConfBase GetMCMolBases OEChem::oemolistream GetMCMolTitle OEChem::OEMCMolBase GetMCSCore OEMedChem::OEMCSMolSimScore GetMCSCorrespondence OEMedChem::OEMatchedPairTransformExtractOptions GetMCSSimTypeString OEMedChem::OEMCSSimFuncBase OEMedChem::OEMCSTanimotoSim OEMedChem::OEMCSTverskySim GetMemoryType OEGraphSim::OEFastFPDatabase GetMemoryTypeString OEGraphSim::OEFastFPDatabase GetMethod OEBio::OESequenceAlignment OEPB::OEArea OEShape::OEBestOverlay OEShape::OEOverlap GetMid OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetMin OEGraphSim::OEFPHistogram GetMinAtoms OEChem::OECliqueSearch OEChem::OEMCSSearch GetMinColor OESystem::OEColorGradientBase GetMinContactFraction OEBio::OEPerceiveInteractionOptions GetMinCovalentFraction OEBio::OEPerceiveInteractionOptions GetMinDistance OEGraphSim::OEFPTypeParams GetMinFontSize OEDepict::OEImageBase GetMinFragLimit OEMedChem::OEMCSFragDatabaseOptions GetMinHBondContactFraction OEBio::OEPerceiveInteractionOptions GetMinimizeType OEShape::OEBestOverlay GetMinLigAtoms OEBio::OEMolComplexCategorizer OESpruce::OEDesignUnitSplitOptions GetMinMMPLimit OEMedChem::OEMatchedPairTransformExtractOptions GetMinProbability OEDocking::OEPositOptions GetMinScore OESpruce::OEBioUnitExtractionOptions GetMinSubstituentLimit OEMedChem::OEMatchedPairTransformExtractOptions GetMinSurfaceArea OESpruce::OEPocketOptions GetMinValue OEGrapheme::OE2DPropMap OESystem::OEColorGradientBase GetMissingFrags OEConfGen::OEMakeFragLib GetMMFFEnergy OESz::OESingleConfResult GetMMFFTerms OEFF::OEMMFFIEFFOptions GetMMFFType OEChem::OEMMFFTypeResult GetMMFFTypeCheck OEMolProp::OEFilter GetMMPOptions OEMedChem::OECreateMMPIndexOptions GetModelNumber OEChem::OEResidue GetMol OEChem::oemolthreadbase GetMolBases OEChem::oemolistream GetMolBuilderOptions OEConfGen::OEOmegaOptions GetMolDatabaseFilename OEGraphSim::OEFastFPDatabaseParams GetMolecule OEBio::OEInteractionHintContainer OEChem::OEMolDatabase OEChem::OESubSearchDatabase OEDepict::OEMolDisplayBase OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairTransform OEPB::OEZap OEProton::OETautomerMolFunction OEShape::OEShapeQueryBase GetMoleculeIndex OEGraphSim::OEFastFPDatabase GetMolecules OEBio::OEInteractionHintContainer GetMoleculeString OEChem::OEMolDatabase GetMoleculeTitle OEMedChem::OEMatchedPairTransform GetMolIdx OEFastROCS::OEShapeDatabaseScore GetMolStream OEChem::oemolithread OEChem::oemolothread GetMoverClass OEBio::OEPlaceHydrogensMoverNote GetMoverNotes OEBio::OEPlaceHydrogensDetails GetMultiplier OEShape::OEColorOptions GetMutations OESpruce::OEDesignUnitMutationOptions GetName OEBio::OEAtomMatchResidueID OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintTypeBase OEBio::OEReceptorProteinConstraint OEChem::OEAtomBase OEChem::OEResidue OEChem::OESubSearchScreenTypeBase OEDepict::OESVGClass OEDocking::OEDock OEDocking::OEPosit OEDocking::OEProteinConstraint OEDocking::OEScore OEGrapheme::OEColorForceFieldDisplay OEMolPotential::OEInteraction OEProton::OEChargeEngineBase OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter OESystem::OERole GetNbr OEChem::OEBondBase GetNbrs OEChem::OENearestNbrs GetNegativeColor OEGrapheme::OE2DPropMap GetNegativeImageGrid OEBio::OEReceptor GetNegativeImageType OEDocking::OEMakeReceptorOptions GetNextToken OEChem::OETokenizerBase GetNoFlipPredicate OEBio::OEPlaceHydrogensOptions GetNonRingOptions OEConfGen::OEFragBuilderOptions GetNormal OESpicoli::OESurface GetNormals OESpicoli::OESurface GetNormalsElement OESpicoli::OESurface GetNPolyMax OEShape::OEHermiteOptions GetNucleicAcid OEBio::OEDesignUnit GetNumBestHits OEShape::OEROCSOptions GetNumBins OEFastROCS::OEDBTracer OEFastROCS::OEDBTracerBase OEFastROCS::OEFastROCSHistogram GetNumBits OEGraphSim::OEFPTypeParams GetNumClashes OEDocking::OESinglePoseResult GetNumClusters OEBio::OEPlaceHydrogensDetails GetNumColorAtomStarts OEFastROCS::OEShapeDatabaseOptions GetNumColumns OEChem::OECSVHeader GetNumContacts OEDocking::OESinglePoseResult GetNumCycles OESz::OESzybkiResults GetNumDevices OEFastROCS::OEShapeDatabase GetNumericGradDelta OEMolAM1::OEAM1Options GetNumFixAtoms OESz::OESzybkiResults GetNumFlips OEBio::OEPlaceHydrogensDetails GetNumGrids OESystem::OEFixedMultiGrid GetNumHeavyAtomStarts OEFastROCS::OEShapeDatabaseOptions GetNumHydrogensStandardized OEBio::OEPlaceHydrogensDetails GetNumInertialStarts OEFastROCS::OEShapeDatabaseOptions GetNumMatchedPairs OEMedChem::OECreateMMPIndexStatus GetNumMols OEMedChem::OECreateMMPIndexStatus GetNumMovers OEBio::OEPlaceHydrogensDetails GetNumOfStarts OEShape::OEStarts GetNumOpenThreads OEFastROCS::OEShapeDatabase GetNumPoses OEDocking::OEPositResults GetNumProcessors OEChem::OECreateSubSearchDatabaseOptions OEGraphSim::OECreateFastFPDatabaseOptions OEGraphSim::OEFPDatabaseOptions GetNumRandomStarts OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay OEShape::OERandomStarts GetNumRotors OESz::OESzybkiResults GetNumSCFCycles OEMolAM1::OEAM1Results GetNumStarts OEFastROCS::OEShapeDatabaseOptions GetNumThreads OEMedChem::OECreateMMPIndexOptions GetNumTriangles OESpicoli::OESurface GetNumUniqueConfs OESz::OEFreeFormConfResults GetNumUserStarts OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay GetNumVertices OESpicoli::OESurface GetOccupancy OEChem::OEResidue GetOERelease OESystem::OEHeader GetOEResidue OEBio::OEHierChain OEBio::OEHierFragment OEBio::OEHierResidue GetOEVersion OESystem::OEHeader GetOffset OEDepict::OEImageFrame GetOmegaOptions OESz::OEFreeFormConfOptions GetOptimizationInclSurfaceAreaTerm OESpruce::OELoopBuilderOptions GetOptimizationMaxLoops OESpruce::OELoopBuilderOptions GetOptimizationShell OESpruce::OELoopBuilderOptions GetOptimizationStage1IterMultiplier OESpruce::OELoopBuilderOptions GetOptimizationStage2IterMultiplier OESpruce::OELoopBuilderOptions GetOptimizationTolerance OESpruce::OELoopBuilderOptions GetOptimizationType OESz::OEProteinLigandOptOptions GetOptimizationUseSolventModel OESpruce::OELoopBuilderOptions GetOptimize OEProton::OEAM1BCCCharges OEProton::OEAM1Charges GetOptimizeExpProtons OESpruce::OEProtonateDesignUnitOptions GetOptimizeOptions OESz::OEFreeFormConfOptions GetOptimizerType OESz::OESzybkiOptOptions GetOption OESystem::OEOptions GetOptions OEChem::OEConfRMSD OEConfGen::OEFragBuilder OEConfGen::OEMacrocycleBuilder OEConfGen::OEMacrocycleOmega OEConfGen::OEMolBuilder OEConfGen::OEOmega OEDepict::OE2DMolDisplay OEDepict::OEImageTable OEDepict::OELegendLayout OEDepict::OEReport OEGrapheme::OE2DActiveSiteDisplay OEMedChem::OEMCSFragDatabase OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMatchedPairTransformExtractOptions OEMolAM1::OEAM1 OEShape::OEHermite OESystem::OEOptions OESzmap::OESzmapEngine GetOptOptions OESz::OESzybkiOptions GetOrder OEChem::OEBondBase GetOrderPriority OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter GetOrientation OEDepict::OEMultiPageImageFile GetOriginalBestClusterScore OEBio::OEPlaceHydrogensMoverNote GetOStream OEChem::oemolothread GetOtherFilter OEBio::OESplitMolComplexOptions GetOuterContourLevel OEBio::OEReceptor GetOuterDielectric OEPB::OEZap GetOuterMask OEPB::OEET GetOutFile OEChem::OERefInputAppOptions OEChem::OESimpleAppOptions GetOutOfPlaneParams OEMolPotential::OEFFParams GetOverlap OEShape::OEOverlapResults GetOverlapColor OEGrapheme::OEShapeOverlapDisplayOptions GetOverlapDisplayStyle OEGrapheme::OEShapeOverlapDisplayOptions GetOverlapFunc OEShape::OEOverlayOptions GetOverlayConf OEShape::OEROCSResult GetOverlayConfs OEShape::OEROCSResult GetOverlayOptions OEShape::OEMultiRefOverlay OEShape::OEOverlay OEShape::OEROCSOptions GetPackedColor OESystem::OEColor GetPackingResidues OEBio::OEDesignUnit OEBio::OEIridiumData GetPage OEDepict::OEMultiPageImageFile OEDepict::OEReport GetPageHeight OEDepict::OEMultiPageImageFile OEDepict::OEReport OEDepict::OEReportOptions GetPageMargin OEDepict::OEReportOptions GetPages OEDepict::OEMultiPageImageFile OEDepict::OEReport GetPageWidth OEDepict::OEMultiPageImageFile OEDepict::OEReport OEDepict::OEReportOptions GetParameter OESystem::OEInterface OESystem::OEOptions GetParameters OESystem::OEInterface OESystem::OEOptions GetParent OEChem::OEAtomBase OEChem::OEAtomBondSet OEChem::OEBondBase OEChem::OEGroupBase GetParentAtom OEChem::OEQAtomBase GetParentBond OEChem::OEQBondBase GetPartialCharge OEChem::OEAtomBase GetPartOccupancyLigand OEBio::OEIridiumData GetPartOccupancyProtein OEBio::OEIridiumData GetPattern OEChem::OECliqueSearch OEChem::OEMCSSearch OEChem::OESubSearch GetPatternAtoms OEChem::OEMatchBase GetPatternBonds OEChem::OEMatchBase GetPen OEDepict::OEHighlightByLasso OEGrapheme::OEPlotMarker GetPenaltyForceConstant OESz::OETorsionScanOptions GetPerceiveBondStereo OEDepict::OEPrepareDepictionOptions GetPercent OEProton::OEELFOptions GetPercentage OEProton::OEELFCharges GetPerformPrep OEShape::OEROCSOptions GetPermissiveBCCs OEProton::OEAM1BCCCharges GetPhi OEBio::OERamachandranAnalysis OEChem::OEEuler GetpKaNormalize OEMolProp::OEFilter GetPlaceHydrogensOptions OESpruce::OEProtonateDesignUnitOptions GetPlatform OESystem::OEHeader GetPocketPredicate OESpruce::OEPocket GetPocketSurface OESpruce::OEPocket GetPoint OEDepict::OE2DPathPoint GetPoints OEDepict::OE2DPath GetPointType OEDepict::OE2DPathPoint GetPose OEDocking::OESinglePoseResult GetPoserCacheCount OEDocking::OEPositOptions GetPoseRelaxMode OEDocking::OEPositOptions GetPosition OEDepict::OEHighlightByLasso GetPositiveColor OEGrapheme::OE2DPropMap GetPositMethod OEDocking::OESinglePoseResult GetPositMethods OEDocking::OEPositOptions GetPossibleCovalent OEBio::OEIridiumData GetPotential OESpicoli::OESurface GetPotentialElement OESpicoli::OESurface GetPotentialName OESpicoli::OESurface GetPrefactor OESystem::OEGaussian OESystem::OEGaussianBase GetPrefactors OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase GetPreferAuthorRecord OESpruce::OEBioUnitExtractionOptions GetPreOptimizeOptions OESz::OEFreeFormConfOptions GetPrepOptions OESpruce::OEMakeDesignUnitOptions GetProbabilities OESzmap::OESzmapResults GetProbability OEBio::OERotamer OEDocking::OESinglePoseResult OESz::OESingleConfResult GetProbabilityOrder OESzmap::OESzmapResults GetProbe OESzmap::OESzmapEngineOptions GetProbeMol OESzmap::OESzmapEngineOptions GetProbeName OESzmap::OESzmapEngineOptions GetProbeRadius OEPB::OEZap OESpicoli::OESurface GetProcessorID OEMedChem::OEMatchedPairAnalyzer GetProcessorType OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairAnalyzerOptions GetProducts OEChem::OELibraryGen GetProgram OESystem::OEHeader GetPromoteUnknowns OEBio::OESplitMolComplexOptions GetProperty OEChem::OEMolPropertyList OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay GetPropertyFont OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay GetPropertyOffset OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay GetProtectiveGroupLabelFont OEDepict::OE2DMolDisplayOptions GetProtectiveGroupStyle OEDepict::OE2DMolDisplayOptions GetProtein OEBio::OEDesignUnit OESz::OESzybki GetProteinConstraints OEBio::OEReceptor GetProteinDesolvationEnergy OEPB::OEBindResults GetProteinDielectric OESz::OESzybkiProteinOptions GetProteinElectrostaticModel OESz::OESzybkiProteinOptions GetProteinFilter OEBio::OESplitMolComplexOptions GetProteinFlexibilityRange OESz::OESzybkiProteinOptions GetProteinFlexibilityType OESz::OESzybkiProteinOptions GetProteinOptions OESz::OESzybkiOptions GetProteinRMSD OESz::OEProteinLigandOptResults OESz::OESzybkiResults GetProtonate OESpruce::OEDesignUnitPrepOptions GetProtonateOptions OESpruce::OEDesignUnitPrepOptions GetProxyGridCutoff OEShape::OEAnalyticOptions GetPsi OEBio::OERamachandranAnalysis OEChem::OEEuler GetPtr OEChem::OEConstCoords OEChem::OEMutableCoords GetQAtoms OEChem::OEQAtomBase OEChem::OEQMol OEChem::OEQMolBase GetQBonds OEChem::OEQAtomBase OEChem::OEQMol OEChem::OEQMolBase GetQuat OEFastROCS::OEShapeDatabaseScore GetQuaternion OEChem::OEQuaternion GetQuerySurfaceArcFxn OEGrapheme::OEColorOverlapDisplayOptions OEGrapheme::OEShapeOverlapDisplayOptions GetQuiet OEChem::OEParseSmilesOptions GetR OESystem::OEColor GetRacemicStereo OEChem::OEInChIOptions GetRacemicType OEProton::OETautomerOptions GetRad OEDocking::OESphereBase OEMath::OESphere GetRadical OEDepict::OE2DAtomDisplay GetRadiiApproximation OEShape::OEBestOverlay OEShape::OEOverlap OEShape::OEShapeOptions GetRadius OEChem::OEAtomBase OEGrapheme::OESurfaceArc GetRadiusMargin OEProton::OESpreadMetalCharges GetRadiusRatio OEGrapheme::OE2DPropMap GetRamaCategory OEBio::OERamachandranAnalysis GetRamaScore OEBio::OERamachandranAnalysis GetRamaType OEBio::OERamachandranAnalysis GetRandomSeed OEConfGen::OEMacrocycleBuilderOptions OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay OEShape::OERandomStarts GetRangeIncrement OEConfGen::OESliceEnsembleOptions GetRankPredicate OEShape::OEROCSOptions GetRankTautomers OEProton::OETautomerOptions GetRawScores OEGraphSim::OEFastFPDatabase GetReadFailureCt OEChem::oemolistream GetReadFxns OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase getreasonabletautomers.java Example Code GetReceptor OEBio::OEDesignUnit GetReceptorIndex OEDocking::OESinglePoseResult GetReconnectedMetals OEChem::OEInChIOptions GetReentrant OESystem::OESkewGrid GetRefChains OESpruce::OESecondaryStructureSuperposition OESpruce::OEStructuralSuperposition GetRefColorTversky OEShape::OEOverlapResults GetRefConfIdx OEShape::OEBestOverlayScore GetReferenceCoords OEBio::OEPlaceHydrogensMoverNote GetRefFile OEChem::OERefInputAppOptions GetRefGrid OEShape::OEBestOverlay GetRefHermiteOptions OEShape::OEHermiteShapeFunc GetRefMol OEShape::OEBestOverlay GetRefSelfColor OEShape::OEBestOverlay OEShape::OEOverlapResults GetRefSelfOverlap OEShape::OEOverlapResults GetRefSymmetry OEShape::OEBestOverlay GetRefTolerance OEConfGen::OEMacrocycleBuilderOptions GetRefTversky OEShape::OEColorResults OEShape::OEOverlapResults GetRefTverskyCombo OEShape::OEOverlapResults GetRegion OESpruce::OEStructuralSuperposition GetRegionType OEMedChem::OEBemisMurckoOptions GetRelativeEnergy OESz::OESingleConfResult GetRelativeStereo OEChem::OEInChIOptions GetRelaxed OEDocking::OESinglePoseResult GetRelLnQ OESz::OESingleConfResult GetRemoveAttractiveVdWForces OESz::OESzybkiGeneralOptions GetRemoveCoulombTerms OESz::OESzybkiGeneralOptions GetRemoveUnmappedFragments OEChem::OELibraryGen GetRenderHint OESystem::OEAnnotation GetRenderInteractiveLegend OEGrapheme::OE2DActiveSiteDisplayOptions GetRepairRequestedHint OEProton::OEChargeEngineBase GetRequired OESystem::OEParameter GetRequirements OEProton::OEChargeEngineBase GetResidue OEBio::OEHierChain OEBio::OEHierFragment OEBio::OEHierView OEGrapheme::OENearestResidue GetResidueCategoryData OEBio::OEMolComplexCategorizer OEBio::OEMolComplexCategorizerBase GetResidueID OESz::OEProteinFlexOptions GetResidueIndex OEBio::OERotamer GetResidueName OEBio::OEHierResidue GetResidueNumber OEBio::OEAtomMatchResidueID OEBio::OEHierResidue OEChem::OEResidue GetResidues OEBio::OEHierFragment OEBio::OEHierView OESpruce::OEPocket GetResidueSVGMarkupFunctor OEGrapheme::OE2DActiveSiteDisplayOptions GetResolution OEBio::OEIridiumData OEDocking::OEDockOptions OEGrapheme::OE2DPropMap OESpicoli::OESurface GetRestrictToRefSite OESpruce::OEDesignUnitEnumerateSitesOptions GetResults OEMolAM1::OEAM1 GetResultsForConformations OESz::OEFreeFormConfResults OESz::OESzybkiEnsembleResults GetRetainBondStereo OEChem::OEExtractRingTemplateOptions GetRetainExistingBuiltInTemplates OEChem::OE2DRingDictionaryCreatorOptions GetRetainExistingTemplates OEChem::OE2DRingDictionaryCreatorOptions OEChem::OEExtractRingTemplateOptions GetReturn OEPlatform::OEThread GetReturnCode OEDocking::OEPositResults OESz::OEFreeFormSolvResults OESz::OEProteinLigandOptResults GetReturnSelectedConfs OEProton::OEELFCharges GetRevision OESpruce::OEStructureMetadata GetRevisionDate OESpruce::OEStructureMetadata GetRFree OEBio::OEIridiumData GetRGBA OESystem::OEColor GetRingFragLimit OEMedChem::OEMCSFragDatabaseOptions GetRingOptions OEConfGen::OEFragBuilderOptions GetRMS OEConfGen::OEFragOptions GetRMSD OEDepict::OEAlignmentResult OESpruce::OEStructuralSuperposition OESz::OESzybkiResults GetRMSDCutoff OEDepict::OEAlignmentOptions GetRMSRange OEConfGen::OESliceEnsembleOptions GetRMSThreshold OEConfGen::OESliceEnsembleOptions GetROCSOptions OEShape::OEROCS GetRoles OESystem::OERoleSet GetRotamerLibrary OESpruce::OESidechainBuilderOptions GetRotateAroundBonds OEDepict::OEAlignmentOptions GetRotateTo2DReference OEGrapheme::OEDepictionFrom3DOptions GetRotationalEntropy OESz::OESingleConfResult GetRotationAngle OEDepict::OEFont GetRotEntropy OESz::OESzybkiResults GetRotMatrix OEChem::OERotMatrix OEFastROCS::OEShapeDatabaseScore OEShape::OEBestOverlayScore OESpruce::OESecondaryStructureSuperposition OESpruce::OEStructuralSuperposition GetRotorOffset OEConfGen::OETorDriveOptions GetRotorPredicate OEConfGen::OETorDriveOptions GetRow OEChem::OEMolDatabase GetRunType OESz::OESzybkiOptions GetRxnRole OEChem::OEAtomBase GetSaltConcentration OEPB::OEET OEPB::OEZap OESz::OESzybkiSolventOptions GetSampleHydrogens OEConfGen::OEMolBuilderOptions GetSaveRange OEChem::OECliqueSearch GetSaveStereo OEProton::OETautomerOptions GetScale OEDepict::OE2DMolDisplay OEDepict::OE2DMolDisplayOptions OEGrapheme::OEPlotMarker GetSCFTolerance OEMolAM1::OEAM1Options GetScore OEBio::OEPlaceHydrogensMoverNote OEBio::OESequenceAlignment OEFastROCS::OEShapeDatabaseScore OEGraphSim::OESimScore OEGraphSim::OESimScorePair OEMedChem::OEMCSMolSimScore OESpruce::OEStructuralSuperposition GetScoreMethod OEDocking::OEDockOptions GetScores OEFastROCS::OEShapeDatabase OEGraphSim::OEFPDatabase OEGraphSim::OEFastFPDatabase OEMedChem::OEMCSFragDatabase OEShape::OEBestOverlayResults GetScoreType OEFastROCS::OEShapeDatabaseOptions OEShape::OEColorOptions OEShape::OEShapeOptions GetScreenType OEChem::OECreateSubSearchDatabaseOptions OEChem::OESubSearchDatabase OEChem::OESubSearchScreen OEChem::OESubSearchScreenTypeBase GetScreenTypeString OEChem::OESubSearchScreenTypeBase GetSDData OEMedChem::OEMatchedPair GetSDEnergy OEConfGen::OETorDriveOptions GetSDTag OEMolProp::OEFilter GetSearchStatus OEChem::OESubSearchResult OEGraphSim::OESimSearchResult GetSecondaryStructure OEChem::OEResidue GetSeed OESystem::OERandom GetSelfColor OEShape::OEColorOverlap GetSelfOverlap OEShape::OEHermite GetSemiMethod OEMolAM1::OEAM1Options GetSeparateResidues OEBio::OESplitMolComplexOptions GetSeqAlignExtendPenalty OESpruce::OELoopBuilderOptions, [1] GetSeqAlignGapPenalty OESpruce::OELoopBuilderOptions GetSeqAlignMethod OESpruce::OELoopBuilderOptions GetSequence OESpruce::OESequenceMetadata GetSequenceID OEChem::OEResidue GetSequenceIdentity OEBio::OESequenceAlignment GetSequenceMetadata OESpruce::OEStructureMetadata GetSequenceSimilarity OEBio::OESequenceAlignment GetSerialNumber OEChem::OEResidue GetSetting OEChem::OEMolParameter OEChem::OEPredicateParameter OESystem::OEMultiParameter OESystem::OETypedParameter GetSettings OESystem::OETypedParameter GetSettingsVector OESystem::OEPODParameter GetShapeFunc OEShape::OEOverlapFunc GetShapeGaussians OEShape::OEShapeQueryBase GetShapeGrid OEShape::OEShapeQueryBase GetShapeGridSpacing OEFastROCS::OEShapeDatabase GetShapeOptions OEShape::OEShapeFunc GetShapeScore OEFastROCS::OEShapeDatabaseScore GetShapeTanimoto OEFastROCS::OEShapeDatabaseScore GetShapeTversky OEFastROCS::OEShapeDatabaseScore GetSheffieldParameters OESz::OESzybki GetSidechainBuilderOptions OESpruce::OEDesignUnitBuildOptions GetSimFunc OEFastROCS::OEShapeDatabaseOptions OEFastROCS::OEShapeDatabaseScore OEGraphSim::OEFPDatabaseOptions GetSimTypeString OEGraphSim::OESimFuncBase OEGraphSim::OETanimotoSim OEGraphSim::OETverskySim GetSinglePoseResults OEDocking::OEPositResults GetSiteResidues OEBio::OEDesignUnit OESpruce::OESuperpositionOptions GetSiteSize OESpruce::OEDesignUnitEnumerateSitesOptions GetSize OEChem::OEMolPropertyList OEChem::OESubSearchScreenTypeBase OEDepict::OEFont OESystem::OEBaseData OESystem::OEBaseDataT OESystem::OEBitVector OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetSizeLimit OEProton::OEAM1BCCCharges OEProton::OEAM1Charges GetSkipRefinement OEConfGen::OEMacrocycleBuilderOptions GetSliceEnsembleOptions OEConfGen::OEMacrocycleOmegaOptions OEConfGen::OEOmegaOptions OEConfGen::OETorDriver GetSmallStep OESystem::OEDots GetSMARTS OEMedChem::OEMatchedPairTransformExtractOptions GetSmarts OEBio::OEReceptorConstraintFeature OEDocking::OEFeature OEGraphSim::OEFPPattern GetSmiles OESpruce::OEHeterogenMetadata GetSoluteDielectric OESz::OESzybkiGeneralOptions GetSoluteDielectricConstant OESheff::OESheffieldOptions GetSolvationFreeEnergy OESz::OEFreeFormSolvResults GetSolvationType OESz::OETorsionScanOptions GetSolvEnergy OESz::OESingleConfResult GetSolvent OEBio::OEDesignUnit GetSolventDielectric OESz::OESzybkiSolventOptions GetSolventDielectricConstant OESheff::OESheffieldOptions GetSolventModel OESz::OESzybkiSolventOptions GetSolventOptions OESz::OEFreeFormConfOptions OESz::OESzybkiOptions GetSortByBitCounts OEChem::OECreateSubSearchDatabaseOptions GetSortedScores OEFastROCS::OEShapeDatabase OEGraphSim::OEFPDatabase OEGraphSim::OEFastFPDatabase OEGraphSim::OESimSearchResult OEMedChem::OEMCSFragDatabase GetSourceMol OEBio::OEAltLocationFactory GetSpaceGroup OEBio::OECrystalSymmetryParams OESystem::OESkewGrid GetSpacing OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetSparseMatrix OEGraphSim::OEFastFPDatabase GetSpheres OEDocking::OEFeature GetSplitCovalent OEBio::OESplitMolComplexOptions GetSplitCovalentCofactors OEBio::OESplitMolComplexOptions GetSplitOptions OESpruce::OEMakeDesignUnitOptions GetStackSize OEPlatform::OEThread GetStandardizeBondLen OEBio::OEPlaceHydrogensOptions GetStart OEDepict::OE2DPath GetStartFactor OEConfGen::OERingFragOptions GetStartingMaterial OEChem::OELibraryGen GetStartResidueInsertCode OESpruce::OESequenceMetadata GetStartResidueNumber OESpruce::OESequenceMetadata GetStarts OEShape::OEOverlayOptions OEShape::OEStarts GetState OEBio::OEAltLocationFactory GetStateIdx OEBio::OEPlaceHydrogensMoverNote GetStateName OEBio::OEPlaceHydrogensMoverNote GetStereo OEChem::OEAtomBase OEChem::OEBondBase OEChem::OEInChIOptions GetStickWidthScale OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByStick OEDepict::OEHighlightOverlayByBallAndStick GetStippleFactor OEDepict::OEPen GetStops OESystem::OEColorGradientBase GetStretchBendParams OEMolPotential::OEFFParams GetStretchParams OEMolPotential::OEFFParams GetStrict OEChem::OEParseSmilesOptions OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase GetStrictAtomTypes OEConfGen::OEMolBuilderOptions GetStrictMode OESpruce::OESidechainBuilderOptions GetStrictProlineMatch OESpruce::OELoopBuilderOptions GetStrictProtonationMode OESpruce::OEDesignUnitPrepOptions GetStrictStereo OEConfGen::OEOmegaOptions GetString OEChem::oemolothread GetStringData OESystem::OEBase GetStringDefault OESystem::OEParameter GetStringDefaults OESystem::OEParameter GetStringValue OESystem::OEParameter GetStringValues OESystem::OEParameter GetStructureID OESpruce::OEStructureMetadata GetStructureQuality OEBio::OEDesignUnit GetStubColumnCell OEDepict::OEImageTable GetStubColumnCells OEDepict::OEImageTable GetStubColumnColor OEDepict::OEImageTableOptions GetStubColumnFont OEDepict::OEImageTableOptions GetStyle OEDepict::OEFont OEGrapheme::OEPlotMarker GetSubChainID OEChem::OEResidue GetSubstituentSearch OEMedChem::OEBemisMurckoOptions GetSuperAtomLabelFont OEDepict::OE2DMolDisplayOptions GetSuperAtomStyle OEDepict::OE2DMolDisplayOptions GetSuperpose OESpruce::OEBioUnitExtractionOptions OESpruce::OEMakeDesignUnitOptions GetSuperpositionMethod OESpruce::OEMakeDesignUnitOptions GetSuperpositionType OESpruce::OESuperpositionOptions GetSuppressHydrogens OEDepict::OEAlignmentOptions OEDepict::OEPrepareDepictionOptions OEGrapheme::OEAlignedDepictionFrom3DOptions OEGrapheme::OEDepictionFrom3DOptions GetSurfaceArcFxn OEGrapheme::OEShapeQueryDisplayOptions GetSurfaceArea OESpruce::OEPocket GetSVGClass OEDepict::OEImageBase GetSVGGroup OEDepict::OEImageBase GetSVGGroups OEDepict::OEImageBase GetSVGMagnifyResidueInHover OEGrapheme::OE2DActiveSiteDisplayOptions GetSymmetrize OEProton::OEAM1BCCCharges OEProton::OEAM1Charges GetSymmetryClass OEChem::OEAtomBase GetSymmetryThreshold OEShape::OEBestOverlay OEShape::OEInertialStarts GetSzybkiGeneralOptions OESz::OEFreeFormConfOptions GetTable OEMolProp::OEFilter GetTag OEChem::OESDDataPair OESystem::OEBaseData GetTaggedComponents OEBio::OEDesignUnit GetTags OEBio::OEDesignUnit GetTanimoto OEShape::OEColorResults OEShape::OEOverlapResults OESpruce::OESecondaryStructureSuperposition GetTanimotoCombo OEFastROCS::OEShapeDatabaseScore OEShape::OEOverlapResults GetTarget OEBio::OEDesignUnit GetTargetAtoms OEChem::OEMatchBase GetTargetBonds OEChem::OEMatchBase GetTargetComponentID OEBio::OEDesignUnit OESpruce::OEDesignUnitSplitOptions GetTargetComponentTag OEBio::OEDesignUnit GetTargetMask OEBio::OEReceptor OEDocking::OEMakeReceptorOptions GetTautomers OESpruce::OEHeterogenMetadata GetTemperature OESz::OEFreeFormConfResults OESz::OESzybkiEnsembleResults OESz::OESzybkiGeneralOptions GetText OEDepict::OEHighlightLabel OESystem::OEColor GetTheta OEChem::OEEuler GetTimeLimit OEConfGen::OEFragOptions GetTimeout OEChem::OEInChIOptions GetTitle OEBio::OEDesignUnit OEBio::OEInteractionHintContainer OEChem::OEConfBase OEChem::OEMolBase OEChem::OEMolDatabase OEChem::OESubSearchDatabase OEGrapheme::OEShapeOverlapDisplay OEGrapheme::OEShapeQueryDisplay OEMolPotential::OEFFParams OEMolPotential::OEForceField OEShape::OEColorForceField OEShape::OEShapeQueryBase OEShape::OEShapeQueryPublic OESpicoli::OESurface OESpruce::OEHeterogenMetadata OESystem::OEAnnotation OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetTitleFont OEDepict::OE2DMolDisplayOptions GetTitleFontScale OEDepict::OE2DMolDisplayOptions GetTitleHeight OEDepict::OE2DMolDisplayOptions GetTitleLocation OEDepict::OE2DMolDisplayOptions GetTitles OEChem::OEMolDatabase gettitles.java Example Code GetTitleSeparator OEChem::OELibraryGen gettoken OEPlatform::oeistream GetTolerance OEOpt::OEOptimizer1 OEOpt::OEOptimizer2 GetTorDriveOptions OEConfGen::OEOmegaOptions OEConfGen::OETorDriver GetTorLib OEConfGen::OETorDriveOptions GetTorRule OEConfGen::OETorLib GetTorRules OEConfGen::OETorLib GetTorsion OEChem::OEConfBase GetTorsionDrive OEConfGen::OEOmegaOptions GetTorsionParams OEMolPotential::OEFFParams GetToSDData OEMedChem::OEMatchedPair GetTotal OEFastROCS::OEDBTracer GetTotalEnergy OEFF::OEComplexEnergies OESz::OESingleConfResult OESz::OESzybkiResults GetTotalEnergyWithHarmConstraint OESz::OESzybkiResults GetTotalEntropy OESz::OEFreeFormConfResults OESz::OESzybkiEnsembleResults GetTotalHCount OEChem::OEAtomBase GetTotalMols OEMedChem::OECreateMMPIndexStatus GetTotalRMSD OESz::OEProteinLigandOptResults GetTracer OEFastROCS::OEShapeDatabaseOptions GetTransform OEBio::OEDesignUnit OEChem::OEConfBase OEMedChem::OEMatchedPairTransform GetTransforms OEChem::OETrans GetTransformThreshold OESpruce::OELoopBuilderOptions GetTranslation OEChem::OETranslation OEFastROCS::OEShapeDatabaseScore OEShape::OEBestOverlayScore OESpruce::OESecondaryStructureSuperposition OESpruce::OEStructuralSuperposition GetTriangle OESpicoli::OESurface GetTriangles OESpicoli::OESurface GetTrianglesElement OESpicoli::OESurface GetTversky OEShape::OEColorResults OEShape::OEOverlapResults GetTverskyAlpha OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabaseOptions GetTverskyBeta OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabaseOptions GetTverskyCombo OEFastROCS::OEShapeDatabaseScore GetType OEBio::OEReceptorProteinConstraint OEChem::OEAtomBase OEChem::OEBondBase OEChem::OEExprBase OEChem::OELingoSim OEDocking::OEProteinConstraint OEShape::OEColorForceField OESpruce::OEHeterogenMetadata OESystem::OEAnnotation OESystem::OEScalarGrid OESystem::OESkewGrid GetTypeCheck OEMolProp::OEFilter GetTypedParameter OESystem::OEInterface GetTypeName OEShape::OEColorForceField GetTypes OEShape::OEColorForceField GetU11 OEChem::OEAnisoUij GetU12 OEChem::OEAnisoUij GetU13 OEChem::OEAnisoUij GetU22 OEChem::OEAnisoUij GetU23 OEChem::OEAnisoUij GetU33 OEChem::OEAnisoUij GetUnboundLigandArea OEPB::OESimpleBindResults GetUnboundLigandAreaEnergy OEPB::OESimpleBindResults GetUnboundLigandCoulombEnergy OEPB::OEBindResults GetUnboundLigandZapEnergy OEPB::OESimpleBindResults GetUnboundProteinArea OEPB::OESimpleBindResults GetUnboundProteinAreaEnergy OEPB::OESimpleBindResults GetUnboundProteinCoulombEnergy OEPB::OEBindResults GetUnboundProteinZapEnergy OEPB::OESimpleBindResults GetUnhashed OEGraphSim::OEFPPattern GetUnindexedMols OEMedChem::OECreateMMPIndexStatus GetUnitCell OESystem::OESkewGrid GetUnsaturatedHeteroBonds OEMedChem::OEBemisMurckoOptions GetUseAttract OEMolPotential::OENonBondIntcsOptions GetUseCoulomb OEMolPotential::OENonBondIntcsOptions GetUseGPU OEConfGen::OETorDriveOptions GetUseHydrogens OEPB::OEArea OEShape::OEBestOverlay OEShape::OEOverlap OEShape::OEOverlapPrep GetUseInput3D OESz::OEFreeFormSolvOptions GetUseInputEnsemble OESz::OEFreeFormConfOptions OESz::OEFreeFormSolvOptions GetUseMaxHits OEShape::OEROCSOptions GetUseMMFF94s OEFF::OEMMFFIEFFOptions GetUseOptimalLambdas OEShape::OEHermiteOptions GetUsePackingResidues OESpruce::OELoopBuilderOptions GetUseProxyGrid OEShape::OEAnalyticOptions GetUserStarts OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay GetUseSinglePointPB OESz::OETorsionScanOptions GetUseSolventCorr OESz::OEFreeFormConfOptions GetUseVdW OEMolPotential::OENonBondIntcsOptions GetValence OEChem::OEAtomBase GetValenceCorrection OEChem::OELibraryGen GetValidateKekule OEChem::OELibraryGen OEChem::OEUniMolecularRxn GetValue OEChem::OEMolParameter OEChem::OEPredicateParameter OEChem::OESDDataPair OEGrapheme::OEColorGradientLabel OEMolProp::OEXLogPResult OEPlatform::OEHalfFloat OEPlatform::OEOnce OESystem::OEColorStop OESystem::OEMultiParameter OESystem::OETypedParameter GetValues OEMolPotential::OEInteraction OESystem::OEFixedGrid OESystem::OEFixedMultiGrid OESystem::OESkewGrid OESystem::OETypedParameter GetValuesVector OESystem::OEPODParameter GetVar OEFF::OEComplexFF OEMolPotential::OEInterMolFunc1 OEOpt::OEAdaptor GetVariogram OEGraphSim::OEFPVariogram OEGraphSim::OEFastFPDatabase GetVdWCutoff OEMolPotential::OENonBondIntcsOptions GetVdwParams OEMolPotential::OEFFParams GetVdwRadius OEMolPotential::OEFFParams GetVerbose OEMedChem::OECreateMMPIndexOptions OEPB::OEZap OEProton::OEFormalChargeOptions OESz::OESzybkiGeneralOptions GetVersion OEChem::OESubSearchScreenTypeBase OEGraphSim::OEFPTypeParams OESystem::OEHeader GetVersionString OEChem::OESubSearchScreenTypeBase GetVertex OESpicoli::OESurface GetVertexClique OESpicoli::OESurface GetVertexCliqueElement OESpicoli::OESurface GetVertices OESpicoli::OESurface GetVerticesElement OESpicoli::OESurface GetVibEntropy OESz::OESzybkiResults GetVibrationalEntropy OESz::OESingleConfResult GetVisibility OESystem::OEParameter GetVolume OEMath::OEBox OEMath::OESphere GetWarnings OESz::OEFreeFormSolvResults GetWarnNoLigand OEBio::OESplitMolComplexOptions GetWarts OEConfGen::OEFlipperOptions OEConfGen::OEOmegaOptions OEProton::OEFormalChargeOptions GetWaterFilter OEBio::OESplitMolComplexOptions GetWaterProcessing OEBio::OEPlaceHydrogensOptions GetWeight OEBio::OEInteractionHint GetWidth OEDepict::OE2DMolDisplay OEDepict::OE2DMolDisplayOptions OEDepict::OEImage OEDepict::OEImageBase OEDepict::OEImageFrame OEGrapheme::OE2DActiveSiteDisplay OESystem::OEGaussian OESystem::OEGaussianBase GetWidths OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase GetWriteFxns OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase GetWriteIdx OEChem::OEMolDatabaseSaveOptions GetX OEDepict::OE2DPoint OEDocking::OESphereBase OEMath::OESphere OESystem::OEGaussian OESystem::OEGaussianBase OESystem::OEGridBase GetXDim OEMath::OEBox OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetXIdx OESystem::OEGridBase GetXInc OESystem::OEGridBase GetXMax OEDocking::OEBox OEDocking::OEBoxBase OEMath::OEBox OESystem::OEGridBase GetXMid OEMath::OEBox OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetXMin OEDocking::OEBox OEDocking::OEBoxBase OEMath::OEBox OESystem::OEGridBase GetY OEDepict::OE2DPoint OEDocking::OESphereBase OEMath::OESphere OESystem::OEGaussian OESystem::OEGaussianBase OESystem::OEGridBase GetYDim OEMath::OEBox OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetYIdx OESystem::OEGridBase GetYInc OESystem::OEGridBase GetYMax OEDocking::OEBox OEDocking::OEBoxBase OEMath::OEBox OESystem::OEGridBase GetYMid OEMath::OEBox OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetYMin OEDocking::OEBox OEDocking::OEBoxBase OEMath::OEBox OESystem::OEGridBase GetZ OEDocking::OESphereBase OEMath::OESphere OESystem::OEGaussian OESystem::OEGaussianBase OESystem::OEGridBase GetZap OEPB::OEBind GetZapEnergy OEPB::OESimpleBindResults GetZDim OEMath::OEBox OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetZIdx OESystem::OEGridBase GetZInc OESystem::OEGridBase GetZMax OEDocking::OEBox OEDocking::OEBoxBase OEMath::OEBox OESystem::OEGridBase GetZMid OEMath::OEBox OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetZMin OEDocking::OEBox OEDocking::OEBoxBase OEMath::OEBox OESystem::OEGridBase GetZValue OEBio::OECrystalSymmetryParams GONNET GRASP GridIdxToElement OESystem::OEGridBase GridIdxToSpatialCoord OESystem::OEGridBase

H

Has OEChem::OEMolPropertyFxn OESystem::OEInterface HasAlphaBetaUnsat OEChem::OEAtomBase HasAltLoc OEBio::OEDesignUnit HasAtom OEBio::OEInteractionHintFragment OEChem::OEAtomBondSet OEChem::OEGroupBase HasBadClash OEBio::OEPlaceHydrogensMoverNote HasBendParams OEMolPotential::OEFFParams HasBond OEChem::OEAtomBondSet OEChem::OEGroupBase HasCalculatedGeometry OEBio::OEInteractionHint HasColor OEShape::OEShapeQueryBase HasCompareMols OEChem::OEConfTestBase OEChem::OEDefaultConfTest HasComponent OEBio::OEDesignUnit HasCustomConstraints OEBio::OEReceptor HasCutoff OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions OEShape::OEROCSOptions HasCutoffGT OEFastROCS::OEShapeDatabaseOptions HasCutoffLT OEFastROCS::OEShapeDatabaseOptions HasData OESystem::OEBase HasDupParameters OESystem::OEOptions HasEntropy OESz::OESzybkiEnsembleResults HasFixPattern OEConfGen::OEConfFixOptions HasFlexibleResidues OESz::OESzybkiProteinOptions HasFlippedBadClusterClash OEBio::OEPlaceHydrogensMoverNote HasHeader OEDepict::OEImageTableOptions HasHyperlink OEDepict::OEFont HasIndexableFragmentHeavyAtomRange OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMatchedPairAnalyzerOptions HasInnerContourLevel OEBio::OEReceptor HasInteraction OEBio::OEInteractionHintContainer HasIridiumData OEBio::OEStructureQuality HasLabel OEDepict::OE2DAtomDisplay HasLigand OEBio::OEDesignUnit HasLigandConstraints OESpruce::OESuperpositionOptions HasMatchedPair OEMedChem::OEMatchedPairTransform HasMetal OEBio::OEDesignUnit HasMolecule OEShape::OEShapeQueryBase HasNegativeImageGrid OEBio::OEReceptor HasNucleicAcid OEBio::OEDesignUnit

HasOption OESystem::OEOptions HasOriginalBadClusterClash OEBio::OEPlaceHydrogensMoverNote HasOuterContourLevel OEBio::OEReceptor HasPackingResidues OEBio::OEDesignUnit HasParameter OESystem::OEOptions HasPerceived OEChem::OEMolBase HasProperties OEChem::OEMolPropertyList HasProperty OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay HasProtectiveGroupStyle OEDepict::OE2DMolDisplayOptions HasProtein OEBio::OEDesignUnit HasProteinConstraints OEBio::OEReceptor HasReceptor OEBio::OEDesignUnit HasRole OESystem::OERoleSet HasSDData OEMedChem::OEMatchedPair HasShape OEShape::OEShapeQueryBase HasShapeGrid OEShape::OEShapeQueryBase HasSiteResidues OEBio::OEDesignUnit HasSolvent OEBio::OEDesignUnit HasSpaceGroup OESystem::OESkewGrid HasStereoSpecified OEChem::OEAtomBase OEChem::OEBondBase HasStretchParams OEMolPotential::OEFFParams HasStructureQuality OEBio::OEDesignUnit HasStubColumn OEDepict::OEImageTableOptions HasTarget OEBio::OEDesignUnit HasTitle OEBio::OEDesignUnit OEChem::OEConfBase HasTorRule OEConfGen::OETorLib HasTorsionParams OEMolPotential::OEFFParams HasTransform OEBio::OEDesignUnit HasUnitCell OESystem::OESkewGrid HasVdwParams OEMolPotential::OEFFParams HBonds OEPlaceHydrogens Helix hermiteexpansion.java Example Code hermitetanimoto.java Example Code Hierarchical View

I

IdentifyConformer OESz::OEFreeFormConfAdvanced implicit hydrogens implicitmillsdeannoringsexample.java Example Code InChI InChIKey IncrementCount OESystem::OEErrorHandlerImplBase IncrementReadFailureCt OEChem::oemolistream inertialatheavyatomstartsexample.java Example Code, [1] Info OESystem::OEErrorHandler Init OEChem::OECliqueSearch OEChem::OELibraryGen OEChem::OELingoSim OEChem::OEMCSSearch OEChem::OESubSearch OEChem::OEUniMolecularRxn OEShape::OEColorForceField Initialize OEDocking::OEDock OEDocking::OEPosit OEDocking::OEScore installation integer atom type integer bond type Invert OEMedChem::OEMatchedPairTransform IsActiveTerm OESz::OESzybkiResults IsAngle OEMolPotential::OEBendParams IsAromatic OEChem::OEAtomBase OEChem::OEBondBase IsAtomsSet OESpicoli::OESurface IsBitOn OESystem::OEBitVector IsBodyPage OEDepict::OEReport IsBond OEMolPotential::OEStretchParams IsCarbon OEChem::OEAtomBase IsCharged OEBio::OEHBondInteractionHint IsChiral OEChem::OEAtomBase OEChem::OEBondBase IsClosed OEDepict::OE2DPath IsColorSet OESpicoli::OESurface IsConnected OEChem::OEAtomBase IsConverged OEMolAM1::OEAM1Results IsCurvatureSet OESpicoli::OESurface IsDataType OEBio::OEDesignUnit OEBio::OEInteractionHint OEBio::OEInteractionHintFragment OEChem::OEAtomBase OEChem::OEBondBase OEChem::OEMolBase OEChem::OEMolDatabase OEChem::OEQAtomBase OEChem::OEQBondBase OEChem::OEQMolBase OEDepict::OE2DMolDisplay OEDepict::OEAtomDisplayBase OEDepict::OEBondDisplayBase OEDepict::OEMolDisplayBase OESpicoli::OESurface OESystem::OEAnnotation OESystem::OEBase OESystem::OEBinaryIOHandler OESystem::OEContainer OESystem::OEFixedGrid OESystem::OEFixedMultiGrid OESystem::OEGaussian OESystem::OEGaussianBase OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase OESystem::OEGrid OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OEMultiGrid OESystem::OEScalarGrid OESystem::OESkewGrid IsDeleted OEChem::OEAtomBase OEChem::OEBondBase OEChem::OEConfBase OEChem::OEGroupBase OEChem::OEMCMolBase OEChem::OEMolBase OEChem::OEMolDatabase IsDirectory OEPlatform::OEFile IsDistanceSet OESpicoli::OESurface IsEmpty OEChem::OEAtomBondSet OEChem::OEGroupBase OEDepict::OEImage OEShape::OEShapeQueryBase OESystem::OEBitVector OESystem::OEColorGradientBase IsEquivalent OEChem::OEExprBase IsExecutable OEPlatform::OEFile IsFaceNormalsSet OESpicoli::OESurface IsFile OEPlatform::OEFile IsFlippable OEBio::OEPlaceHydrogensMoverNote IsFlipped OEBio::OEPlaceHydrogensMoverNote IsFocusTargetSet OEPB::OEZap IsGridPage OEDepict::OEReport IsHalogen OEChem::OEAtomBase IsHetAtom OEChem::OEResidue IsHydrogen OEChem::OEAtomBase

IsIndexed OEMedChem::OEMCSFragDatabase OEMedChem::OEMatchedPairAnalyzer IsInGrid OESystem::OEGridBase IsInitialized OEDocking::OEDock OEDocking::OEPosit OEDocking::OEScore IsInLittleEndian OEGraphSim::OEFastFPDatabaseParams IsInRing OEChem::OEAtomBase OEChem::OEBondBase IsInside OEMath::OEBox OEMath::OESphere IsInter OEBio::OEInteractionHint IsIntra OEBio::OEInteractionHint IsIonizable OEBio::OEPlaceHydrogensMoverNote IsIonized OEBio::OEPlaceHydrogensMoverNote IsLegalString OESystem::OEParameter IsLink OEPlatform::OEFile IsMetal OEChem::OEAtomBase IsMultiPage OEDepict::OEImageFileCreatorBase IsNitrogen OEChem::OEAtomBase IsNormalsSet OESpicoli::OESurface isotopic mass IsOxygen OEChem::OEAtomBase IsPair OEMolPotential::OEVdwParams IsPhosphorus OEChem::OEAtomBase IsPolar OEChem::OEAtomBase IsPolarHydrogen OEChem::OEAtomBase IsPotentialSet OESpicoli::OESurface IsReadable OEPlatform::OEFile IsRedundant OEMolPotential::OEQuatAdaptor IsRegular OESystem::OESkewGrid IsRestrained OEBio::OEPlaceHydrogensMoverNote IsRotor OEChem::OEBondBase IsRxn OEChem::OEMolBase IsSet OESystem::OEParameter IsSetToString OESystem::OEParameter IsSingleton OEBio::OEPlaceHydrogensDetails IsSpacingSet OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid IsSulfur OEChem::OEAtomBase IsTitleSet OESystem::OEGridBase OESystem::OESkewGrid IsTorsion OEMolPotential::OETorsionParams IsUnique OESz::OESzybkiResults IsValid OEBio::OECationPiInteractionHint OEBio::OEChelatorInteractionHint OEBio::OEClashInteractionHint OEBio::OEContactInteractionHint OEBio::OECovalentInteractionHint OEBio::OEHBondInteractionHint OEBio::OEHalogenBondInteractionHint OEBio::OEInteractionHint OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintContainer OEBio::OEInteractionHintTypeBase OEBio::OELigandInteractionHintComponent OEBio::OEPlaceHydrogensDetails OEBio::OEProteinInteractionHintComponent OEBio::OEReceptor OEBio::OESaltBridgeInteractionHint OEBio::OEStackingInteractionHint OEChem::OECSVHeader OEChem::OEConfRMSD OEChem::OELingoSim OEChem::OEMatchBase OEChem::OESubSearchDatabase OEChem::OESubSearchResult OEChem::OESubSearchScreen OEDepict::OE2DMolDisplay OEDepict::OE2DPath OEDepict::OEAlignmentResult OEDepict::OENearestAtom OEDepict::OENearestBond OEGraphSim::OEFPTypeParams OEGraphSim::OEFastFPDatabase OEGraphSim::OEFastFPDatabaseParams OEGraphSim::OESimSearchResult OEGrapheme::OE2DActiveSiteDisplay OEGrapheme::OENearestResidue OEGrapheme::OEShapeOverlapDisplay OEGrapheme::OEShapeQueryDisplay OEMolPotential::OEBendParams OEMolPotential::OEOutOfPlaneParams OEMolPotential::OEStretchParams OEMolPotential::OETorsionParams OEMolPotential::OEVdwParams OEProton::OEChargeEngineBase OEProton::OEDesignUnitCharges IsValid() OEMolProp::OEXLogPResult IsVertexCliqueSet OESpicoli::OESurface IsVisible OEDepict::OEAtomDisplayBase OEDepict::OEBondDisplayBase OEDepict::OEImageFileBase OEDepict::OESVGGroup IsWritable OEPlatform::OEFile IsXMidSet OESystem::OEGridBase IsYMidSet OESystem::OEGridBase IsZMidSet OESystem::OEGridBase itf interface definition specification

J

Join OEPlatform::OEThread

K

Kekule form Kekule SMILES

kekulization

L

Lap OESystem::OECycleTimer OESystem::OEStopwatch OESystem::OEWallTimer LastBit OESystem::OEBitVector length OEPlatform::oestream libgen.java Example Code licensing ligandentropy.java Example Code ligandflexproteinnewton.java Example Code

ligandmultipleoptions.java Example Code LINGO, [1] Linux Load OEFF::OEFF14SBSmirnoffParams OEMolSmirnoff::OESmirnoffParams OESystem::OEParameter LoadDefault OESystem::OEParameter LoadPotentialGrid OESz::OESzybki LoadValue OESystem::OEParameter

M

MACCS macOS macrocycle.java Example Code make MakeAltMol OEBio::OEAltLocationFactory MakeCurrentAltMol OEBio::OEAltLocationFactory makefastfp.java Example Code makefastfp.txt Example Code Makefile makefraglib.java Example Code MakePrimaryAltMol OEBio::OEAltLocationFactory makereceptor.java Example Code Manhattan similarity measure marching cubes Match OEChem::OECliqueSearch OEChem::OEMCSSearch OEChem::OESubSearch match2img.java Example Code match2img.txt Example Code matchedpairtransform.java Example Code matchedpairtransformlist.java Example Code matchedpairtransformprobe.java Example Code maximum atom index maximum bond index maximum common substructure search MCMol OEChem::OEMol mcs3dalign.java Example Code mcsalign2d.java Example Code mcsalign2d.txt Example Code mcsfragdatabase.java Example Code MCSS MDL query mdlquery2img.java Example Code

mdlquery2img.txt Example Code mdlreaction2img.java Example Code mdlreaction2img.txt Example Code Mean OEGraphSim::OEFPHistogram MeetsCutoff OEShape::OEROCSOptions MinimizeRMSD OEChem::OEConfRMSD minpath.java Example Code ModifyOptions OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairAnalyzerOptions mol2img.java Example Code mol2img.txt Example Code mol2nam_example.java Example Code mol2nam_example.txt Example Code molchunk.java Example Code molcount.java Example Code molecule dimension molecule energy molecule title, [1] MoleculeToCores OEMedChem::OEMCSFragDatabase molextract.java Example Code molfilter.java Example Code molgrep.java Example Code molpropcsv.java Example Code molpropsddata.java Example Code molproptable.java Example Code mols2img.java Example Code mols2img.txt Example Code mols2pdf.java Example Code mols2pdf.txt Example Code molstats.java Example Code Msg OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase

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nam2mol_example.java Example Code nam2mol_example.txt Example Code NegateBits OESystem::OEBitVector neutralionization.java Example Code NewAtom OEChem::OEMolBase NewBody OEDepict::OEReport NewBond OEChem::OEMolBase NewCell OEDepict::OEReport NewConf OEChem::OEMCMolBase NewGroup OEChem::OEMolBase NewPage OEDepict::OEMultiPageImageFile NewSVGClass OEDepict::OEImageBase NewSVGGroup OEDepict::OEImageBase Next OEPlatform::OEDirectoryScan NextBit OESystem::OEBitVector NextFloat OESystem::OERandom NextInt OESystem::OERandom non-terminal atom Null OESystem::OEProtectedBuffer NumAtoms OEBio::OEInteractionHintFragment OEChem::OEAtomBondSet OEChem::OEGroupBase OEChem::OEMatch OEChem::OEMatchBase OEChem::OEMolBase OEDepict::OEAlignmentResult OEMolPotential::OEInteraction NumAutomorphs OEChem::OEConfRMSD number of atoms number of bonds NumBins OEGraphSim::OEFPHistogram NumBodyPages OEDepict::OEReport NumBonds OEChem::OEAtomBondSet OEChem::OEGroupBase OEChem::OEMatch OEChem::OEMatchBase OEChem::OEMolBase OEDepict::OEAlignmentResult NumColorTypes OEGrapheme::OEColorForceFieldDisplay NumCols OEDepict::OEImageGrid OEGrapheme::OE2DActiveSiteLegendDisplayOptions OEGrapheme::OEColorForceFieldLegendDisplayOptions NumColsPerPage OEDepict::OEReport OEDepict::OEReportOptions NumColumns OEDepict::OEImageTable OEDepict::OEImageTableOptions NumConfs OEChem::OEMCMolBase OEFastROCS::OEShapeDatabase OESz::OESzybkiEnsembleResults NumDataPoints OEGrapheme::OERamachandranPlot NumDataTags OEMedChem::OEMatchedPair

NumFeatures OEBio::OEReceptorCustomConstraints OEDocking::OECustomConstraints NumFingerPrints OEGraphSim::OEFPDatabase OEGraphSim::OEFastFPDatabase OEGraphSim::OEFastFPDatabaseParams NumFragments OEBio::OEInteractionHintContainer OEMedChem::OEMCSFragDatabase NumGaussians OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase NumGridPages OEDepict::OEReport NumGroups OEChem::OEMolBase NumIndexNodes OEMedChem::OEMatchedPairAnalyzer NumInteractions OEBio::OEInteractionHintContainer NumMatchedPairs OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairTransform NumMatches OEChem::OESubSearchDatabase OEChem::OESubSearchResult NumMolecules OEBio::OEInteractionHintContainer OEChem::OESubSearchDatabase NumMols OEChem::OEMolDatabase OEMedChem::OEMCSFragDatabase OEMedChem::OEMatchedPairAnalyzer NumOrientations OESzmap::OESzmapEngineOptions OESzmap::OESzmapResults NumPages OEDepict::OEMultiPageImageFile OEDepict::OEReport NumPossibleProducts OEChem::OELibraryGen NumProcessors OEChem::OESubSearchDatabase NumProteinConstraints OEBio::OEReceptor NumReactants OEChem::OELibraryGen NumRings OEChem::OE2DRingDictionary NumRoles OESystem::OERoleSet NumRows OEDepict::OEImageGrid OEDepict::OEImageTable OEDepict::OEImageTableOptions OEGrapheme::OE2DActiveSiteLegendDisplayOptions OEGrapheme::OEColorForceFieldLegendDisplayOptions NumRowsPerPage OEDepict::OEReport OEDepict::OEReportOptions NumSamples OEGraphSim::OEFPHistogram NumScreened OEChem::OESubSearchResult NumSearched OEChem::OESubSearchResult OEGraphSim::OESimSearchResult NumSmarts OEBio::OEReceptorConstraintFeature OEDocking::OEFeature NumSpheres OEBio::OEReceptorConstraintFeature OEDocking::OEFeature NumStops OESystem::OEColorGradientBase NumTargets OEChem::OESubSearchResult OEGraphSim::OESimSearchResult NumTotalMatches OEChem::OESubSearchResult NumValues OEMolPotential::OEInteraction NumVar OEOpt::OEFunc0 nxnshape.java Example Code

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OE_DIR, [1], [2], [3] OE_LICENSE, [1], [2], [3], [4] OEAddExplicitHydrogens OEAltGroup OEAltLocation OEAltLocationFactory OEAM1BCC::OEBCCPartialCharges OEAM1BCC::OEBCCType OEAM1BCC::OEBCCType::AM1 OEAM1BCC::OEBCCType::PM3 OEAM1BCC::OESymmetrizePartialCharges OEAssignAromaticFlags OEAtomBase OEAtomIdxSelected OEBio::OEAltGroup Constructors GetGroupCount GetGroupID GetLocationCount GetLocations SetGroupID operator bool operator= OEBio::OEAltLocation Constructors GetGroupID GetLocationCount GetLocationID SetLocationID operator bool operator= OEBio::OEAltLocationFactory Constructors GetAltAtoms GetAtomMapSize GetBondMapSize GetCurrentAtoms GetCurrentLocations GetGroup GetGroupCount GetGroups GetLocation GetLocationCodes GetSourceMol GetState MakeAltMol MakeCurrentAltMol MakePrimaryAltMol SetAlt SetPrimaryAlt SetState operator= OEBio::OEAltLocationState Constructors ToHexString operator bool operator= OEBio::OEAltLocFactOption OEBio::OEAltLocFactOption::None OEBio::OEAltLocFactOption::TrustInputBonds OEBio::OEAssumption OEBio::OEAssumption::BondedResidue OEBio::OEAssumption::Default OEBio::OEAssumption::None OEBio::OEAssumption::PDBOrder OEBio::OEAssumption::ResPerceived OEBio::OEAtomMatchResidue Constructors CreateCopy operator() OEBio::OEAtomMatchResidueID Constructors GetAlternateLocation() GetChainID GetFragmentNumber GetInsertCode GetName GetResidueNumber SetAlternateLocation SetChainID SetFragmentNumber SetInsertCode SetName SetResidueNumber OEBio::OEBuildUnitCell OEBio::OECalculateDPI OEBio::OECationPiInteractionHint Constructors CreateCopy IsValid operator= OEBio::OECationPiInteractionHintType OEBio::OECationPiInteractionHintType::LigandCation OEBio::OECationPiInteractionHintType::LigandPi OEBio::OECationPiInteractionHintType::ProteinCation OEBio::OECationPiInteractionHintType::ProteinPi OEBio::OEChelatorInteractionHint Constructors CreateCopy GetChelatorType IsValid operator= OEBio::OEChelatorInteractionHintType OEBio::OEChelatorInteractionHintType::IntramolecularProtein OEBio::OEChelatorInteractionHintType::LigandChelates OEBio::OEChelatorInteractionHintType::ProteinChelates OEBio::OEClashInteractionHint Constructors CreateCopy IsValid operator= OEBio::OEClearMolComplexSDData OEBio::OEClearPlaceHydrogensMetadata OEBio::OECombineMolComplexFragments OEBio::OEConfigureSplitMolComplexOptions OEBio::OEContactInteractionHint Constructors CreateCopy IsValid operator= OEBio::OECopyCrystalSymmetry OEBio::OECountMolComplexSites OEBio::OECovalentInteractionHint Constructors CreateCopy IsValid operator= OEBio::OECrystalSymmetryParams Constructors GetA GetAlpha GetB GetBeta GetC GetGamma GetSpaceGroup GetZValue SetA SetAlpha SetB SetBeta SetC SetGamma SetSpaceGroup SetZValue OEBio::OEDesignUnit Clear ClearReceptor Constructors CreateCopy GetComponent GetComponentID GetComponentTag GetComponents GetComponentsWithin GetDataType GetIDs GetLigand GetNucleicAcid GetPackingResidues GetProtein GetReceptor GetSiteResidues GetSolvent GetStructureQuality GetTaggedComponents GetTags GetTarget GetTargetComponentID GetTargetComponentTag GetTitle GetTransform HasAltLoc HasComponent HasLigand HasMetal HasNucleicAcid HasPackingResidues HasProtein HasReceptor HasSiteResidues HasSolvent HasStructureQuality HasTarget HasTitle HasTransform IsDataType SetTitle operator bool operator= OEBio::OEDesignUnitComponents OEBio::OEDesignUnitComponents::All OEBio::OEDesignUnitComponents::Cofactors OEBio::OEDesignUnitComponents::CounterIons OEBio::OEDesignUnitComponents::Default OEBio::OEDesignUnitComponents::Excipients OEBio::OEDesignUnitComponents::Ligand OEBio::OEDesignUnitComponents::Lipids OEBio::OEDesignUnitComponents::ListComponents OEBio::OEDesignUnitComponents::MacroMolComponents OEBio::OEDesignUnitComponents::Metals OEBio::OEDesignUnitComponents::MolComponents OEBio::OEDesignUnitComponents::Nucleic OEBio::OEDesignUnitComponents::OtherCofactors OEBio::OEDesignUnitComponents::OtherLigands OEBio::OEDesignUnitComponents::OtherNucleics OEBio::OEDesignUnitComponents::OtherProteins OEBio::OEDesignUnitComponents::PackingResidues OEBio::OEDesignUnitComponents::Polymers OEBio::OEDesignUnitComponents::PostTranslational OEBio::OEDesignUnitComponents::Protein OEBio::OEDesignUnitComponents::Solvent OEBio::OEDesignUnitComponents::Sugars OEBio::OEDesignUnitComponents::TargetComplex OEBio::OEDesignUnitComponents::TargetComplexNoSolvent OEBio::OEDesignUnitComponents::Undefined OEBio::OEDesignUnitComponents::Unknown OEBio::OEDesignUnitFileType OEBio::OEDesignUnitFileType::OEDesignUnit OEBio::OEDesignUnitFileType::Undefined OEBio::OEExpandCrystalSymmetry OEBio::OEFilterMolComplexFragments OEBio::OEGetActiveSiteInteractionHintTypes OEBio::OEGetAlignment OEBio::OEGetAlignmentMethodName OEBio::OEGetAlignments OEBio::OEGetAtomMatchResidueIDs OEBio::OEGetCalculatedInteractionGeometries OEBio::OEGetChis OEBio::OEGetCrystalSymmetry OEBio::OEGetDesignUnitComponentID OEBio::OEGetDesignUnitComponentName OEBio::OEGetDesignUnitComponentNamesFromMask OEBio::OEGetInteractions OEBio::OEGetIridiumCategoryFromName OEBio::OEGetIridiumCategoryName OEBio::OEGetMolComplexComponents OEBio::OEGetMolComplexFilterCategoryName OEBio::OEGetMolComplexFragments OEBio::OEGetPhi OEBio::OEGetPlaceHydrogensMetadata OEBio::OEGetPlaceHydrogensMoverClassName OEBio::OEGetProteinTorsionName OEBio::OEGetPsi OEBio::OEGetRamachandranCategoryName OEBio::OEGetRamachandranTypeName OEBio::OEGetResidueAtom OEBio::OEGetResidueAtoms OEBio::OEGetResidueDatabaseCategoryName OEBio::OEGetResidues OEBio::OEGetRotamers OEBio::OEGetSecondaryStructureID OEBio::OEGetSecondaryStructureName OEBio::OEGetSecondaryStructureStrandID OEBio::OEGetSecondaryStructureType OEBio::OEGetSimpleAlignment OEBio::OEGetSpaceGroup OEBio::OEGetSpaceGroupNumber OEBio::OEGetTorsion OEBio::OEHalogenBondInteractionHint Constructors CreateCopy IsValid operator= OEBio::OEHalogenBondInteractionHintType OEBio::OEHalogenBondInteractionHintType::LigandElectrophile OEBio::OEHalogenBondInteractionHintType::LigandNucleophile OEBio::OEHalogenBondInteractionHintType::ProteinElectrophile OEBio::OEHalogenBondInteractionHintType::ProteinNucleophile OEBio::OEHasAlternateLocation Constructors CreateCopy operator() OEBio::OEHasBondedResidues OEBio::OEHasCrystalSymmetry OEBio::OEHasInteractionHint Constructors CreateCopy operator() operator= OEBio::OEHasInteractionHintType Constructors CreateCopy operator() operator= OEBio::OEHasPDBAtomIndex Constructors CreateCopy operator() OEBio::OEHasPlaceHydrogensMetadata OEBio::OEHasResidueInteractionHint Constructors CreateCopy operator() operator= OEBio::OEHasSecondaryStructure Constructors CreateCopy operator() OEBio::OEHBondInteractionHint Constructors CreateCopy GetHBondType IsCharged IsValid operator= OEBio::OEHBondInteractionHintType OEBio::OEHBondInteractionHintType::Clash OEBio::OEHBondInteractionHintType::ClashAcceptorAcceptor OEBio::OEHBondInteractionHintType::ClashDonorDonor OEBio::OEHBondInteractionHintType::IntramolecularLigand OEBio::OEHBondInteractionHintType::IntramolecularProtein OEBio::OEHBondInteractionHintType::LigandAccepts OEBio::OEHBondInteractionHintType::LigandDonates OEBio::OEHBondInteractionHintType::NonIdealLigandAccepts OEBio::OEHBondInteractionHintType::NonIdealLigandDonates OEBio::OEHBondInteractionHintType::NonIdealProteinAccepts OEBio::OEHBondInteractionHintType::NonIdealProteinDonates OEBio::OEHBondInteractionHintType::ProteinAccepts OEBio::OEHBondInteractionHintType::ProteinDonates OEBio::OEHBondInteractionHintType::UnpairedLigandAcceptor OEBio::OEHBondInteractionHintType::UnpairedLigandDonor OEBio::OEHBondInteractionHintType::UnpairedProteinAcceptor OEBio::OEHBondInteractionHintType::UnpairedProteinDonor OEBio::OEHierChain Constructors GetAtom GetChainID GetFragments GetOEResidue GetResidue operator= OEBio::OEHierFragment Constructors GetAtom GetFragmentNumber GetOEResidue GetResidue GetResidues operator= OEBio::OEHierResidue Constructors GetAtom GetAtoms GetOEResidue GetResidueName GetResidueNumber operator= OEBio::OEHierView Constructors GetAtom GetAtoms GetChains GetFragments GetResidue GetResidues operator= OEBio::OEInteractionHint Constructors CreateCopy GetBgnFragment GetCalculatedGeometries GetCalculatedGeometry GetDataType GetDetails GetEndFragment GetFragment GetInteractionType GetWeight HasCalculatedGeometry IsDataType IsInter IsIntra IsValid SetDetails SetWeight operator= OEBio::OEInteractionHintComponentTypeBase Constructors CreateCopy GetName IsValid operator!= operator= operator== OEBio::OEInteractionHintContainer AddMolecule Constructors DeleteInteraction DeleteInteractions GetInteractions GetMolecule GetMolecules GetTitle HasInteraction IsValid NumFragments NumInteractions NumMolecules SetTitle operator bool OEBio::OEInteractionHintFragment AddAtom Constructors CreateCopy GetAtom GetAtoms GetComponentType GetDataType HasAtom IsDataType NumAtoms operator= OEBio::OEInteractionHintTypeBase Constructors CreateCopy GetName IsValid operator!= operator= operator== OEBio::OEIridiumCategory OEBio::OEIridiumCategory::HT OEBio::OEIridiumCategory::MT OEBio::OEIridiumCategory::NA OEBio::OEIridiumCategory::NT OEBio::OEIridiumData Clear Constructors DetermineCategory GetAltConfs GetAsDensity GetCategory GetDPI GetExcipients GetHasMTZ GetIrrationalRFree GetLigandDensity GetPackingResidues GetPartOccupancyLigand GetPartOccupancyProtein GetPossibleCovalent GetRFree GetResolution SetAltConfs SetAsDensity SetCategory SetDPI SetExcipients SetHasMTZ SetIrrationalRFree SetLigandDensity SetPackingResidues SetPartOccupancyLigand SetPartOccupancyProtein SetPossibleCovalent SetRFree SetResolution operator bool operator= OEBio::OEIsAlphaCarbon OEBio::OEIsBackboneAtom Constructors CreateCopy operator() OEBio::OEIsCationPiInteractionHint Constructors CreateCopy operator() OEBio::OEIsChelatorInteractionHint Constructors CreateCopy operator() OEBio::OEIsClashInteractionHint Constructors CreateCopy operator() OEBio::OEIsContactInteractionHint Constructors CreateCopy operator() OEBio::OEIsCovalentInteractionHint Constructors CreateCopy operator() OEBio::OEIsCTerminalAtom Constructors CreateCopy operator() OEBio::OEIsDisulfideBond Constructors CreateCopy operator() OEBio::OEIsHalogenBondInteractionHint Constructors CreateCopy operator() OEBio::OEIsHBondInteractionHint Constructors CreateCopy operator() OEBio::OEIsHetAtom Constructors CreateCopy operator() OEBio::OEIsInterInteractionHint Constructors CreateCopy operator() OEBio::OEIsIntermolecularChelatorInteractionHint Constructors CreateCopy operator() OEBio::OEIsIntermolecularHBondInteractionHint Constructors CreateCopy operator() OEBio::OEIsIntraInteractionHint Constructors CreateCopy operator() OEBio::OEIsIntramolecularChelatorInteractionHint Constructors CreateCopy operator() OEBio::OEIsIntramolecularHBondInteractionHint Constructors CreateCopy operator() OEBio::OEIsNonIdealHBondInteractionHint Constructors CreateCopy operator() OEBio::OEIsNTerminalAtom Constructors CreateCopy operator() OEBio::OEIsNucleicAcidBase CreateCopy operator() OEBio::OEIsNucleicAcidPhosphate CreateCopy operator() OEBio::OEIsNucleicAcidSugar CreateCopy operator() OEBio::OEIsReadableDesignUnit OEBio::OEIsSaltBridgeInteractionHint Constructors CreateCopy operator() OEBio::OEIsStackingInteractionHint Constructors CreateCopy operator() OEBio::OEIsStandardNucleicAcidResidue OEBio::OEIsStandardProteinResidue OEBio::OEIsTypicalPrimaryLocationCode OEBio::OEIsUnpairedLigandInteractionHint Constructors CreateCopy operator() OEBio::OEIsUnpairedProteinInteractionHint Constructors CreateCopy operator() OEBio::OEIsValidActiveSite OEBio::OEIsWater Constructors CreateCopy operator() OEBio::OEIsWriteableDesignUnit OEBio::OELigandInteractionHintComponent Constructors CreateCopy GetMaxHeavyAtom IsValid SetMaxHeavyAtom operator= OEBio::OEMakeAltMolOption OEBio::OEMakeAltMolOption::None OEBio::OEMakeAltMolOption::RemoveAltCodes OEBio::OEMolComplexCategorizer AddLigandName ClearLigandSubSearch Constructors CreateCopy GetBundleCofactors GetLigandSubSearch GetMaxLigAtoms GetMaxLigResidues GetMaxPeptideResidues GetMaxProteinAtoms GetMinLigAtoms GetResidueCategoryData SetBundleCofactors SetLigandSubSearch SetMaxLigAtoms SetMaxLigResidues SetMaxPeptideResidues SetMaxProteinAtoms SetMinLigAtoms SetResidueCategoryData UsingExplicitLigandName operator() operator= OEBio::OEMolComplexCategorizerBase CreateCopy GetBundleCofactors GetResidueCategoryData UsingExplicitLigandName operator() OEBio::OEMolComplexChainRoleFactory OEBio::OEMolComplexData OEBio::OEMolComplexData::CovalentLigandSDTag OEBio::OEMolComplexData::CovalentSDTag OEBio::OEMolComplexData::PartOrderSDTag OEBio::OEMolComplexData::SDTagPrefix OEBio::OEMolComplexData::SiteNumberSDTag OEBio::OEMolComplexData::SurfaceWatersNumberSDTag OEBio::OEMolComplexFilter Constructors CreateCopy operator() operator= OEBio::OEMolComplexFilterCategory OEBio::OEMolComplexFilterCategory::Anything OEBio::OEMolComplexFilterCategory::ChainA OEBio::OEMolComplexFilterCategory::Cofactor OEBio::OEMolComplexFilterCategory::CofactorAndLigand OEBio::OEMolComplexFilterCategory::CounterIon OEBio::OEMolComplexFilterCategory::Covalent OEBio::OEMolComplexFilterCategory::DNA_RNA OEBio::OEMolComplexFilterCategory::Ligand OEBio::OEMolComplexFilterCategory::Lipid OEBio::OEMolComplexFilterCategory::Metal OEBio::OEMolComplexFilterCategory::Misc OEBio::OEMolComplexFilterCategory::Model1 OEBio::OEMolComplexFilterCategory::Nothing OEBio::OEMolComplexFilterCategory::Nucleotide OEBio::OEMolComplexFilterCategory::Peptide OEBio::OEMolComplexFilterCategory::ProtComplex OEBio::OEMolComplexFilterCategory::Protein OEBio::OEMolComplexFilterCategory::Saccharide OEBio::OEMolComplexFilterCategory::Site1 OEBio::OEMolComplexFilterCategory::Solution OEBio::OEMolComplexFilterCategory::SurfaceWaters1 OEBio::OEMolComplexFilterCategory::Underdefined OEBio::OEMolComplexFilterCategory::Unknown OEBio::OEMolComplexFilterCategory::Water OEBio::OEMolComplexFilterFactory OEBio::OEMolComplexModelRoleFactory OEBio::OEMolComplexOrderRoleFactory OEBio::OEMolComplexRoleFactory OEBio::OEMolComplexSiteRoleFactory OEBio::OEMolComplexSurfaceWatersRoleFactory OEBio::OEPerceiveInteractionHints OEBio::OEPerceiveInteractionOptions Constructors GetExtendedSaltBridgeDistance GetMaxAcceptorAngle GetMaxAtomPairDistance GetMaxCationPiAngle GetMaxCationPiDistance GetMaxChargeAidedHBondDistance GetMaxContactFraction GetMaxCovalentFraction GetMaxDonorAngle GetMaxHBondDistance GetMaxHalogenAngle GetMaxHalogenBondDistance GetMaxMetalBondDistance GetMaxNonIdealAcceptorAngle GetMaxNonIdealDonorAngle GetMaxNonIdealHBondDistance GetMaxPiStackAngle GetMaxPiStackDistance GetMaxSaltBridgeDistance GetMaxTStackAngle GetMaxTStackDistance GetMaxUnpairedAngle GetMaxUnpairedDistance GetMinContactFraction GetMinCovalentFraction GetMinHBondContactFraction SetMaxAcceptorAngle SetMaxCationPiAngle SetMaxCationPiDistance SetMaxChargeAidedHBondDistance SetMaxContactFraction SetMaxCovalentFraction SetMaxDonorAngle SetMaxHBondDistance SetMaxHalogenAngle SetMaxHalogenBondDistance SetMaxMetalBondDistance SetMaxNonIdealAcceptorAngle SetMaxNonIdealDonorAngle SetMaxNonIdealHBondDistance SetMaxPiStackAngle SetMaxPiStackDistance SetMaxSaltBridgeDistance SetMaxTStackAngle SetMaxTStackDistance SetMaxUnpairedAngle SetMaxUnpairedDistance SetMinContactFraction SetMinCovalentFraction SetMinHBondContactFraction OEBio::OEPerceiveSecondaryStructure OEBio::OEPlaceHydrogens OEBio::OEPlaceHydrogensDetails ClusterHasBadClash Constructors Describe GetClusterScore GetFlipBias GetMoverNotes GetNumClusters GetNumFlips GetNumHydrogensStandardized GetNumMovers IsSingleton IsValid operator= OEBio::OEPlaceHydrogensMoverClass OEBio::OEPlaceHydrogensMoverClass::AmideNO OEBio::OEPlaceHydrogensMoverClass::AroCH3 OEBio::OEPlaceHydrogensMoverClass::AroN OEBio::OEPlaceHydrogensMoverClass::Background OEBio::OEPlaceHydrogensMoverClass::COOH OEBio::OEPlaceHydrogensMoverClass::DH OEBio::OEPlaceHydrogensMoverClass::Imidazole OEBio::OEPlaceHydrogensMoverClass::Max OEBio::OEPlaceHydrogensMoverClass::N OEBio::OEPlaceHydrogensMoverClass::NH2 OEBio::OEPlaceHydrogensMoverClass::NH3 OEBio::OEPlaceHydrogensMoverClass::NHsp2Only OEBio::OEPlaceHydrogensMoverClass::NHsp2sp3 OEBio::OEPlaceHydrogensMoverClass::NHsp3Only OEBio::OEPlaceHydrogensMoverClass::SCH3 OEBio::OEPlaceHydrogensMoverClass::Water OEBio::OEPlaceHydrogensMoverNote Constructors Describe GetAngle GetFlippedBestClusterScore GetLabel GetMoverClass GetOriginalBestClusterScore GetReferenceCoords GetScore GetStateIdx GetStateName HasBadClash HasFlippedBadClusterClash HasOriginalBadClusterClash IsFlippable IsFlipped IsIonizable IsIonized IsRestrained operator= OEBio::OEPlaceHydrogensOptions Constructors GetAddMetadata GetAltsMustBeCompatible GetBadClashOverlapDistance GetBypassPredicate GetFlipBias GetFlipBiasScale GetFlipPredicate GetMaxSubstateCutoff GetNoFlipPredicate GetStandardizeBondLen GetWaterProcessing SetAddMetadata SetAltsMustBeCompatible SetBadClashOverlapDistance SetBypassPredicate SetFlipBiasScale SetFlipPredicate SetMaxSubstateCutoff SetNoFlipPredicate SetStandardizeBondLen SetWaterProcessing operator= OEBio::OEPlaceHydrogensWaterProcessing OEBio::OEPlaceHydrogensWaterProcessing::Default OEBio::OEPlaceHydrogensWaterProcessing::Focused OEBio::OEPlaceHydrogensWaterProcessing::FullSearch OEBio::OEPlaceHydrogensWaterProcessing::Ignore OEBio::OEProteinConstraintType OEBio::OEProteinConstraintType::Acceptor OEBio::OEProteinConstraintType::Chelator OEBio::OEProteinConstraintType::Contact OEBio::OEProteinConstraintType::Donor OEBio::OEProteinConstraintType::Lipophilic OEBio::OEProteinConstraintType::Unknown OEBio::OEProteinInteractionHintComponent Constructors CreateCopy IsValid operator= OEBio::OEProtTorType OEBio::OEProtTorType::Chi1 OEBio::OEProtTorType::Chi2 OEBio::OEProtTorType::Chi3 OEBio::OEProtTorType::Chi4 OEBio::OEProtTorType::Chi5 OEBio::OEProtTorType::Max OEBio::OEProtTorType::Omega OEBio::OEProtTorType::Phi OEBio::OEProtTorType::Psi OEBio::OEProtTorType::Unknown OEBio::OERamaCategory OEBio::OERamaCategory::Allowed OEBio::OERamaCategory::Favored OEBio::OERamaCategory::Outlier OEBio::OERamaCategory::Unknown OEBio::OERamachandranAnalysis Constructors GetPhi GetPsi GetRamaCategory GetRamaScore GetRamaType OEBio::OERamaType OEBio::OERamaType::CisPro OEBio::OERamaType::General OEBio::OERamaType::Glycine OEBio::OERamaType::IleVal OEBio::OERamaType::PrePro OEBio::OERamaType::TransPro OEBio::OERamaType::Unknown OEBio::OEReadDesignUnit OEBio::OEReceptor AddProteinConstraint Clear ClearCustomConstraints ClearProteinConstraint ClearProteinConstraints Constructor GetCustomConstraints GetInnerContourLevel GetNegativeImageGrid GetOuterContourLevel GetProteinConstraints GetTargetMask HasCustomConstraints HasInnerContourLevel HasNegativeImageGrid HasOuterContourLevel HasProteinConstraints IsValid NumProteinConstraints SetCustomConstraints SetInnerContourLevel SetOuterContourLevel operator= OEBio::OEReceptorConstraintFeature AddNewSphere AddSmarts ClearSmarts ClearSpheres Constructor CreateCopy DeleteSmarts DeleteSphere GetEnabled GetFeatureName GetFeatureSpheres GetSmarts NumSmarts NumSpheres SetEnabled SetFeatureName operator= OEBio::OEReceptorCustomConstraints AddFeature Clear Constructors DeleteFeature GetFeatures NumFeatures operator= OEBio::OEReceptorProteinConstraint GetAtom GetEnabled GetName GetType SetAtom SetEnabled SetName SetType OEBio::OEResidueCategoryData AddToDB AllInDB ClearDBCategory Constructors FoundInDB GetEntries RemoveFromDB Size operator= OEBio::OEResidueDatabaseCategory OEBio::OEResidueDatabaseCategory::AminoAcid OEBio::OEResidueDatabaseCategory::Cofactor OEBio::OEResidueDatabaseCategory::CofactorAndLigand OEBio::OEResidueDatabaseCategory::Ligand OEBio::OEResidueDatabaseCategory::Lipid OEBio::OEResidueDatabaseCategory::Max OEBio::OEResidueDatabaseCategory::Metal OEBio::OEResidueDatabaseCategory::Misc OEBio::OEResidueDatabaseCategory::NucleicAcid OEBio::OEResidueDatabaseCategory::Polymer OEBio::OEResidueDatabaseCategory::Saccharide OEBio::OERMSD OEBio::OERoleMolComplexFilterFactory OEBio::OERotamer GetChi1 GetChi2 GetChi3 GetChi4 GetProbability GetResidueIndex OEBio::OERotamerLibrary OEBio::OERotamerLibrary::Default OEBio::OERotamerLibrary::Dunbrack OEBio::OERotamerLibrary::Richardson OEBio::OERotamerLibrary::Richardson_2016 OEBio::OESaltBridgeInteractionHint Constructors CreateCopy IsValid operator= OEBio::OESaltBridgeInteractionHintType OEBio::OESaltBridgeInteractionHintType::LigandNegative OEBio::OESaltBridgeInteractionHintType::LigandPositive OEBio::OESaltBridgeInteractionHintType::ProteinNegative OEBio::OESaltBridgeInteractionHintType::ProteinPositive OEBio::OESaltBridgeInteractionHintType::UnpairedLigand OEBio::OESaltBridgeInteractionHintType::UnpairedLigandNegative OEBio::OESaltBridgeInteractionHintType::UnpairedLigandPositive OEBio::OESaltBridgeInteractionHintType::UnpairedProtein OEBio::OESaltBridgeInteractionHintType::UnpairedProteinNegative OEBio::OESaltBridgeInteractionHintType::UnpairedProteinPositive OEBio::OESecondaryStructure OEBio::OESecondaryStructure::Any OEBio::OESecondaryStructure::Helix OEBio::OESecondaryStructure::Helix310 OEBio::OESecondaryStructure::HelixAlpha OEBio::OESecondaryStructure::HelixLeft OEBio::OESecondaryStructure::HelixPi OEBio::OESecondaryStructure::Sheet OEBio::OESecondaryStructure::StrandSense OEBio::OESecondaryStructure::Turn OEBio::OESecondaryStructure::Turn3 OEBio::OESecondaryStructure::Turn4 OEBio::OESecondaryStructure::Turn5 OEBio::OESecondaryStructure::Unassigned OEBio::OESecondaryStructurePacked OEBio::OESeqAlignmentMethod OEBio::OESeqAlignmentMethod::BLOSUM62 OEBio::OESeqAlignmentMethod::GONNET OEBio::OESeqAlignmentMethod::Identity OEBio::OESeqAlignmentMethod::None OEBio::OESeqAlignmentMethod::PAM250 OEBio::OESequenceAlignment Clear Constructors GetBackboneMatch GetCAlphaMatch GetChainID GetExtend GetGap GetMaxSeqIdx GetMethod GetScore GetSequenceIdentity GetSequenceSimilarity operator bool operator= OEBio::OESetCrystalSymmetry OEBio::OESetRotamer OEBio::OESetTorsion OEBio::OESetupSplitMolComplexOptions OEBio::OESplitMolComplex OEBio::OESplitMolComplexOptions Constructors GetAddRGroup GetAdjustHCount GetAssumptions GetCategorizer GetCollectProteinByChain GetCombinedFilter GetLigandFilter GetMaxBindingSiteDist GetMaxSurfaceWaterDist GetOtherFilter GetPromoteUnknowns GetProteinFilter GetSeparateResidues GetSplitCovalent GetSplitCovalentCofactors GetWarnNoLigand GetWaterFilter ResetFilters SetAddRGroup SetAdjustHCount SetAssumptions SetCategorizer SetCollectProteinByChain SetLigandFilter SetMaxBindingSiteDist SetMaxSurfaceWaterDist SetPromoteUnknowns SetProteinFilter SetSeparateResidues SetSplitCovalent SetSplitCovalentCofactors SetWarnNoLigand SetWaterFilter operator!= operator= operator== OEBio::OESplitMolComplexParam OEBio::OESplitMolComplexParam::DoNotOverride OEBio::OESplitMolComplexSetup OEBio::OESplitMolComplexSetup::All OEBio::OESplitMolComplexSetup::CovBondTreatment OEBio::OESplitMolComplexSetup::CovCofactor OEBio::OESplitMolComplexSetup::CovLig OEBio::OESplitMolComplexSetup::LigFilter OEBio::OESplitMolComplexSetup::LigName OEBio::OESplitMolComplexSetup::MaxSiteDist OEBio::OESplitMolComplexSetup::MaxSurfDist OEBio::OESplitMolComplexSetup::ModelNum OEBio::OESplitMolComplexSetup::ProtFilter OEBio::OESplitMolComplexSetup::SeparateRes OEBio::OESplitMolComplexSetup::SiteNum OEBio::OESplitMolComplexSetup::SurfWat OEBio::OESplitMolComplexSetup::WatFilter OEBio::OEStackingInteractionHint Constructors CreateCopy IsValid operator= OEBio::OEStackingInteractionHintType OEBio::OEStackingInteractionHintType::Pi OEBio::OEStackingInteractionHintType::T OEBio::OEStructureQuality Clear Constructors GetIridiumData HasIridiumData SetIridiumData operator bool operator= OEBio::OESubsetDesignUnit OEBio::OESwapAIEResidueAtoms OEBio::OESymmetryCartesianToFractional OEBio::OESymmetryFractionalToCartesian OEBio::OETransformDesignUnit OEBio::OEUpdateDesignUnit OEBio::OEWriteAlignment OEBio::OEWriteDesignUnit OEBondBase OEBondIdxSelected OEBuildMDLQueryExpression OEBuildMDLQueryExpressions OEChem::OE2DRingDictionary AddRings Constructors NumRings OEChem::OE2DRingDictionaryCreatorOptions Constructors GetAddCarbonSkeleton GetAddCarbonSkeletonWithBondStereo GetRetainExistingBuiltInTemplates GetRetainExistingTemplates SetAddCarbonSkeleton SetAddCarbonSkeletonWithBondStereo SetRetainExistingBuiltInTemplates SetRetainExistingTemplates operator= OEChem::OE3DToAtomStereo OEChem::OE3DToBondStereo OEChem::OE3DToInternalStereo OEChem::OEAbsCanonicalConfTest CombineMols CompareMols CreateCopy OEChem::OEAbsoluteConfTest CombineMols CompareMols Constructors CreateCopy OEChem::OEAcyclicPath OEChem::OEAddCustomFASTAResidue OEChem::OEAddExplicitHydrogens OEChem::OEAddMols OEChem::OEAddPDBData OEChem::OEAddSDData OEChem::OEAnisoUij Constructors GetU11 GetU12 GetU13 GetU22 GetU23 GetU33 SetU11 SetU12 SetU13 SetU22 SetU23 SetU33 OEChem::OEApplyStateFromRef OEChem::OEAroModel OEChem::OEAroModel::Daylight OEChem::OEAroModel::MDL OEChem::OEAroModel::MMFF OEChem::OEAroModel::OpenEye OEChem::OEAroModel::Tripos OEChem::OEAssignAromaticFlags OEChem::OEAssignBondiVdWRadii OEChem::OEAssignCovalentRadii OEChem::OEAssignDelphiRadii OEChem::OEAssignFormalCharges OEChem::OEAssignHonigIonicCavityRadii OEChem::OEAssignHybridization OEChem::OEAssignImplicitHydrogens OEChem::OEAssignMDLHydrogens OEChem::OEAssignPaulingVdWRadii OEChem::OEAssignRadii OEChem::OEAssignResidueNumbers OEChem::OEAssignSerialNumbers OEChem::OEAssignZap7Radii OEChem::OEAssignZap9Radii OEChem::OEAtomBase AddBond Clear GetAtomicNum GetAtoms GetAxial GetBond GetBonds GetDegree GetExplicitDegree GetExplicitHCount GetExplicitValence GetFormalCharge GetHvyDegree GetHvyValence GetHyb GetIdx GetImplicitHCount GetIntType GetIsotope GetMapIdx GetName GetParent GetPartialCharge GetRadius GetRxnRole GetStereo GetSymmetryClass GetTotalHCount GetType GetValence HasAlphaBetaUnsat HasStereoSpecified IsAromatic IsCarbon IsChiral IsConnected IsDataType IsDeleted IsHalogen IsHydrogen IsInRing IsMetal IsNitrogen IsOxygen IsPhosphorus IsPolar IsPolarHydrogen IsSulfur OrderBonds RemoveBond SetAromatic SetAtomicNum SetAxial SetChiral SetFormalCharge SetHyb SetImplicitHCount SetInRing SetIntType SetIsotope SetMapIdx SetName SetPartialCharge SetRadius SetRxnRole SetStereo SetSymmetryClass SetType Sweep operator= OEChem::OEAtomBondSet Add AddAtom AddAtoms AddBond AddBonds Clear ClearAtoms ClearAtomsAndBonds ClearBonds Constructors CreateCopy GetAtoms GetBonds GetParent HasAtom HasBond IsEmpty NumAtoms NumBonds Remove RemoveAtom RemoveAtoms RemoveBond RemoveBonds Sweep Translate operator= OEChem::OEAtomGetMDLParity OEChem::OEAtomGetResidue OEChem::OEAtomGetSmallestRingSize OEChem::OEAtomIsInAgent CreateCopy operator() OEChem::OEAtomIsInAromaticRingSize OEChem::OEAtomIsInChain CreateCopy operator() OEChem::OEAtomIsInProduct CreateCopy operator() OEChem::OEAtomIsInReactant CreateCopy operator() OEChem::OEAtomIsInResidue Constructors CreateCopy operator() OEChem::OEAtomIsInRing CreateCopy operator() OEChem::OEAtomIsInRingSize OEChem::OEAtomSetMDLParity OEChem::OEAtomSetResidue OEChem::OEAtomStereo OEChem::OEAtomStereo::All OEChem::OEAtomStereo::Left OEChem::OEAtomStereo::LeftHanded OEChem::OEAtomStereo::Right OEChem::OEAtomStereo::RightHanded OEChem::OEAtomStereo::Tetra OEChem::OEAtomStereo::Tetrahedral OEChem::OEAtomStereo::Undefined OEChem::OEBAtomIntTypeOpts OEChem::OEBDefaultOpts OEChem::OEBGZipCompressOpts OEChem::OEBondBase Clear GetBgn GetBgnIdx GetEnd GetEndIdx GetIdx GetIntType GetNbr GetOrder GetParent GetStereo GetType HasStereoSpecified IsAromatic IsChiral IsDataType IsDeleted IsInRing IsRotor SetAromatic SetBgn SetChiral SetEnd SetInRing SetIntType SetOrder SetStereo SetType SwapEnds Sweep operator= OEChem::OEBondGetSmallestRingSize OEChem::OEBondIsInAromaticRingSize OEChem::OEBondIsInChain CreateCopy operator() OEChem::OEBondIsInRing CreateCopy operator() OEChem::OEBondIsInRingSize OEChem::OEBondStereo OEChem::OEBondStereo::All OEChem::OEBondStereo::Cis OEChem::OEBondStereo::CisTrans OEChem::OEBondStereo::DoubleEither OEChem::OEBondStereo::Hash OEChem::OEBondStereo::Trans OEChem::OEBondStereo::Undefined OEChem::OEBondStereo::Wavy OEChem::OEBondStereo::Wedge OEChem::OEBRotCompressOpts OEChem::OEBuildMDLQueryExpressions OEChem::OECalcCartesianCoord OEChem::OECalcInternalCoord OEChem::OECalculateMolecularWeight OEChem::OECanonicalOrderAtoms OEChem::OECanonicalOrderBonds OEChem::OECenter OEChem::OECheckAtomValence OEChem::OECheckAtomValences OEChem::OEChem OEChem::OEChem::FzFalse OEChem::OEChem::FzMaybe OEChem::OEChem::FzTrue OEChem::OEChem::OEAroModelDaylight OEChem::OEChem::OEAroModelMDL OEChem::OEChem::OEAroModelMMFF OEChem::OEChem::OEAroModelOpenEye OEChem::OEChem::OEAroModelTripos OEChem::OEChemGetArch OEChem::OEChemGetLicensee OEChem::OEChemGetPlatform OEChem::OEChemGetRelease OEChem::OEChemGetSite OEChem::OEChemGetVersion OEChem::OEChemIsLicensed OEChem::OECIPAtomStereo OEChem::OECIPAtomStereo::NotStereo OEChem::OECIPAtomStereo::R OEChem::OECIPAtomStereo::S OEChem::OECIPAtomStereo::UnspecStereo OEChem::OECIPBondStereo OEChem::OECIPBondStereo::E OEChem::OECIPBondStereo::NotStereo OEChem::OECIPBondStereo::UnspecStereo OEChem::OECIPBondStereo::Z OEChem::OEClear2DRingDictionary OEChem::OEClearAromaticFlags OEChem::OEClearChiralPerception OEChem::OEClearPartialCharges OEChem::OEClearPDBData OEChem::OEClearResidue OEChem::OEClearResidues OEChem::OEClearRotorCompressData OEChem::OEClearSDData OEChem::OECliqueSearch AddConstraint ClearConstraints Constructors GetMaxMatches GetMinAtoms GetPattern GetSaveRange Init Match SetMCSFunc SetMaxMatches SetMinAtoms SetSaveRange operator bool operator= OEChem::OEConfBase AddAtom AddBond ClearCoords Delete GetCoords GetCoordsPtr GetIdx GetMCMol GetTitle GetTorsion GetTransform HasTitle IsDeleted RemoveAtom RemoveBond SetCoords SetTorsion Transform operator= OEChem::OEConfRMSD CalculateRMSD Constructors GetOptions IsValid MinimizeRMSD NumAutomorphs OEChem::OEConfRMSDOptions Constructors GetIgnoreHydrogens GetIgnoreTerminalHeavy GetMaxMatches SetIgnoreHydrogens SetIgnoreTerminalHeavy SetMaxMatches operator= OEChem::OEConfTestBase CombineMols CompareMols CreateCopy HasCompareMols OEChem::OEConstCoords Constructors GetPtr operator const T * OEChem::OECoordArray Constructors operator double * operator= OEChem::OECoordsType OEChem::OECoordsType::DoubleType OEChem::OECoordsType::FloatType OEChem::OECoordsType::HalfFloatType OEChem::OECoordsType::LongDoubleType OEChem::OECoordsType::MaxType OEChem::OECoordsType::Undefined OEChem::OECopyMol OEChem::OECopyPDBData OEChem::OECopySDData OEChem::OECorrectAcidProtonGeometry OEChem::OECount OEChem::OECreateAbsSmiString OEChem::OECreateCanSmiString OEChem::OECreateCSVHeader OEChem::OECreateInChI OEChem::OECreateInChIKey OEChem::OECreateIsoSmiString OEChem::OECreateMolDatabaseIdx OEChem::OECreateSlnString OEChem::OECreateSmiString OEChem::OECreateSubSearchDatabaseFile OEChem::OECreateSubSearchDatabaseOptions Constructors GetKeepTitle GetNumProcessors GetScreenType GetSortByBitCounts SetKeepTitle SetNumProcessors SetSortByBitCounts OEChem::OECSVHeader Clear Constructors GetColumnName GetColumnNames GetNumColumns IsValid operator bool operator= OEChem::OEDefaultConfTest CombineMols CompareMols CreateCopy HasCompareMols OEChem::OEDefaultImplicitHCount OEChem::OEDefaultMDLHCount OEChem::OEDeleteEverythingExceptTheFirstLargestComponent OEChem::OEDeletePDBData OEChem::OEDeleteSDData OEChem::OEDetermineAromaticRingSystems OEChem::OEDetermineComponents OEChem::OEDetermineConnectivity OEChem::OEDetermineReactants OEChem::OEDetermineRingSystems OEChem::OEDisassembleExpressions OEChem::OEDoubleBondCount OEChem::OEDoubleBondOCount OEChem::OEElementHistogram OEChem::OEElemNo OEChem::OEElemNo::Ac OEChem::OEElemNo::Ag OEChem::OEElemNo::Al OEChem::OEElemNo::Am OEChem::OEElemNo::Ar OEChem::OEElemNo::As OEChem::OEElemNo::At OEChem::OEElemNo::Au OEChem::OEElemNo::B OEChem::OEElemNo::Ba OEChem::OEElemNo::Be OEChem::OEElemNo::Bh OEChem::OEElemNo::Bi OEChem::OEElemNo::Bk OEChem::OEElemNo::Br OEChem::OEElemNo::C OEChem::OEElemNo::Ca OEChem::OEElemNo::Cd OEChem::OEElemNo::Ce OEChem::OEElemNo::Cf OEChem::OEElemNo::Cl OEChem::OEElemNo::Cm OEChem::OEElemNo::Cn OEChem::OEElemNo::Co OEChem::OEElemNo::Cr OEChem::OEElemNo::Cs OEChem::OEElemNo::Cu OEChem::OEElemNo::D OEChem::OEElemNo::Db OEChem::OEElemNo::Ds OEChem::OEElemNo::Du OEChem::OEElemNo::Dy OEChem::OEElemNo::Er OEChem::OEElemNo::Es OEChem::OEElemNo::Eu OEChem::OEElemNo::F OEChem::OEElemNo::Fe OEChem::OEElemNo::Fl OEChem::OEElemNo::Fm OEChem::OEElemNo::Fr OEChem::OEElemNo::Ga OEChem::OEElemNo::Gd OEChem::OEElemNo::Ge OEChem::OEElemNo::H OEChem::OEElemNo::He OEChem::OEElemNo::Hf OEChem::OEElemNo::Hg OEChem::OEElemNo::Ho OEChem::OEElemNo::Hs OEChem::OEElemNo::I OEChem::OEElemNo::In OEChem::OEElemNo::Ir OEChem::OEElemNo::K OEChem::OEElemNo::Kr OEChem::OEElemNo::La OEChem::OEElemNo::Li OEChem::OEElemNo::Lp OEChem::OEElemNo::Lr OEChem::OEElemNo::Lu OEChem::OEElemNo::Lv OEChem::OEElemNo::MAXELEM OEChem::OEElemNo::Mc OEChem::OEElemNo::Md OEChem::OEElemNo::Mg OEChem::OEElemNo::Mn OEChem::OEElemNo::Mo OEChem::OEElemNo::Mt OEChem::OEElemNo::N OEChem::OEElemNo::Na OEChem::OEElemNo::Nb OEChem::OEElemNo::Nd OEChem::OEElemNo::Ne OEChem::OEElemNo::Nh OEChem::OEElemNo::Ni OEChem::OEElemNo::No OEChem::OEElemNo::Np OEChem::OEElemNo::O OEChem::OEElemNo::Og OEChem::OEElemNo::Os OEChem::OEElemNo::P OEChem::OEElemNo::Pa OEChem::OEElemNo::Pb OEChem::OEElemNo::Pd OEChem::OEElemNo::Pm OEChem::OEElemNo::Po OEChem::OEElemNo::Pr OEChem::OEElemNo::Pt OEChem::OEElemNo::Pu OEChem::OEElemNo::Ra OEChem::OEElemNo::Rb OEChem::OEElemNo::Re OEChem::OEElemNo::Rf OEChem::OEElemNo::Rg OEChem::OEElemNo::Rh OEChem::OEElemNo::Rn OEChem::OEElemNo::Ru OEChem::OEElemNo::S OEChem::OEElemNo::Sb OEChem::OEElemNo::Sc OEChem::OEElemNo::Se OEChem::OEElemNo::Sg OEChem::OEElemNo::Si OEChem::OEElemNo::Sm OEChem::OEElemNo::Sn OEChem::OEElemNo::Sr OEChem::OEElemNo::T OEChem::OEElemNo::Ta OEChem::OEElemNo::Tb OEChem::OEElemNo::Tc OEChem::OEElemNo::Te OEChem::OEElemNo::Th OEChem::OEElemNo::Ti OEChem::OEElemNo::Tl OEChem::OEElemNo::Tm OEChem::OEElemNo::Ts OEChem::OEElemNo::U OEChem::OEElemNo::V OEChem::OEElemNo::W OEChem::OEElemNo::Xe OEChem::OEElemNo::Xx OEChem::OEElemNo::Y OEChem::OEElemNo::Yb OEChem::OEElemNo::Zn OEChem::OEElemNo::Zr OEChem::OEEuler Constructors CreateCopy Extract GetAngles GetInverse GetPhi GetPsi GetTheta SetPhi SetPsi SetTheta operator= OEChem::OEEulerRotate OEChem::OEExactGraphMatch OEChem::OEExpandSuperAtoms OEChem::OEExprBase Constructors CreateCopy GetType IsEquivalent OEChem::OEExprOpts OEChem::OEExprOpts::Aromaticity OEChem::OEExprOpts::AtomicNumber OEChem::OEExprOpts::AutomorphAtoms OEChem::OEExprOpts::AutomorphBonds OEChem::OEExprOpts::BondOrder OEChem::OEExprOpts::Chiral OEChem::OEExprOpts::DefaultAtoms OEChem::OEExprOpts::DefaultBonds OEChem::OEExprOpts::Degree OEChem::OEExprOpts::EqAromatic OEChem::OEExprOpts::EqCAliphaticONS OEChem::OEExprOpts::EqCHalogen OEChem::OEExprOpts::EqCPSAcidRoot OEChem::OEExprOpts::EqDoubleTriple OEChem::OEExprOpts::EqHalogen OEChem::OEExprOpts::EqKetoneSulfoneRoot OEChem::OEExprOpts::EqMetal OEChem::OEExprOpts::EqNotAromatic OEChem::OEExprOpts::EqON OEChem::OEExprOpts::EqONS OEChem::OEExprOpts::EqPS OEChem::OEExprOpts::EqSingleDouble OEChem::OEExprOpts::ExactAtoms OEChem::OEExprOpts::ExactBonds OEChem::OEExprOpts::ExplicitDegree OEChem::OEExprOpts::FormalCharge OEChem::OEExprOpts::HCount OEChem::OEExprOpts::HvyDegree OEChem::OEExprOpts::Hybridization OEChem::OEExprOpts::ImplicitHCount OEChem::OEExprOpts::IntType OEChem::OEExprOpts::Mass OEChem::OEExprOpts::RingMember OEChem::OEExprOpts::StrictFormalCharge OEChem::OEExprOpts::StringType OEChem::OEExprOpts::SymmetryClass OEChem::OEExprOpts::Valence OEChem::OEExprType OEChem::OEExprType::AllowedElements OEChem::OEExprType::And OEChem::OEExprType::Aromatic OEChem::OEExprType::AromBondOrder OEChem::OEExprType::AromElem OEChem::OEExprType::AromElemMinDegree OEChem::OEExprType::AromOrBondOrder OEChem::OEExprType::AromRingElem OEChem::OEExprType::BondOrder OEChem::OEExprType::Charge OEChem::OEExprType::Chiral OEChem::OEExprType::Connect OEChem::OEExprType::Const OEChem::OEExprType::DefaultEdge OEChem::OEExprType::Degree OEChem::OEExprType::DoubleAromBond OEChem::OEExprType::ElemCharge OEChem::OEExprType::Element OEChem::OEExprType::ElemMinDegree OEChem::OEExprType::ElemMinHCount OEChem::OEExprType::Halogen OEChem::OEExprType::HCount OEChem::OEExprType::Hyb OEChem::OEExprType::Implicit OEChem::OEExprType::IntType OEChem::OEExprType::Mass OEChem::OEExprType::Metal OEChem::OEExprType::MinDegree OEChem::OEExprType::MinHCount OEChem::OEExprType::Not OEChem::OEExprType::Or OEChem::OEExprType::Recurs OEChem::OEExprType::Ring OEChem::OEExprType::RingBondCount OEChem::OEExprType::RingBondOrder OEChem::OEExprType::RingDefaultEdge OEChem::OEExprType::RingElem OEChem::OEExprType::Saturation OEChem::OEExprType::SingleAromBond OEChem::OEExprType::Size OEChem::OEExprType::Stereo OEChem::OEExprType::StringType OEChem::OEExprType::SymmetryClass OEChem::OEExprType::TerminalAtom OEChem::OEExprType::Undefined OEChem::OEExprType::Valence OEChem::OEExtractRingTemplateOptions Constructors GetRetainBondStereo GetRetainExistingTemplates SetRetainBondStereo SetRetainExistingTemplates operator= OEChem::OEExtractRingTemplates OEChem::OEFastaToMol OEChem::OEFileStringParameter Constructors operator= OEChem::OEFileStringType OEChem::OEFileStringType::DU OEChem::OEFileStringType::Mol OEChem::OEFileStringType::Mol3D OEChem::OEFileStringType::MolReceptor OEChem::OEFindRingAtomsAndBonds OEChem::OEFormalPartialCharges OEChem::OEFormat OEChem::OEFormat::CAN OEChem::OEFormat::CDX OEChem::OEFormat::CIF OEChem::OEFormat::CSV OEChem::OEFormat::Default OEChem::OEFormat::FASTA OEChem::OEFormat::INCHI OEChem::OEFormat::INCHIKEY OEChem::OEFormat::ISM OEChem::OEFormat::MAXFORMAT OEChem::OEFormat::MDL OEChem::OEFormat::MF OEChem::OEFormat::MMCIF OEChem::OEFormat::MMOD OEChem::OEFormat::MOL2 OEChem::OEFormat::MOL2H OEChem::OEFormat::MOPAC OEChem::OEFormat::OEB OEChem::OEFormat::OEZ OEChem::OEFormat::PDB OEChem::OEFormat::RDF OEChem::OEFormat::SDF OEChem::OEFormat::SKC OEChem::OEFormat::SLN OEChem::OEFormat::SMI OEChem::OEFormat::UNDEFINED OEChem::OEFormat::USM OEChem::OEFormat::XYZ OEChem::OEFuzzVal OEChem::OEFuzzVal::False OEChem::OEFuzzVal::Maybe OEChem::OEFuzzVal::True OEChem::OEFuzzy Constructors operator bool operator! operator!= operator&& operator== operator|| OEChem::OEGasteigerInitialCharges OEChem::OEGasteigerPartialCharges OEChem::OEGenerate2DCoordinates OEChem::OEGetAbsTorsion OEChem::OEGetAminoAcidCode OEChem::OEGetAngle OEChem::OEGetAnisou OEChem::OEGetAtomComment OEChem::OEGetAtomicNum OEChem::OEGetAtomicSymbol OEChem::OEGetAutomorphs OEChem::OEGetAverageWeight OEChem::OEGetBondiVdWRadius OEChem::OEGetCenterAndExtents OEChem::OEGetCenterOfMass OEChem::OEGetComment OEChem::OEGetCovalentRadius OEChem::OEGetDefaultIFlavor OEChem::OEGetDefaultMass OEChem::OEGetDefaultOFlavor OEChem::OEGetDelphiRadius OEChem::OEGetDimensionFromCoords OEChem::OEGetDistance OEChem::OEGetDistance2 OEChem::OEGetDoubleBondNeighbor OEChem::OEGetFileExtension OEChem::OEGetFileType OEChem::OEGetFormatExtension OEChem::OEGetFormatString OEChem::OEGetHonigIonicCavityRadius OEChem::OEGetHybridization OEChem::OEGetHydrogenCounts OEChem::OEGetIsotopicWeight OEChem::OEGetMCSExhaustiveSearchTruncationLimit OEChem::OEGetMDLDimensionFromCoords OEChem::OEGetMolDatabaseIdxFileName OEChem::OEGetMolDBIdx OEChem::OEGetNbrAtom Constructors CreateCopy operator() OEChem::OEGetNearestNbrs OEChem::OEGetOEGraphMol OEChem::OEGetOEMol OEChem::OEGetOEQMol OEChem::OEGetOtherNeighbor OEChem::OEGetPackedCoords OEChem::OEGetPathLength OEChem::OEGetPaulingVdWRadius OEChem::OEGetPDBAtomIndex OEChem::OEGetPDBAtomName OEChem::OEGetPDBBaseData OEChem::OEGetPDBData OEChem::OEGetPDBDataPairs OEChem::OEGetRadiiTypeName OEChem::OEGetResidueIndex OEChem::OEGetResidueIndexFromCode OEChem::OEGetResidueName OEChem::OEGetSDBaseData OEChem::OEGetSDData OEChem::OEGetSDDataPairs OEChem::OEGetSingleBondNeighbor OEChem::OEGetSmallestSubtree OEChem::OEGetSmiStringOrder OEChem::OEGetSoleBond OEChem::OEGetSoleDoubleBond OEChem::OEGetSoleNeighbor OEChem::OEGetSoleSingleBond OEChem::OEGetSoleTripleBond OEChem::OEGetSubSearchScreenType OEChem::OEGetSubtree OEChem::OEGetTokenizer OEChem::OEGetTorsion OEChem::OEGetTorsions OEChem::OEGetTripleBondNeighbor OEChem::OEGetUniMolecularRxnIter OEChem::OEGraphMol Constructors SCMol operator OEMolBase & operator= OEChem::OEGroupBase AddAtom AddBond Clear DeleteAtom DeleteBond GetAtoms GetBonds GetGroupDefinition GetGroupType GetParent HasAtom HasBond IsDeleted IsEmpty NumAtoms NumBonds SetGroupType Sweep OEChem::OEGroupType OEChem::OEGroupType::Component OEChem::OEGroupType::MDLAbsStereo OEChem::OEGroupType::MDLAndStereo OEChem::OEGroupType::MDLOrStereo OEChem::OEGroupType::Undefined OEChem::OEGroupType::UserDefined OEChem::OEHasAlphaBetaUnsat Constructors CreateCopy operator() OEChem::OEHasAnisou CreateCopy operator() OEChem::OEHasAtomicNum Constructors CreateCopy operator() OEChem::OEHasAtomInGroup Constructors CreateCopy operator() OEChem::OEHasAtomName Constructors CreateCopy operator() OEChem::OEHasAtomStereoHydrogens OEChem::OEHasAtomStereoSpecified Constructors CreateCopy operator() OEChem::OEHasBondInGroup Constructors CreateCopy operator() OEChem::OEHasBondStereoHydrogens OEChem::OEHasBondStereoSpecified Constructors CreateCopy operator() OEChem::OEHasChainID Constructors CreateCopy operator() OEChem::OEHasDoubleBond OEChem::OEHasDoubleBondO OEChem::OEHasExplicitHydrogenExpression OEChem::OEHasExplicitHydrogens OEChem::OEHasFormalCharge Constructors CreateCopy operator() OEChem::OEHasFragmentNumber Constructors CreateCopy operator() OEChem::OEHasGroupType Constructors CreateCopy operator()