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 OEBioisostere::OEDBBuffer OEBioisostere::OEDBBuilder OEChem::OEAtomBondSet OEChem::OEIsMember OEChem::OEIsMemberPtr OEChem::OEMolPropertyList OEChem::OEVectorBindings OESiteHopper::OESiteHopperDatabase 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 AddColor OEChem::OEMolStyleColorer AddColorer OEShape::OEColorForceField AddColorGaussian OEShape::OEShapeQuery AddColorGaussians OEShape::OEShapeQuery AddConstMol OEMedChem::OEMCSFragDatabase AddConstraint OEChem::OECliqueSearch OEChem::OEMCSSearch OEChem::OESubSearch AddCSV OEBioisostere::OEDBBuilder AddCurveSegment OEDepict::OE2DPath AddCutoff OEShape::OEROCSOptions AddData OESystem::OEBase AddDefault OESystem::OETypedParameter AddDetail OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter AddDirectory OESiteHopper::OESiteHopperDatabase AddExcipientCode OESpruce::OEDesignUnitSplitOptions AddFeature 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::OEConstParameter OESystem::OEMultiParameter AddLegalRange OESystem::OEParameter AddLegalValue OESystem::OEParameter AddLigand OEModels::OEROCSQueryModelBuilder AddLigandName OEBio::OEMolComplexCategorizer AddLineSegment OEDepict::OE2DPath AddLipidCode OESpruce::OEDesignUnitSplitOptions AddMarkedValue OEGrapheme::OEColorGradientDisplayOptions AddMarkedValues OEGrapheme::OEColorGradientDisplayOptions AddMatchedPair OEMedChem::OEMatchedPairTransform AddMol OEFastROCS::OEShapeDatabase OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMCSFragDatabase AddMolecule OEBio::OEInteractionHintContainer OEGrapheme::OERamachandranPlot OEShape::OEROCS AddMolFunc OEMolPotential::OEGenericFF OEMolPotential::OEGenericFF2 AddMutation OESpruce::OEDesignUnitMutationOptions

AddNewFeature OEBio::OEReceptorCustomConstraints AddNewSphere OEBio::OEReceptorConstraintFeature AddNormalizationRule OEMolProp::OEFilter AddOption OESystem::OEOptions AddPair OEChem::OEMatch AddParameter OESystem::OEInterface OESystem::OEOptions AddParameterPrefix OESystem::OEOptions AddParameterSuffix OESystem::OEOptions AddProteinConstraint OEBio::OEReceptor AddRamachandran OEGrapheme::OERamachandranPlot AddReceptor OEDocking::OEPosit AddRings OEChem::OE2DRingDictionary AddRole OESystem::OERoleSet AddRow OEMath::OEMatrix AddSample OEGraphSim::OEFPHistogram OEGraphSim::OEFPVariogram AddScore OEEon::OEEonHitlistBuilder OEEon::OEEonOverlayResults OEShape::OEBestOverlayResults OEShape::OEROCSResult AddScores OEBioisostere::OEHitlistBuilder OEEon::OEEonHitlistBuilder 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::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 AMI anisou.java Example Code AnnotatePose OEDocking::OEDock OEDocking::OEScore apo protein apo proteins 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::OEInteractParams OEMolPotential::OEInterCoulombPotential OEMolPotential::OEInterNonBondPotBase OEMolPotential::OEInterNonBondPotential OEMolPotential::OEInterVdwPotential OEMolPotential::OENonBondIntcsOptions OEMolPotential::OENonBondPotBase OEMolPotential::OENonBondPotential OEMolPotential::OEOutOfPlanePotential OEMolPotential::OEStretchPotential OEMolPotential::OETorsionPotential OEMolPotential::OEVdwPotential asymmetric unit 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 AUC AutoMapRxn OEChem::OERxnAutomapper

B

B-factor backbone.java Example Code bemismurckoperception.java Example Code besthit.java Example Code BestOverlay OEEon::OEEonOverlay OEEon::OEEonPBOverlay OEShape::OEFlexiOverlay 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 biological unit 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 OEBioisostere::OEBroodMolBuilder OEBioisostere::OEHitlistBuilder OEConfGen::OEConformerBuilder OEConfGen::OEFragBuilder OEConfGen::OEMacrocycleBuilder OEConfGen::OEMacrocycleOmega OEConfGen::OEMolBuilder OEConfGen::OEOmega OEEon::OEEonHitlistBuilder OEModels::OEROCSQueryModelBuilder 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 CalculateNumOfMicrostates OEProton::OEMultistatepKaModel CalculateRMSD OEChem::OEConfRMSD Cancel OEChem::OESubSearchResult canonical isomeric SMILES canonical SMILES 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 OEEon::OEEonOverlayResults OEMath::OEMatrix OEMolPotential::OEInteractParams OEMolPotential::OEMolFunc OEShape::OEBestOverlayResults OEShape::OEColorForceField OEShape::OEShapeQuery OESpicoli::OESurface OESpruce::OESuperpose 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 ClearAtomColorer OEChem::OE3DMolStyle ClearAtomLabelColorer OEChem::OE3DMolStyle ClearAtomLabelDataTag OEChem::OE3DMolStyle ClearAtomLabelText OEChem::OE3DMolStyle ClearAtomLabelType OEChem::OE3DMolStyle ClearAtoms OEChem::OEAtomBondSet ClearAtomsAndBonds OEChem::OEAtomBondSet ClearAtomStyle OEChem::OE3DMolStyle 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 ClearColors OEChem::OEMolStyleColorer ClearComponent OEBio::OEDesignUnit ClearConstraints OEChem::OECliqueSearch OEChem::OEMCSSearch OEChem::OESubSearch ClearContourStyle OEChem::OE3DMolStyle 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 ClearGridContourColorer OEChem::OE3DMolStyle ClearGridType OEChem::OE3DMolStyle ClearHarmonicConstraints OESz::OESzybki ClearHeterogenMetadata OESpruce::OEStructureMetadata ClearHydrogenVisibility OEChem::OE3DMolStyle ClearIndexableFragmentRange OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions ClearIndexedMols OEMedChem::OEMCSFragDatabase ClearInteractions OEShape::OEColorForceField ClearInteractionStyle OEChem::OE3DMolStyle ClearKeywords OESpruce::OEStructureMetadata ClearLabels OEGrapheme::OEColorGradientDisplayOptions ClearLigandConstraints OESpruce::OESuperpositionOptions ClearLigands OEModels::OEROCSQueryModelBuilder 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 ClearProteinColorer OEChem::OE3DMolStyle ClearProteinConstraint OEBio::OEReceptor ClearProteinConstraints OEBio::OEReceptor ClearProteinStyle OEChem::OE3DMolStyle 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 ClearSurfaceAlpha OEChem::OE3DMolStyle ClearSurfaceArcFxn OEGrapheme::OEShapeQueryDisplayOptions ClearSurfaceColorer OEChem::OE3DMolStyle ClearSurfaceStyle OEChem::OE3DMolStyle ClearSurfaceType OEChem::OE3DMolStyle 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 OESiteHopper::OESiteHopperDatabase 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 interface definition 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] conformer conformers 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::OEPositProbability OEDocking::OEScore OEDocking::OEShapeFit OEDocking::OEShapeFitOptions OEDocking::OEShapeFitResults OEGraphSim::OESimSearchResult OEMath::OEKernelPLS OEMath::OESphere OEModels::OEROCSQueryModelBuilder OEModels::OEROCSQueryModelOptions OEShape::OEFlexiOverlapOptions OEShape::OEFlexiOverlapResults OEShape::OEFlexiOverlay OEShape::OEFlexiOverlayOptions OEShape::OEOverlapPrepOptions OESz::OEFixedProteinLigandOptimizer OESz::OEFlexProteinLigandOptimizer OESz::OEProteinFlexOptions OESz::OEProteinLigandOptOptions OESz::OETorsionScanner 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::OEHalogenBondInteractionHint OEBio::OEHasAlternateLocation OEBio::OEHasInteractionHint OEBio::OEHasInteractionHintType OEBio::OEHasPDBAtomIndex OEBio::OEHasResidueInteractionHint OEBio::OEHasSecondaryStructure OEBio::OEHBondInteractionHint OEBio::OEHierChain OEBio::OEHierFragment OEBio::OEHierResidue OEBio::OEHierView OEBio::OEInteractionHint OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintContainer OEBio::OEInteractionHintFragment OEBio::OEInteractionHintTypeBase OEBio::OEIridiumData OEBio::OEIsBackboneAtom OEBio::OEIsCationPiInteractionHint OEBio::OEIsChelatorInteractionHint OEBio::OEIsClashInteractionHint OEBio::OEIsContactInteractionHint OEBio::OEIsCovalentInteractionHint OEBio::OEIsCTerminalAtom OEBio::OEIsDisulfideBond OEBio::OEIsHalogenBondInteractionHint OEBio::OEIsHBondInteractionHint OEBio::OEIsHetAtom OEBio::OEIsInterInteractionHint OEBio::OEIsIntermolecularChelatorInteractionHint OEBio::OEIsIntermolecularHBondInteractionHint OEBio::OEIsIntraInteractionHint OEBio::OEIsIntramolecularChelatorInteractionHint OEBio::OEIsIntramolecularHBondInteractionHint OEBio::OEIsNonIdealHBondInteractionHint OEBio::OEIsNTerminalAtom OEBio::OEIsSaltBridgeInteractionHint OEBio::OEIsStackingInteractionHint OEBio::OEIsStandardAminoAcid OEBio::OEIsStandardNucleicAcid 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 OEBioisostere::OEBroodBuildOptions OEBioisostere::OEBroodDBFilter OEBioisostere::OEBroodDBPacket OEBioisostere::OEBroodFragPrep OEBioisostere::OEBroodGeneralOptions OEBioisostere::OEBroodHit OEBioisostere::OEBroodHitlistOptions OEBioisostere::OEBroodMolBuilder OEBioisostere::OEBroodOverlay OEBioisostere::OEBroodQuery OEBioisostere::OEBroodScore OEBioisostere::OEBroodScoreOptions OEBioisostere::OEDBBuffer OEBioisostere::OEDBBuilder OEBioisostere::OEDBReader OEBioisostere::OEDBScreenOptions OEBioisostere::OEDBWriter OEBioisostere::OEExtrinsicPropOptions OEBioisostere::OEFragConfReader OEBioisostere::OEFragmentOptions OEBioisostere::OEFragOverlay OEBioisostere::OEHitlistBuilder OEBioisostere::OEIntrinsicPropOptions OEBioisostere::OEMolPropertyOptions OEChem::OE2DRingDictionary OEChem::OE2DRingDictionaryCreatorOptions OEChem::OE3DMolStyle OEChem::OEAbsoluteConfTest OEChem::OEAnisoUij OEChem::OEAtomBondSet OEChem::OEAtomIsInResidue OEChem::OECliqueSearch OEChem::OEConfRMSD OEChem::OEConfRMSDOptions OEChem::OEConstCoords OEChem::OECoordArray OEChem::OECreateSubSearchDatabaseOptions OEChem::OECSVHeader OEChem::OEEuler OEChem::OEExprBase OEChem::OEExtractRingTemplateOptions OEChem::OEFileStringParameter OEChem::OEFuzzy OEChem::OEGetNbrAtom OEChem::OEGraphMol OEChem::OEHasAlphaBetaUnsat OEChem::OEHasAtomicNum OEChem::OEHasAtomInGroup OEChem::OEHasAtomName OEChem::OEHasAtomStereoSpecified 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::OEIsomericConfTest OEChem::OEIsProductGroup OEChem::OEIsReactantGroup OEChem::OEIsRGroup OEChem::OEIsRotor OEChem::OEIsRxnComponentGroup OEChem::OELibraryGen OEChem::OELingoSim OEChem::OEMatch OEChem::OEMatchFunc OEChem::OEMatchPair OEChem::OEMCSFuncParameter OEChem::OEMCSMaxAtomsCompleteCycles OEChem::OEMCSMaxBondsCompleteCycles OEChem::OEMCSSearch OEChem::OEMMFFTypeResult OEChem::OEMol OEChem::OEMolDatabase OEChem::OEMolDatabaseSaveOptions OEChem::OEMolDBException OEChem::OEMolGDPropertyFxn OEChem::oemolistream OEChem::oemolithread OEChem::oemolostream OEChem::oemolothread OEChem::OEMolParameter OEChem::OEMolPropertyList OEChem::OEMolReaderParameter OEChem::OEMolSDPropertyFxn OEChem::OEMolStyleColorer 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::OERxnAutomapper OEChem::OERxnAutomapperOptions OEChem::OESDDataPair OEChem::OESimilarByRMSD OEChem::OESimpleAppOptions OEChem::OESubSearch OEChem::OESubSearchDatabase OEChem::OESubSearchQuery OEChem::OESubSearchResult OEChem::OESubSearchScreen OEChem::OETorsion OEChem::OETrans OEChem::OETranslation OEChem::OEUnaryToBinaryAnd OEChem::OEUnaryToBinaryOr OEChem::OEUnAtomPredParameter OEChem::OEUnBondPredParameter OEChem::OEUniMolecularRxn OEChem::OEUniMolecularRxnOptions OEChem::OEVectorBindings OEConfGen::OEConfFixOptions OEConfGen::OEConformerBuilder OEConfGen::OEConfSlicer OEConfGen::OEFlipperClassicOptions 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::OEThompsonOptions OEConfGen::OETorDriveOptions OEConfGen::OETorDriver OEConfGen::OETorLib OEConfGen::OETorLibParameter OEConstr::OEDihedralQuadPenalty 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 OEEon::OEEonHit OEEon::OEEonHitlistBuilder OEEon::OEEonHitlistOptions OEEon::OEEonOverlapScore OEEon::OEEonOverlay OEEon::OEEonOverlayResults OEEon::OEEonOverlayScore OEEon::OEEonPBFunc OEEon::OEEonPBOptions OEEon::OEEonPBOverlay OEEon::OEEonPBResults OEFastROCS::OEDBTracer OEFastROCS::OEFastROCSHistogram OEFastROCS::OEShapeDatabase OEFastROCS::OEShapeDatabaseOptions OEFastROCS::OEShapeDatabaseScore OEFF::OEComplexEnergies OEFF::OEComplexFF OEFF::OEComplexFFParameter OEFF::OEFF14SBParsley OEFF::OEFF14SBParsleyComplex OEFF::OEFF14SBParsleyParams OEFF::OEFF14SBSage OEFF::OEFF14SBSageComplex OEFF::OEFF14SBSageParams OEFF::OEFF14SBSmirnoff OEFF::OEFF14SBSmirnoffComplex OEFF::OEFF14SBSmirnoffParams OEFF::OEForceFieldParameter OEFF::OEMMFFAmberComplex OEFF::OEMMFFComplex OEFF::OEMMFFIEFF OEFF::OEMMFFIEFFOptions OEFF::OEMMFFSheffield OEFF::OEMMFFSheffieldOptions OEFF::OESmirnoffComplex 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 OEGraphSim::OECreateFastFPDatabaseOptions OEGraphSim::OEFastFPDatabase OEGraphSim::OEFastFPDatabaseParams OEGraphSim::OEFingerPrint OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions OEGraphSim::OEFPHistogram OEGraphSim::OEFPPattern OEGraphSim::OEFPTypeBase OEGraphSim::OEFPTypeParams OEGraphSim::OEFPVariogram OEGraphSim::OESimFuncBase OEGraphSim::OESimScore OEGraphSim::OESimScorePair OEGraphSim::OETanimotoSim OEGraphSim::OETverskySim OEMath::OEBox OEMath::OEMatrix OEMath::OESquareMatrix OEMedChem::OEBemisMurckoOptions OEMedChem::OECreateMMPIndexOptions OEMedChem::OECreateMMPIndexStatus OEMedChem::OEMatchedPair OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMatchedPairTransform OEMedChem::OEMatchedPairTransformExtractOptions OEMedChem::OEMCSFragDatabase OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMCSMolSimScore OEMedChem::OEMCSSimFuncBase OEMedChem::OEMCSTanimotoSim OEMedChem::OEMCSTverskySim 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::OEInteraction OEMolPotential::OEInteractParams OEMolPotential::OEInterAdaptor OEMolPotential::OEInterCoulombPotential OEMolPotential::OEInterNonBondPotBase OEMolPotential::OEInterNonBondPotential OEMolPotential::OEInterVdwPotential 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::OESage OEMolSmirnoff::OESageParams OEMolSmirnoff::OESmirnoff OEMolSmirnoff::OESmirnoffParams OEOpt::OEBFGSOpt OEOpt::OECGLineMinimize OEOpt::OEConjGradOpt OEOpt::OEDFPOpt OEOpt::OEFComponent OEOpt::OEFletcherReevesOpt OEOpt::OEHestenesStiefelOpt OEOpt::OEMaxStepLineMinimize OEOpt::OENewtonOpt OEOpt::OENRLineSearch 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::oeifstream OEPlatform::oeigzstream OEPlatform::oeiofstream OEPlatform::oeisstream OEPlatform::oeistdstream OEPlatform::oeistream OEPlatform::oeiwrapperstream OEPlatform::OELockCondition OEPlatform::oemultiostream OEPlatform::OEMutex OEPlatform::oeofstream OEPlatform::oeogzstream OEPlatform::oeosstream OEPlatform::oeostdstream OEPlatform::oeostream OEPlatform::oeowrapperstream OEPlatform::OESpinlock OEPlatform::oestream OEPlatform::OEThread OEPlatform::OEThreadLocal OEPlatform::OETryMutex 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::OEMultistatepKaModel OEProton::OEMultistatepKaModelOptions 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::OEColorFFParameter 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::OERandomStarts OEShape::OERefColorTverskyCutoff OEShape::OERefTverskyComboCutoff OEShape::OERefTverskyCutoff OEShape::OEROCS OEShape::OEROCSOptions OEShape::OEROCSResult OEShape::OEShapeGridOptions OEShape::OEShapeOptions OEShape::OEShapeQuery OEShape::OEShapeQueryPublic OEShape::OESubrocsStarts OEShape::OETanimotoComboCutoff OEShape::OETanimotoCutoff OESheff::OESheffield OESheff::OESheffieldOptions OESiteHopper::OESiteHopperDatabase OESiteHopper::OESiteHopperDatabaseOptions OESiteHopper::OESiteHopperPatchOptions OESiteHopper::OESiteHopperResults OESiteHopper::OESiteHopperScore OESiteHopper::OESiteHopperSearch OESiteHopper::OESiteHopperSearchBase OESiteHopper::OESiteHopperSearchOptions 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::OESpruceFilter OESpruce::OESpruceFilterOptions OESpruce::OEStructuralSuperposition OESpruce::OEStructureMetadata OESpruce::OESuperpose OESpruce::OESuperposeOptions OESpruce::OESuperposeResults OESpruce::OESuperpositionOptions OESpruce::OEValidateDesignUnit OESystem::OEAnd OESystem::OEAnnotation OESystem::OEBase OESystem::OEBaseData OESystem::OEBaseDataT OESystem::OEBinaryAnd OESystem::OEBinaryIOHandler OESystem::OEBinaryNot OESystem::OEBinaryOr OESystem::OEBInitializer 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::OEInterface OESystem::OEIntParameter OESystem::OEIter OESystem::OEIterBase OESystem::OELinearColorGradient OESystem::OELogarithmicColorGradient OESystem::OEMultiGrid OESystem::OEMultiParameter OESystem::OENot OESystem::OEOr OESystem::OEOwnedPtr OESystem::OEPredIter OESystem::oeprogressstream 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 OESz::OEBoundEntropyOptions OESz::OEEntropyResults OESz::OEFreeFormConf OESz::OEFreeFormConfAdvanced OESz::OEFreeFormConfOptions OESz::OEFreeFormConfResults OESz::OEFreeFormSolvOptions OESz::OEFreeFormSolvResults OESz::OELigandEntropyOptions OESz::OEProteinLigandOptResults OESz::OERestrictionEnergyResult OESz::OESingleConfResult OESz::OESzybki OESz::OESzybkiEnsembleResults OESz::OESzybkiGeneralOptions OESz::OESzybkiOptions OESz::OESzybkiOptOptions 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::OEHalogenBondInteractionHint OEBio::OEHasAlternateLocation OEBio::OEHasInteractionHint OEBio::OEHasInteractionHintType OEBio::OEHasPDBAtomIndex OEBio::OEHasResidueInteractionHint OEBio::OEHasSecondaryStructure OEBio::OEHBondInteractionHint OEBio::OEInteractionHint OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintFragment OEBio::OEInteractionHintTypeBase OEBio::OEIsBackboneAtom OEBio::OEIsCationPiInteractionHint OEBio::OEIsChelatorInteractionHint OEBio::OEIsClashInteractionHint OEBio::OEIsContactInteractionHint OEBio::OEIsCovalentInteractionHint OEBio::OEIsCTerminalAtom OEBio::OEIsDisulfideBond OEBio::OEIsHalogenBondInteractionHint OEBio::OEIsHBondInteractionHint OEBio::OEIsHetAtom OEBio::OEIsInterInteractionHint OEBio::OEIsIntermolecularChelatorInteractionHint OEBio::OEIsIntermolecularHBondInteractionHint OEBio::OEIsIntraInteractionHint OEBio::OEIsIntramolecularChelatorInteractionHint OEBio::OEIsIntramolecularHBondInteractionHint OEBio::OEIsNonIdealHBondInteractionHint OEBio::OEIsNTerminalAtom OEBio::OEIsNucleicAcidBase OEBio::OEIsNucleicAcidPhosphate OEBio::OEIsNucleicAcidSugar OEBio::OEIsSaltBridgeInteractionHint OEBio::OEIsStackingInteractionHint OEBio::OEIsStandardAminoAcid OEBio::OEIsStandardNucleicAcid 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::OEHasAtomicNum OEChem::OEHasAtomInGroup OEChem::OEHasAtomName OEChem::OEHasAtomStereoSpecified 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::OEIsomericConfTest OEChem::OEIsOxygen OEChem::OEIsPhosphorus OEChem::OEIsPolar OEChem::OEIsPolarHydrogen OEChem::OEIsProductGroup OEChem::OEIsReactantGroup OEChem::OEIsRGroup OEChem::OEIsRotor OEChem::OEIsRxnComponentGroup OEChem::OEIsSulfur OEChem::OEIsTermHeavyAtom OEChem::OEIsValidAtomValence OEChem::OEIsValidMDLAtomValence OEChem::OEMatch OEChem::OEMatchBase OEChem::OEMatchFunc OEChem::OEMCSFunc OEChem::OEMCSMaxAtoms OEChem::OEMCSMaxAtomsCompleteCycles OEChem::OEMCSMaxBonds OEChem::OEMCSMaxBondsCompleteCycles 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 OEEon::OEHighestChargeTanimoto OEEon::OEHighestShapeChargeTanimotoCombo OEEon::OEHighestShapeTanimoto 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 OEGraphSim::OESimFuncBase OEGraphSim::OETanimotoSim OEGraphSim::OETverskySim OEMedChem::OEBemisMurckoOptions OEMedChem::OEMatchedPair OEMedChem::OEMatchedPairTransform OEMedChem::OEMCSSimFuncBase OEMedChem::OEMCSTanimotoSim OEMedChem::OEMCSTverskySim 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 OESiteHopper::OESiteHopperDatabaseOptions OESiteHopper::OESiteHopperPatchOptions OESiteHopper::OESiteHopperSearchOptions 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 cube cubes CUDA customcolorffprep.java Example Code CXSMILES cyclic membership

D

Daylight, [1] Daylight SMARTS 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 design unit Destructor OEDocking::OEBoxBase OEDocking::OEFeature OEDocking::OESphereBase OEEon::OEEonHit OEEon::OEEonHitlistBuilder OEEon::OEEonOverlapScore OEEon::OEEonOverlay OEEon::OEEonOverlayResults OEEon::OEEonOverlayScore OEEon::OEEonPBFunc OEEon::OEEonPBOverlay OEEon::OEEonPBResults

DetermineCategory OEBio::OEIridiumData Dice similarity measure Dihedral DirContents OEPlatform::OEFile DirPath OEPlatform::OEFile Dock OEDocking::OEPosit dock docking dockmolecules.java Example Code, [1] 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

E

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 Estimate OEDocking::OEPositProbability 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, [1] 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 generatemultiplepose.java, [1] 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, [1] 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 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 simplesmirnoff.java simplevacuum.java singleconformer.java singleconformermacrocycle.java sizefilter.java smartsalign.java smartsalign2d.java smartsalign2d.txt 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 excipient excludedvolume.java Example Code excludedvolume.txt Example Code Exists OEPlatform::OEFile Expand OEBioisostere::OEDBBuilder 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 ExtractTransform OEFastROCS::OEShapeDatabaseScore

F

Factory OESystem::OEInterface FASTA Fatal OESystem::OEErrorHandler fd OEPlatform::oeifstream OEPlatform::oeofstream feature release file formats FileName OEPlatform::OEFile Filter OEBioisostere::OEDBBuilder Finalize OEBioisostere::OEDBBuffer FindDupParameters OESystem::OEOptions FindSimilarConfs OESz::OEFreeFormConf findsimilarconfs.java Example Code fingerprint Finish OEBioisostere::OEDBWriter FirstBit OESystem::OEBitVector Fit OEDocking::OEShapeFit OEMath::OEKernelPLS FixAtoms OESz::OESzybki flexibleprotein.java Example Code

flexresidues.java Example Code floe floes 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 FromString OEChem::OE3DMolStyle Full OESystem::OEBoundedBuffer OESystem::OEUnboundedBuffer Functor

G

g++ Gasteiger charge gcc Generate OEBioisostere::OEDBBuilder generate2d.java Example Code GenerateConfs OEConfGen::OETorDriver GenerateMicrostates OEProton::OEMultistatepKaModel GenerateMissingFrags OEConfGen::OEMakeFragLib generatemultiplepose.java Example Code, [1] 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 get_name OEDataFlow::OEFieldTypeHandler GetA OEBio::OECrystalSymmetryParams OESheff::OESheffieldOptions OESystem::OEColor GetAbbottBioScore OEBioisostere::OEBroodHit GetActive OEChem::OEMCMolBase GetAddCarbonSkeleton OEChem::OE2DRingDictionaryCreatorOptions GetAddCarbonSkeletonWithBondStereo OEChem::OE2DRingDictionaryCreatorOptions GetAddCount OEBioisostere::OEHitlistBuilder OEEon::OEEonHitlistBuilder 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 GetAlteredTag OEChem::OEUniMolecularRxnOptions 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 GetAromaticJCT OEBioisostere::OEIntrinsicPropOptions GetAromaticRingCount OEBioisostere::OEBroodHit GetAromaticStyle OEDepict::OE2DMolDisplayOptions GetAsDensity OEBio::OEIridiumData GetAssignBondiRadii OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions GetAssignColor OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions 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 GetAtomAdjTypeAtNeutralpH OEProton::OEMultistatepKaModel GetAtomColor OEDepict::OE2DMolDisplayOptions GetAtomColorer OEChem::OE3DMolStyle 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 GetAtomLabelColorer OEChem::OE3DMolStyle GetAtomLabelDataTag OEChem::OE3DMolStyle GetAtomLabelFont OEDepict::OE2DMolDisplayOptions GetAtomLabelFontScale OEDepict::OE2DMolDisplayOptions GetAtomLabelMonochrome OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByLasso OEDepict::OEHighlightByStick OEDepict::OEHighlightOverlayByBallAndStick GetAtomLabelPrecision OEChem::OE3DMolStyle GetAtomLabelText OEChem::OE3DMolStyle GetAtomLabelType OEChem::OE3DMolStyle GetAtomList OEChem::OEMolBase GetAtomMapSize OEBio::OEAltLocationFactory GetAtompKaRange OEProton::OEMultistatepKaModel GetAtomPredicate OEConfGen::OEFlipperClassicOptions 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 OESpruce::OESpruceFilter OESpruce::OEValidateDesignUnit GetAtomsElement OESpicoli::OESurface GetAtomStereoStyle OEDepict::OE2DMolDisplayOptions GetAtomStrength OEShape::OEShapeQueryBase GetAtomStyle OEChem::OE3DMolStyle GetAtomSVGMarkupFunctor OEDepict::OE2DMolDisplayOptions GetAtomTypeIndex OEMolPotential::OEFFParams GetAtomTypeName OEMolPotential::OEFFParams GetAtomTypes OEGraphSim::OEFPTypeParams GetAtomVisibilityFunctor OEDepict::OE2DMolDisplayOptions GetAttachCount OEBioisostere::OEBroodQuery OEBioisostere::OEBroodScore GetAttachCutoff OEBioisostere::OEBroodScoreOptions GetAttachmentPoints OEMedChem::OEMatchedPairTransformExtractOptions GetAttachScale OEBioisostere::OEBroodGeneralOptions GetAttachScore OEBioisostere::OEBroodHit OEBioisostere::OEBroodScore GetAuthor OESpruce::OEStructureMetadata GetAutoConstraints OEDocking::OEMakeReceptorOptions GetAxial OEChem::OEAtomBase GetB OEBio::OECrystalSymmetryParams OESheff::OESheffieldOptions OESystem::OEColor GetB0 OEMath::OEKernelPLS 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 GetBatchMaxRotors OEConfGen::OEThompsonOptions GetBeliefScore OEBioisostere::OEBroodHit GetBendParams OEMolPotential::OEFFParams GetBestHits OEEon::OEEonHitlistOptions GetBestReceptorPoseOnly OEDocking::OEPositOptions 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::OEFlipperClassicOptions 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 OEBioisostere::OEBroodHitlistOptions OESpruce::OEDesignUnitPrepOptions GetBuildSidechains OESpruce::OEDesignUnitBuildOptions GetBuildTails OESpruce::OELoopBuilderOptions GetBuildType OEBioisostere::OEBroodBuildOptions GetBumpCount OEBioisostere::OEHitlistBuilder GetBumpRadius OEBioisostere::OEBroodGeneralOptions 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 GetBValues OEMath::OEKernelPLS GetBypassPredicate OEBio::OEPlaceHydrogensOptions getbyte OEChem::oemolistream OEPlatform::oeistream getByteArray OEChem::oemolostream GetC OEBio::OECrystalSymmetryParams OESheff::OESheffieldOptions 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 GetCheckBond OEBioisostere::OEBroodBuildOptions GetCheckGeometry OEBioisostere::OEBroodScoreOptions 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 OEChem::OEUniMolecularRxnOptions OEProton::OETautomerOptions GetClearCoords OEDepict::OEAlignmentOptions OEDepict::OEPrepareDepictionOptions OEGrapheme::OEAlignedDepictionFrom3DOptions GetClearMapping OEChem::OERxnAutomapperOptions GetClusterScore OEBio::OEPlaceHydrogensDetails GetCoefficients OEShape::OEHermite GetCofactorCodes OESpruce::OEDesignUnitSplitOptions GetCollapseNonSiteAlts OESpruce::OEDesignUnitEnumerateSitesOptions GetCollectProteinByChain OEBio::OESplitMolComplexOptions GetColor OEChem::OEMolStyleColorer 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 OEModels::OEROCSQueryModelOptions OEShape::OEColorOptions OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions OEShape::OEShapeQueryBase OEShape::OEShapeQueryPublic OESiteHopper::OESiteHopperPatchOptions GetColorForceFieldType OEFastROCS::OEShapeDatabase OEFastROCS::OEShapeDatabaseOptions GetColorFunc OEShape::OEOverlapFunc GetColorFuncType OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions GetColorGaussians OEShape::OEShapeQueryBase GetColorGridSpacing OEFastROCS::OEShapeDatabase GetColorOptimization OEFastROCS::OEShapeDatabaseOptions GetColorOptions OEShape::OEColorFunc OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions GetColors OEDepict::OEHighlightOverlayBase OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase GetColorScale OESiteHopper::OESiteHopperResults GetColorScheme OEChem::OEMolStyleColorer GetColorScore OEBioisostere::OEBroodHit OEBioisostere::OEBroodScore OEFastROCS::OEShapeDatabaseScore OEShape::OEOverlapResults GetColorScoreScale OEFastROCS::OEShapeDatabaseOptions GetColorStopLabelFont OEGrapheme::OEColorGradientDisplayOptions GetColorStopLabelFontScale OEGrapheme::OEColorGradientDisplayOptions GetColorStopPrecision OEGrapheme::OEColorGradientDisplayOptions GetColorStopVisibility OEGrapheme::OEColorGradientDisplayOptions GetColorStyle OEDepict::OELegendLayoutOptions GetColorTanimoto OEFastROCS::OEShapeDatabaseScore OEShape::OEOverlapResults OESiteHopper::OESiteHopperResults GetColorTversky OEFastROCS::OEShapeDatabaseScore OEShape::OEOverlapResults GetColorTypes OEGrapheme::OEColorForceFieldDisplay GetColumnName OEChem::OECSVHeader GetColumnNames OEChem::OECSVHeader GetCombinedFilter OEBio::OESplitMolComplexOptions GetComboScore OEBioisostere::OEBroodHit OEBioisostere::OEBroodScore GetCommandLine OESystem::OEHeader GetComment OESystem::OEHeader GetCommentEnergy OEConfGen::OETorDriveOptions GetComplexArea OEPB::OESimpleBindResults GetComplexAreaEnergy OEPB::OESimpleBindResults GetComplexCoulombEnergy OEPB::OEBindResults GetComplexity OEBioisostere::OEBroodHit OEBioisostere::OEExtrinsicPropOptions GetComplexSolvationEnergy OEFF::OEComplexEnergies 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 GetCompositeMolecule OEShape::OEShapeQueryBase GetConf OEChem::OEMCMolBase OEPB::OESimpleBindResults GetConfFixOptions OEConfGen::OEOmegaOptions GetConfFreeEnergyFromEnsemble OESz::OESzybkiResults GetConfGenRMS OESz::OEFreeFormSolvOptions GetConfIdx OEFastROCS::OEShapeDatabaseScore OESz::OESingleConfResult OESz::OESzybkiResults GetConfigurationalEntropy OESz::OEEntropyResults OESz::OESzybkiEnsembleResults GetConfList OEChem::OEMCMolBase OEChem::OEMol GetConformerIndex OEEon::OEEonHit GetConfResult OESz::OEFreeFormConfResults GetConfs OEChem::OEMCMolBase GetConfsPerHit OEShape::OEROCSOptions GetConfTest OEChem::oemolistream GetConnectBufferDistance OESpruce::OELoopBuilderOptions GetConsiderAtomLabelBoundingBox OEDepict::OEHighlightByLasso GetConstraintFeatures OEBio::OEReceptorCustomConstraints GetContactDistance OEMolPotential::OEFFParams GetContext OEMedChem::OEMatchedPairTransformExtractOptions OESzmap::OESzmapEngine GetContourStyle OEChem::OE3DMolStyle GetCoords OEChem::OEConfBase OEChem::OEMolBase OEDepict::OE2DAtomDisplay OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase OESzmap::OESzmapResults GetCoordsPtr OEChem::OEConfBase GetCoordsToInertialFrame OEGrapheme::OEDepictionFrom3DOptions GetCorrSolventOptions OESz::OEFreeFormConfOptions 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 OEEon::OEEonHitlistOptions OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions OEMolPotential::OENonBondIntcsOptions GetCutoffGT OEFastROCS::OEShapeDatabaseOptions GetCutoffLT OEFastROCS::OEShapeDatabaseOptions GetCXSMILES OEChem::OEParseSmilesOptions GetData OEMath::OEMatrix 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 GetDataTypes OEChem::OEMolStyleColorer GetDate OESystem::OEHeader GetDefault OEChem::OEPredicateParameter OESystem::OEMultiParameter OESystem::OETypedParameter GetDefaultBondPen OEDepict::OE2DMolDisplayOptions GetDefaultColor OEChem::OEMolStyleColorer GetDefaultReadFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase GetDefaults OESystem::OETypedParameter GetDefaultsVector OESystem::OEPODParameter GetDefaultWriteFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase GetDegree OEChem::OEAtomBase GetDeleteClashingSolvent OESpruce::OECapBuilderOptions OESpruce::OESidechainBuilderOptions GetDeleteCount OEBioisostere::OEHitlistBuilder GetDeleteFloatingRes OESpruce::OESpruceFilterOptions 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 OESiteHopper::OESiteHopperDatabase OESiteHopper::OESiteHopperScore GetDesolvationEnergy OEFF::OEComplexEnergies OEPB::OEBindResults GetDetail OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter GetDetails OEBio::OEInteractionHint GetDielectric OEEon::OEEonPBOptions 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 GetDuplicateCount OEBioisostere::OEHitlistBuilder GetDuplicateDistance OEShape::OEOverlapPrepOptions GetDuplicateRemoval OESpruce::OEDesignUnitEnumerateSitesOptions GetEgan OEBioisostere::OEBroodHit GetEganEgg OEBioisostere::OEMolPropertyOptions 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 OEBioisostere::OEBroodScore OEChem::OEMolBase OEMolAM1::OEAM1Results OESz::OETorsionScanResult GetEnergyRange OEConfGen::OESliceEnsembleOptions GetEnergyTerm OESz::OESzybkiResults GetEnergyWindow OEConfGen::OEFragOptions OEConfGen::OEMacrocycleOmegaOptions OEConfGen::OEOmegaOptions OEConfGen::OESliceEnsembleOptions GetEnhancedStereo OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions GetEnsembleLigPartialSolvEntropy OESz::OESzybkiEnsembleResults GetEnsembleLigSolvEntropy OESz::OESzybkiEnsembleResults GetEnsembleProtDesolvEntropy OESz::OESzybkiEnsembleResults GetEnsembleValue OESzmap::OESzmapResults GetEntityID OEChem::OEResidue GetEntries OEBio::OEResidueCategoryData GetEntropicEnergy OESz::OESzybkiEnsembleResults GetEntropy OESz::OESzybki GetEntropy(const OEChem::OEMCMolBase&, unsigned int, unsigned int) OESz::OESzybki GetEnumAtoms OEConfGen::OEFlipperOptions GetEnumAtomSpecifiedStereo OEConfGen::OEFlipperOptions GetEnumBonds OEConfGen::OEFlipperOptions GetEnumBondSpecifiedStereo OEConfGen::OEFlipperOptions GetEnumBridgehead OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions GetEnumerateCofactorSites OESpruce::OEDesignUnitEnumerateSitesOptions GetEnumerateSitesOptions OESpruce::OEDesignUnitPrepOptions GetEnumEZ OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions GetEnumNitrogen OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions OEConfGen::OEMolBuilderOptions GetEnumRelativeAtomStereo OEConfGen::OEFlipperOptions GetEnumRing OEConfGen::OEMolBuilderOptions GetEnumRS OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions GetEnumSpecifiedStereo OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions GetEnvironment OESz::OELigandEntropyOptions GetEquilibriumAngle OEMolPotential::OEFFParams GetEquilibriumBondLength OEMolPotential::OEFFParams GetError OEPB::OEZap GetETAttachScore OEBioisostere::OEBroodHit OEBioisostere::OEBroodScore GetETComboScore OEBioisostere::OEBroodHit OEBioisostere::OEBroodScore GetETOverlap OEEon::OEEonOverlapScore OEEon::OEEonOverlayScore GetETPBScore OEBioisostere::OEBroodHit OEBioisostere::OEBroodScore GetETShapeScore OEBioisostere::OEBroodHit OEBioisostere::OEBroodScore GetETTanimoto OEEon::OEEonOverlapScore OEEon::OEEonOverlayScore 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 GetExtendMappedRegions OEChem::OERxnAutomapperOptions GetExtension OEDepict::OEImageFileBase OEDepict::OEImageFileCreatorBase GetExtrinsicMaxOptions OEBioisostere::OEMolPropertyOptions GetExtrinsicMinOptions OEBioisostere::OEMolPropertyOptions 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 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 OESpruce::OESuperposeResults GetFitColorTversky OEShape::OEOverlapResults GetFitConfIdx OEShape::OEBestOverlayScore GetFitHermiteOptions OEShape::OEHermiteShapeFunc GetFitSelfColor OEShape::OEOverlapResults GetFitSelfET OEEon::OEEonOverlapScore OEEon::OEEonOverlayScore GetFitSelfOverlap OEEon::OEEonPBResults OEShape::OEOverlapResults GetFitTversky OEShape::OEColorResults OEShape::OEOverlapResults GetFitTverskyCombo OEShape::OEOverlapResults GetFixBackboneAtoms OESpruce::OESpruceFilterOptions GetFixBondOrder OESpruce::OESpruceFilterOptions GetFixBondsToMetals OESpruce::OESpruceFilterOptions GetFixDeleteH OEConfGen::OEConfFixOptions GetFixedCoords OEDepict::OEAlignmentOptions GetFixedHLayer OEChem::OEInChIOptions GetFixLigandState OESpruce::OESpruceFilterOptions GetFixMaxMatch OEConfGen::OEConfFixOptions GetFixMCS OEConfGen::OEConfFixOptions GetFixMol OEConfGen::OEConfFixOptions GetFixNames OESpruce::OESpruceFilterOptions GetFixPattern OESz::OESzybki GetFixPredicate OEConfGen::OEConfFixOptions OESz::OESzybki GetFixRMS OEConfGen::OEConfFixOptions GetFixSmarts OEConfGen::OEConfFixOptions GetFixSubSearch OEConfGen::OEConfFixOptions GetFixUniqueMatch OEConfGen::OEConfFixOptions GetFixValence OEChem::OEUniMolecularRxnOptions GetFlagTableFailures OEMolProp::OEFilter GetFlavor OEChem::OEMolDatabase OEChem::OEMolDatabaseSaveOptions OEChem::oemolstreambase GetFlexiOverlapOptions OEDocking::OEShapeFitOptions OEShape::OEFlexiOverlayOptions GetFlexiOverlayOptions OEDocking::OEPositOptions 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 GetForceCapping OESpruce::OECapBuilderOptions GetForceField OEConfGen::OEFragBuilderOptions OEConfGen::OETorDriveOptions OEConfGen::OETorDriver OEDocking::OEPoseOptimizerOptions OEShape::OEFlexiOverlapOptions OESz::OEBoundEntropyOptions OESz::OELigandEntropyOptions OESz::OEProteinLigandOptOptions OESz::OESzybkiGeneralOptions OESz::OETorsionScanOptions 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::OEFastFPDatabase OEGraphSim::OEFastFPDatabaseParams OEGraphSim::OEFingerPrint OEGraphSim::OEFPDatabase GetFPTypeString OEGraphSim::OEFPTypeBase GetFPVersion OEGraphSim::OEFPTypeBase GetFPVersionString OEGraphSim::OEFPTypeBase GetFrag OEBioisostere::OEBroodScore OEBioisostere::OEDBBuilder GetFragBuilderOptions OEConfGen::OEMolBuilderOptions GetFragCount OEBioisostere::OEBroodDBPacket OEBioisostere::OEDBReader GetFragGen OEConfGen::OEFragOptions GetFragKeep OEConfGen::OEFragOptions GetFragment OEBio::OEInteractionHint GetFragmentationLimit OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions GetFragmentNumber OEBio::OEAtomMatchResidueID OEBio::OEHierFragment OEChem::OEResidue GetFragments OEBio::OEHierChain OEBio::OEHierView GetFragMol OEBioisostere::OEBroodScore GetFrags OEBioisostere::OEDBBuilder GetFragSmiles OEBioisostere::OEBroodHit OEBioisostere::OEDBBuilder GetFragSmilesCSV OEBioisostere::OEDBBuilder GetFrequency OEBioisostere::OEBroodHit OEBioisostere::OEExtrinsicPropOptions GetFromCT OEConfGen::OEMolBuilderOptions GetFromSDData OEMedChem::OEMatchedPair Getfsp3C OEBioisostere::OEBroodHit GetFullConformationSearch OEDocking::OEPositOptions OEDocking::OEShapeFitOptions GetG OESystem::OEColor GetGamma OEBio::OECrystalSymmetryParams GetGap OEBio::OESequenceAlignment GetGaussians OESystem::OEGaussianContainer OESystem::OEGaussianContainerBase GetGeneralOptions OESz::OESzybkiOptions GetGenerateIdea OEBioisostere::OEBroodHitlistOptions GetGenerateTautomers OESpruce::OEProtonateDesignUnitOptions GetGlobalOffset OEDepict::OEImageBase GetGlobalStrain OESz::OERestrictionEnergyResult GetGradients OESz::OESzybkiResults GetGradTolerance OESz::OEProteinLigandOptOptions OESz::OESzybkiOptOptions GetGraphics OEDepict::OEJavaImageBase GetGridBuffer OEEon::OEEonPBOptions OEPB::OEET GetGridContourColorer OEChem::OE3DMolStyle GetGridOptions OEShape::OEGridColorFunc OEShape::OEGridShapeFunc GetGridSpacing OEEon::OEEonPBOptions OEPB::OEET OEPB::OEZap OEShape::OEOverlap OEShape::OEShapeGridOptions GetGridType OEChem::OE3DMolStyle 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 GetHarmonic OEShape::OEFlexiOverlapOptions 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 GetHeavyAtomCount OEBioisostere::OEIntrinsicPropOptions GetHeavyCount OEBioisostere::OEBroodHit OEBioisostere::OEBroodQuery 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 GetHitCount OEBioisostere::OEHitlistBuilder OEEon::OEEonHitlistBuilder GetHits OEBioisostere::OEHitlistBuilder OEEon::OEEonHitlistBuilder GetHostComponents OEFF::OEComplexEnergies GetHostEnergy OEFF::OEComplexEnergies GetHostSolvationEnergy OEFF::OEComplexEnergies GetHPosition OEDepict::OE2DAtomDisplay GetHvyDegree OEChem::OEAtomBase GetHvyValence OEChem::OEAtomBase GetHyb OEChem::OEAtomBase GetHybridizationLevel OEProton::OETautomerOptions GetHydrogens OEChem::OEInChIOptions GetHydrogenStyle OEDepict::OE2DMolDisplayOptions GetHydrogenVisibility OEChem::OE3DMolStyle GetHydrophobicSolvationFreeEnergy OESz::OEFreeFormSolvResults GetHyperlink OEDepict::OEFont GetID OESiteHopper::OESiteHopperScore OESpruce::OEHeterogenMetadata GetId OEDepict::OESVGGroup GetIDByTitle OESiteHopper::OESiteHopperDatabase GetIdeaGroup OEBioisostere::OEBroodHit GetIdeaRank OEBioisostere::OEBroodHit GetIDs OEBio::OEDesignUnit GetIdx OEBioisostere::OEBroodDBPacket 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 GetIgnoreStereo OEConfGen::OEMolBuilderOptions GetIgnoreTerminalHeavy OEChem::OEConfRMSDOptions GetIllegalRanges OESystem::OEParameter GetIllegalValues OESystem::OEParameter GetImplicitHCount OEChem::OEAtomBase GetIncludeInput OEConfGen::OEOmegaOptions GetIndexableFragmentRangeMax OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions GetIndexableFragmentRangeMin OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions GetIndices OEBioisostere::OEDBReader GetInFile OEChem::OERefInputAppOptions OEChem::OESimpleAppOptions GetInitHitCount OEBioisostere::OEHitlistBuilder GetInitialEnergies OESz::OEProteinLigandOptResults GetInitialOrientation OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay GetInitialRMSGradient OESz::OESzybkiResults GetInitialTotalPotential OESz::OESzybkiResults GetInnerContour OEDepict::OEHighlightByCogwheel GetInnerContourLevel OEBio::OEReceptor GetInnerContourVolume OEBio::OEReceptor GetInnerDielectric OEPB::OEET OEPB::OEZap GetInnerMask OEEon::OEEonPBOptions OEPB::OEET GetInsertCode OEBio::OEAtomMatchResidueID OEChem::OEResidue GetIntData OESystem::OEBase GetInteractions OEBio::OEInteractionHintContainer OEMolPotential::OEMolFunc GetInteractionStyle OEChem::OE3DMolStyle 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 GetInternalEnergy OEShape::OEFlexiOverlapResults GetIntramolecularLigandEnergy OESz::OESzybkiResults GetIntramolecularVdWCutoff OESz::OESzybkiGeneralOptions GetIntrinsicMaxOptions OEBioisostere::OEMolPropertyOptions GetIntrinsicMinOptions OEBioisostere::OEMolPropertyOptions 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::OEBoundEntropyOptions OESz::OELigandEntropyOptions 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 GetLigandSolvationEnergy OEFF::OEComplexEnergies 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 GetLipinski OEBioisostere::OEExtrinsicPropOptions GetLipinskiAcc OEBioisostere::OEBroodHit OEBioisostere::OEExtrinsicPropOptions GetLipinskiDon OEBioisostere::OEBroodHit OEBioisostere::OEExtrinsicPropOptions GetLipinskiFail OEBioisostere::OEBroodHit GetList OEMolPotential::OEInteractParams OESystem::OEInterface GetLnQrot OESz::OESzybkiResults GetLnQrotational OESz::OESingleConfResult GetLnQvib OESz::OESzybkiResults GetLnQvibrational OESz::OESingleConfResult GetLocalDensity OESpruce::OEPocket GetLocalStrain OEBioisostere::OEBroodHit OESz::OERestrictionEnergyResult GetLocation OEBio::OEAltLocationFactory GetLocationCodes OEBio::OEAltLocationFactory GetLocationCount OEBio::OEAltGroup OEBio::OEAltLocation GetLocationID OEBio::OEAltLocation GetLocations OEBio::OEAltGroup GetLogP OEBioisostere::OEExtrinsicPropOptions GetLoopBuilderOptions OESpruce::OEDesignUnitBuildOptions GetLoopClashRejectThreshold OESpruce::OELoopBuilderOptions GetLoopDBFilename OESpruce::OELoopBuilderOptions GetLowestdGConfIdx OESz::OEFreeFormConfResults GetLowestEneResults OESz::OETorsionScanner GetLowestEnergyConfs OESz::OETorsionScanner GetLowestRelEneConfIdx OESz::OEFreeFormConfResults GetMacrocycleBuilderOptions OEConfGen::OEMacrocycleOmegaOptions GetMacroCycOptions OEConfGen::OEFragBuilderOptions GetMakePackingResidues OESpruce::OEDesignUnitSplitOptions GetMapIdx OEChem::OEAtomBase GetMappingMethod OEChem::OERxnAutomapperOptions GetMargin OEDepict::OE2DMolDisplayOptions OEDepict::OEImageGrid OEDepict::OEImageTableOptions OEDepict::OELegendLayoutOptions GetMarkedValuePen OEGrapheme::OEColorGradientDisplayOptions GetMarkedValuePrecision OEGrapheme::OEColorGradientDisplayOptions GetMarkedValues OEGrapheme::OEColorGradientDisplayOptions GetMartin OEBioisostere::OEExtrinsicPropOptions GetMaskCutoff OESzmap::OESzmapEngineOptions GetMass OEDepict::OE2DAtomDisplay GetMatchCount OEBioisostere::OEHitlistBuilder 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::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions 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::OEFlipperClassicOptions OEConfGen::OEFlipperOptions GetMaxChargeAidedHBondDistance OEBio::OEPerceiveInteractionOptions GetMaxChiral OEBioisostere::OEFragmentOptions 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

GetMaxDegree OEBioisostere::OEFragmentOptions GetMaxDisplacement OESz::OESzybkiResults GetMaxDistance OEGraphSim::OEFPTypeParams GetMaxDonorAngle OEBio::OEPerceiveInteractionOptions GetMaxEnumConfs OEConfGen::OEMolBuilderOptions GetMaxFragLimit OEMedChem::OEMCSFragDatabaseOptions GetMaxHalogenAngle OEBio::OEPerceiveInteractionOptions GetMaxHalogenBondDistance OEBio::OEPerceiveInteractionOptions GetMaxHBondDistance OEBio::OEPerceiveInteractionOptions GetMaxHeavy OEBioisostere::OEFragmentOptions GetMaxHeavyAtom OEBio::OELigandInteractionHintComponent GetMaxHits OEBioisostere::OEBroodHitlistOptions OEEon::OEEonHitlistOptions OEShape::OEROCSOptions OESiteHopper::OESiteHopperSearchOptions GetMaxIter OEConfGen::OEMacrocycleOmegaOptions OESz::OEProteinLigandOptOptions OESz::OESzybkiOptOptions OESz::OETorsionScanOptions GetMaxLigAtoms OEBio::OEMolComplexCategorizer OESpruce::OEDesignUnitSplitOptions GetMaxLigResidues OEBio::OEMolComplexCategorizer OESpruce::OEDesignUnitSplitOptions GetMaxLocalStrain OEBioisostere::OEBroodBuildOptions OEDocking::OEShapeFitOptions GetMaxMatches OEChem::OECliqueSearch OEChem::OEConfRMSDOptions OEChem::OEMCSSearch OEChem::OESubSearch OEChem::OESubSearchQuery OEChem::OEUniMolecularRxnOptions GetMaxMetalBondDistance OEBio::OEPerceiveInteractionOptions GetMaxMMPLimit OEMedChem::OEMatchedPairTransformExtractOptions GetMaxMoleculesPerModel OEModels::OEROCSQueryModelOptions GetMaxMolIdx OEChem::OEMolDatabase OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMCSFragDatabase OESiteHopper::OESiteHopperDatabase GetMaxMolWt OEBioisostere::OEFragmentOptions GetMaxNbrDist OEProton::OESpreadMetalCharges GetMaxNonIdealAcceptorAngle OEBio::OEPerceiveInteractionOptions GetMaxNonIdealDonorAngle OEBio::OEPerceiveInteractionOptions GetMaxNonIdealHBondDistance OEBio::OEPerceiveInteractionOptions GetMaxNumDevices OEFastROCS::OEShapeDatabase GetMaxNumMicrostates OEProton::OEMultistatepKaModelOptions GetMaxOptIterations OEFastROCS::OEShapeDatabase GetMaxOptSteps OEDocking::OEShapeFitOptions OEShape::OEFlexiOverlayOptions 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 GetMaxTrials OEConfGen::OEThompsonOptions GetMaxTrialsRange OEConfGen::OEThompsonOptions 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 GetMCSExhaustiveMode OEChem::OERxnAutomapperOptions GetMCSFunc OEConfGen::OEConfFixOptions GetMCSMinAtoms OEConfGen::OEConfFixOptions GetMCSSimTypeString OEMedChem::OEMCSSimFuncBase OEMedChem::OEMCSTanimotoSim OEMedChem::OEMCSTverskySim GetMCSType OEConfGen::OEConfFixOptions GetMemoryType OEGraphSim::OEFastFPDatabase GetMemoryTypeString OEGraphSim::OEFastFPDatabase GetMergeColorAtoms OEModels::OEROCSQueryModelOptions GetMessage OEMolProp::OEFilter GetMessages OESpruce::OESpruceFilter OESpruce::OEValidateDesignUnit GetMetal OEBio::OEDesignUnit GetMethod OEBio::OESequenceAlignment OEPB::OEArea OEShape::OEBestOverlay OEShape::OEOverlap OESpruce::OESuperposeOptions GetMicrostates OEProton::OEMultistatepKaModel GetMid OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetMin OEGraphSim::OEFPHistogram GetMinAtoms OEChem::OECliqueSearch OEChem::OEMCSSearch GetMinColor OESystem::OEColorGradientBase GetMinContactFraction OEBio::OEPerceiveInteractionOptions GetMinCovalentFraction OEBio::OEPerceiveInteractionOptions GetMinDegree OEBioisostere::OEFragmentOptions GetMinDistance OEGraphSim::OEFPTypeParams GetMinFontSize OEDepict::OEImageBase GetMinFragLimit OEMedChem::OEMCSFragDatabaseOptions GetMinFreqHeavy OEBioisostere::OEDBScreenOptions GetMinFrequency OEBioisostere::OEDBScreenOptions GetMinHBondContactFraction OEBio::OEPerceiveInteractionOptions GetMinHeavy OEBioisostere::OEFragmentOptions GetMinimizeSidechains OESpruce::OESidechainBuilderOptions GetMinimizeSidechainsShell OESpruce::OESidechainBuilderOptions 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 GetModelMolecule OEProton::OEMultistatepKaModel GetModelNumber OEChem::OEResidue GetMol OEBioisostere::OEBroodHit OEChem::oemolthreadbase OEEon::OEEonHit 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 OESiteHopper::OESiteHopperDatabase GetMoleculeIndex OEGraphSim::OEFastFPDatabase GetMolecules OEBio::OEInteractionHintContainer GetMoleculeString OEChem::OEMolDatabase GetMoleculeTitle OEMedChem::OEMatchedPairTransform GetMolIdx OEFastROCS::OEShapeDatabaseScore GetMolStream OEChem::oemolithread OEChem::oemolothread GetMolTanimotoCombo OEBioisostere::OEBroodHit GetMolWt OEBioisostere::OEBroodHit OEBioisostere::OEIntrinsicPropOptions 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 GetNCPU OESiteHopper::OESiteHopperSearchOptions GetNegativeColor OEGrapheme::OE2DPropMap GetNegativeImageGrid OEBio::OEReceptor GetNegativeImageType OEDocking::OEMakeReceptorOptions GetNeutralPH OEBioisostere::OEBroodBuildOptions GetNextPacket OEBioisostere::OEDBReader GetNextToken OEChem::OETokenizerBase GetNoFlipPredicate OEBio::OEPlaceHydrogensOptions GetNonBondCutoff OEDocking::OEPoseOptimizerOptions OESz::OEProteinLigandOptOptions GetNonBondOptions OEMolPotential::OENonBondPotBase GetNonPolymerPseudoAtoms OEChem::OEInChIOptions GetNonRingOptions OEConfGen::OEFragBuilderOptions GetNormal OESpicoli::OESurface GetNormalizeAndRescore OESiteHopper::OESiteHopperSearchOptions 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 GetNumColors OEChem::OEMolStyleColorer GetNumColumns OEChem::OECSVHeader OEMath::OEMatrix GetNumContacts OEDocking::OESinglePoseResult GetNumCycles OESz::OESzybkiResults GetNumDevices OEFastROCS::OEShapeDatabase GetNumericGradDelta OEMolAM1::OEAM1Options GetNumFeaturesUsed OEMath::OEKernelPLS GetNumFixAtoms OESz::OESzybkiResults GetNumFlips OEBio::OEPlaceHydrogensDetails GetNumGrids OESystem::OEFixedMultiGrid GetNumHeavyAtomStarts OEFastROCS::OEShapeDatabaseOptions GetNumHydrogensStandardized OEBio::OEPlaceHydrogensDetails GetNumInertialStarts OEFastROCS::OEShapeDatabaseOptions GetNumMatchedPairs OEMedChem::OECreateMMPIndexStatus GetNumModels OEModels::OEROCSQueryModelOptions 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 GetNumRows OEMath::OEMatrix GetNumSCFCycles OEMolAM1::OEAM1Results GetNumStartPoints OEShape::OECartesianStarts GetNumStarts OEFastROCS::OEShapeDatabaseOptions OESz::OETorsionScanOptions 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 OEChem::OERxnAutomapper OEChem::OEUniMolecularRxn OEConfGen::OEFragBuilder OEConfGen::OEMacrocycleBuilder OEConfGen::OEMacrocycleOmega OEConfGen::OEMolBuilder OEConfGen::OEOmega OEDepict::OE2DMolDisplay OEDepict::OEImageTable OEDepict::OELegendLayout OEDepict::OEReport OEGrapheme::OE2DActiveSiteDisplay OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMatchedPairTransformExtractOptions OEMedChem::OEMCSFragDatabase OEMedChem::OEMCSFragDatabaseOptions OEMolAM1::OEAM1 OEShape::OEHermite OESiteHopper::OESiteHopperDatabase 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 GetOuterContourVolume OEBio::OEReceptor GetOuterDielectric OEPB::OEZap GetOuterMask OEEon::OEEonPBOptions OEPB::OEET GetOutFile OEChem::OERefInputAppOptions OEChem::OESimpleAppOptions GetOutOfPlaneParams OEMolPotential::OEFFParams GetOverlap OEEon::OEEonPBResults OEShape::OEOverlapResults GetOverlapColor OEGrapheme::OEShapeOverlapDisplayOptions GetOverlapDisplayStyle OEGrapheme::OEShapeOverlapDisplayOptions GetOverlapDiv OESz::OETorsionScanOptions GetOverlapFunc OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions GetOverlayConf OEShape::OEROCSResult GetOverlayConfs OEShape::OEROCSResult GetOverlayOptions OEShape::OEMultiRefOverlay OEShape::OEOverlay OEShape::OEROCSOptions GetPackedColor OESystem::OEColor GetPackets OEBioisostere::OEDBBuffer 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 GetPatchOptions OESiteHopper::OESiteHopperDatabaseOptions GetPatchScore OESiteHopper::OESiteHopperResults GetPattern OEChem::OECliqueSearch OEChem::OEMCSSearch OEChem::OESubSearch GetPatternAtoms OEChem::OEMatchBase GetPatternBonds OEChem::OEMatchBase GetPDBMetaData OEBio::OEDesignUnit GetPen OEDepict::OEHighlightByLasso OEGrapheme::OEPlotMarker GetPenaltyConstant OEConstr::OEDihedralQuadPenalty GetPenaltyForceConstant OESz::OETorsionScanOptions GetPerceiveBondStereo OEDepict::OEPrepareDepictionOptions GetPercent OEProton::OEELFOptions GetPercentage OEProton::OEELFCharges GetPerformPrep OEShape::OEROCSOptions GetPermissiveBCCs OEProton::OEAM1BCCCharges GetpH OEProton::OEMultistatepKaModelOptions 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::OEShapeFitResults OEDocking::OESinglePoseResult GetPoserCacheCount OEDocking::OEPositOptions GetPoseRelaxMode OEDocking::OEPositOptions GetPoseRelaxOptions 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 GetPrettyLegalValues OESystem::OEParameter GetPriorTemperature OEConfGen::OEThompsonOptions 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 GetProcessCarbons OEProton::OEMultistatepKaModelOptions 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 GetPropertyName OEChem::OEMolStyleColorer GetPropertyOffset OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay GetPropertyOptions OEBioisostere::OEBroodScoreOptions GetProtectiveGroupLabelFont OEDepict::OE2DMolDisplayOptions GetProtectiveGroupStyle OEDepict::OE2DMolDisplayOptions GetProtein OEBio::OEDesignUnit OESz::OESzybki GetProteinColorer OEChem::OE3DMolStyle 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 GetProteinStyle OEChem::OE3DMolStyle 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 GetRank OESiteHopper::OESiteHopperResults 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 OESpruce::OESuperposeResults GetRefColorTversky OEShape::OEOverlapResults GetRefConfIdx OEShape::OEBestOverlayScore GetReferenceCoords OEBio::OEPlaceHydrogensMoverNote GetRefFile OEChem::OERefInputAppOptions GetRefFrag OEBioisostere::OEFragOverlay GetRefGrid OEShape::OEBestOverlay GetRefHermiteOptions OEShape::OEHermiteShapeFunc GetRefMol OEShape::OEBestOverlay GetRefSelfColor OEShape::OEBestOverlay OEShape::OEOverlapResults GetRefSelfET OEEon::OEEonOverlapScore OEEon::OEEonOverlayScore GetRefSelfOverlap OEEon::OEEonPBResults 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 GetRelaxAttempted OEDocking::OESinglePoseResult GetRelaxed OEDocking::OESinglePoseResult GetRelaxStatus OEDocking::OESinglePoseResult GetRelaxStatusStr OEDocking::OESinglePoseResult GetRelLnQ OESz::OESingleConfResult GetRemoveAttractiveVdWForces OESz::OESzybkiGeneralOptions GetRemoveCoulombTerms OESz::OESzybkiGeneralOptions GetRemoveDuplicate OEShape::OEOverlapPrepOptions 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 GetResidueCutoff OESiteHopper::OESiteHopperPatchOptions 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 GetRigidOverlay OEShape::OEFlexiOverlayOptions GetRigidOverlayOptions OEDocking::OEShapeFitOptions OEShape::OEFlexiOverlayOptions GetRingCount OEBioisostere::OEBroodHit GetRingFragLimit OEMedChem::OEMCSFragDatabaseOptions GetRingOnly OEBioisostere::OEBroodScoreOptions GetRingOptions OEConfGen::OEFragBuilderOptions GetRingRatio OEBioisostere::OEBroodHit GetRMS OEConfGen::OEFragOptions GetRMSD OEDepict::OEAlignmentResult OESpruce::OEStructuralSuperposition OESpruce::OESuperposeResults OESz::OESzybkiResults GetRMSDCutoff OEDepict::OEAlignmentOptions GetRMSRange OEConfGen::OESliceEnsembleOptions GetRMSThreshold OEConfGen::OESliceEnsembleOptions GetROCSOptions OEShape::OEROCS GetROCSQueryModelOptions OEModels::OEROCSQueryModelBuilder 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 OESpruce::OESuperposeResults GetRotorCount OEBioisostere::OEBroodHit OEBioisostere::OEIntrinsicPropOptions GetRotorOffset OEConfGen::OETorDriveOptions GetRotorPredicate OEConfGen::OETorDriveOptions GetRow OEChem::OEMolDatabase GetRunType OESz::OESzybkiOptions GetRxnRole OEChem::OEAtomBase GetSaltConcentration OEEon::OEEonPBOptions OEPB::OEET OEPB::OEZap OESz::OESzybkiSolventOptions GetSampleHydrogens OEConfGen::OEMolBuilderOptions GetSaveRange OEChem::OECliqueSearch GetSaveStereo OEProton::OETautomerOptions GetScale OEDepict::OE2DMolDisplay OEDepict::OE2DMolDisplayOptions OEGrapheme::OEPlotMarker GetScaleFactor OESiteHopper::OESiteHopperPatchOptions GetScannedAngles OESz::OETorsionScanner GetSCFTolerance OEMolAM1::OEAM1Options GetScore OEBio::OEPlaceHydrogensMoverNote OEBio::OESequenceAlignment OEDocking::OEShapeFitResults OEFastROCS::OEShapeDatabaseScore OEGraphSim::OESimScore OEGraphSim::OESimScorePair OEMedChem::OEMCSMolSimScore OESpruce::OEStructuralSuperposition GetScoreCutoff OESiteHopper::OESiteHopperSearchOptions GetScoreMethod OEDocking::OEDockOptions GetScores OEEon::OEEonOverlayResults OEFastROCS::OEShapeDatabase OEGraphSim::OEFastFPDatabase OEGraphSim::OEFPDatabase OEMedChem::OEMCSFragDatabase OEShape::OEBestOverlayResults GetScoreType OEBioisostere::OEBroodGeneralOptions 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 GetSecDuplicateCount OEBioisostere::OEHitlistBuilder GetSecondaryStructure OEChem::OEResidue GetSeed OESystem::OERandom GetSelfColor OEShape::OEColorOverlap GetSelfOverlap OEShape::OEHermite GetSemiMethod OEMolAM1::OEAM1Options GetSeparateResidues OEBio::OESplitMolComplexOptions GetSeqAlignExtendPenalty OESpruce::OELoopBuilderOptions GetSeqAlignGapPenalty OESpruce::OELoopBuilderOptions GetSeqAlignMethod OESpruce::OELoopBuilderOptions GetSeqScore OESpruce::OESuperposeResults GetSequence OESpruce::OESequenceMetadata GetSequenceCutoff OESiteHopper::OESiteHopperSearchOptions GetSequenceID OEChem::OEResidue GetSequenceIdentity OEBio::OESequenceAlignment GetSequenceInfo OESiteHopper::OESiteHopperDatabase GetSequenceMetadata OESpruce::OEStructureMetadata GetSequenceSimilarity OEBio::OESequenceAlignment OESiteHopper::OESiteHopperResults GetSerialNumber OEChem::OEResidue GetSetting OEChem::OEMolParameter OEChem::OEPredicateParameter OESystem::OEMultiParameter OESystem::OETypedParameter GetSettings OESystem::OETypedParameter GetSettingsVector OESystem::OEPODParameter GetShapeCutoff OEBioisostere::OEBroodScoreOptions GetShapeFunc OEShape::OEOverlapFunc GetShapeFuncType OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions GetShapeGaussians OEShape::OEShapeQueryBase GetShapeGrid OEShape::OEShapeQueryBase GetShapeGridSpacing OEFastROCS::OEShapeDatabase GetShapeOptions OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions OEShape::OEShapeFunc GetShapeScore OEBioisostere::OEBroodHit OEBioisostere::OEBroodScore OEFastROCS::OEShapeDatabaseScore GetShapeScoreScale OEFastROCS::OEShapeDatabaseOptions GetShapeTanimoto OEFastROCS::OEShapeDatabaseScore OESiteHopper::OESiteHopperResults GetShapeTversky OEFastROCS::OEShapeDatabaseScore GetSheffieldParameters OESz::OESzybki GetSidechainBuilderOptions OESpruce::OEDesignUnitBuildOptions GetSimFunc OEFastROCS::OEShapeDatabaseOptions OEFastROCS::OEShapeDatabaseScore OEGraphSim::OEFPDatabaseOptions GetSimTypeString OEGraphSim::OESimFuncBase OEGraphSim::OETanimotoSim OEGraphSim::OETverskySim GetSinglePointConfs OESz::OETorsionScanner GetSinglePoseResults OEDocking::OEPositResults GetSingleSourceMol OEBioisostere::OEFragmentOptions GetSiteResidues OEBio::OEDesignUnit OESpruce::OESuperpositionOptions GetSiteSize OESiteHopper::OESiteHopperPatchOptions 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 OEBioisostere::OEFragmentOptions OEDocking::OEFeature OEGraphSim::OEFPPattern GetSmiles OESpruce::OEHeterogenMetadata GetSoluteDielectric OESz::OESzybkiGeneralOptions GetSoluteDielectricConstant OESheff::OESheffieldOptions GetSolvationEntropy OESz::OEEntropyResults GetSolvationFreeEnergy OESz::OEFreeFormSolvResults GetSolvationType OESz::OETorsionScanOptions GetSolvEnergy OESz::OESingleConfResult GetSolvent OEBio::OEDesignUnit GetSolventDielectric OESz::OESzybkiSolventOptions GetSolventDielectricConstant OESheff::OESheffieldOptions GetSolventModel OESz::OEProteinLigandOptOptions OESz::OESzybkiSolventOptions GetSolventOptions OESz::OEFreeFormConfOptions OESz::OESzybkiOptions GetSortByBitCounts OEChem::OECreateSubSearchDatabaseOptions GetSortedScores OEFastROCS::OEShapeDatabase OEGraphSim::OEFastFPDatabase OEGraphSim::OEFPDatabase OEGraphSim::OESimSearchResult OEMedChem::OEMCSFragDatabase GetSourceMol OEBio::OEAltLocationFactory GetSourceMolLabel OEBioisostere::OEBroodHit GetSourceMolSmiles OEBioisostere::OEBroodHit GetSp3CFrac OEBioisostere::OEIntrinsicPropOptions GetSpaceGroup OEBio::OECrystalSymmetryParams OESystem::OESkewGrid GetSpacing OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid GetSparseMatrix OEGraphSim::OEFastFPDatabase GetSpecifiedAngle OEConstr::OEDihedralQuadPenalty 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 GetStartPoints OEShape::OECartesianStarts GetStartResidueInsertCode OESpruce::OESequenceMetadata GetStartResidueNumber OESpruce::OESequenceMetadata GetStarts OEShape::OEOverlayOptions OEShape::OEStarts GetState OEBio::OEAltLocationFactory GetStateIdx OEBio::OEPlaceHydrogensMoverNote GetStateName OEBio::OEPlaceHydrogensMoverNote GetStatus OEBioisostere::OEBroodScore GetStereo OEChem::OEAtomBase OEChem::OEBondBase OEChem::OEInChIOptions GetStickWidthScale OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByStick OEDepict::OEHighlightOverlayByBallAndStick GetStippleFactor OEDepict::OEPen GetStops OESystem::OEColorGradientBase GetStrainCount OEBioisostere::OEHitlistBuilder GetStretchBendParams OEMolPotential::OEFFParams GetStretchParams OEMolPotential::OEFFParams GetStrict OEChem::OEParseSmilesOptions OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase GetStrictAtomTypes OEConfGen::OEMolBuilderOptions GetStrictMapping OEChem::OERxnAutomapperOptions GetStrictMode OESpruce::OESidechainBuilderOptions GetStrictProlineMatch OESpruce::OELoopBuilderOptions GetStrictProtonationMode OESpruce::OEDesignUnitPrepOptions GetStrictSmirks OEChem::OEUniMolecularRxnOptions GetStrictStereo OEConfGen::OEOmegaOptions GetString OEChem::OE3DMolStyle 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 GetSurfaceAlpha OEChem::OE3DMolStyle GetSurfaceArcFxn OEGrapheme::OEShapeQueryDisplayOptions GetSurfaceArea OESpruce::OEPocket GetSurfaceColorer OEChem::OE3DMolStyle GetSurfaceCutoff OESiteHopper::OESiteHopperPatchOptions GetSurfaceStyle OEChem::OE3DMolStyle GetSurfaceType OEChem::OE3DMolStyle 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 OEEon::OEEonOverlapScore OEEon::OEEonOverlayScore OEEon::OEEonPBResults OEShape::OEColorResults OEShape::OEOverlapResults OESpruce::OESecondaryStructureSuperposition OESpruce::OESuperposeResults GetTanimotoCombo OEEon::OEEonOverlapScore OEEon::OEEonOverlayScore 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 OEDocking::OESinglePoseResult GetTargetPred OEBio::OEReceptor OEDocking::OEMakeReceptorOptions OEDocking::OESinglePoseResult GetTautomers OEBioisostere::OEBroodBuildOptions OESpruce::OEHeterogenMetadata GetTemperature OESz::OEFreeFormConfResults OESz::OESzybkiEnsembleResults OESz::OESzybkiGeneralOptions GetText OEDepict::OEHighlightLabel OESystem::OEColor GetTheta OEChem::OEEuler GetThompsonOptions OEConfGen::OETorDriveOptions 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 OESiteHopper::OESiteHopperDatabase OESiteHopper::OESiteHopperScore 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 OESz::OETorsionScanOptions GetTorDriveOptions OEConfGen::OEOmegaOptions OEConfGen::OETorDriver GetTorLib OEConfGen::OETorDriveOptions OEDocking::OEPositOptions OEDocking::OEShapeFitOptions 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 GetTotalEntropy in J/(mol K). OESz::OEEntropyResults GetTotalHCount OEChem::OEAtomBase GetTotalMols OEMedChem::OECreateMMPIndexStatus GetTotalRMSD OESz::OEProteinLigandOptResults GetTPSA OEBioisostere::OEBroodHit OEBioisostere::OEIntrinsicPropOptions GetTracer OEFastROCS::OEShapeDatabaseOptions GetTransform OEBio::OEDesignUnit OEChem::OEConfBase OEMedChem::OEMatchedPairTransform OESiteHopper::OESiteHopperScore OESpruce::OESuperposeResults GetTransforms OEChem::OETrans GetTransformThreshold OESpruce::OELoopBuilderOptions GetTranslation OEChem::OETranslation OEFastROCS::OEShapeDatabaseScore OEShape::OEBestOverlayScore OESpruce::OESecondaryStructureSuperposition OESpruce::OEStructuralSuperposition OESpruce::OESuperposeResults GetTranslationalEntropy OESz::OEEntropyResults GetTrialsRangeIncrement OEConfGen::OEThompsonOptions 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 GetUndefinedStereo OEChem::OEInChIOptions GetUnhashed OEGraphSim::OEFPPattern GetUnindexedMols OEMedChem::OECreateMMPIndexStatus GetUnitCell OESystem::OESkewGrid GetUnsaturatedHeteroBonds OEMedChem::OEBemisMurckoOptions GetUnstableCount OEBioisostere::OEHitlistBuilder GetUseBondOrder OEBioisostere::OEBroodScoreOptions GetUseConstraints OESpruce::OESuperposeOptions GetUseCoulomb OEMolPotential::OENonBondIntcsOptions GetUseGPU OEConfGen::OETorDriveOptions OESiteHopper::OESiteHopperSearchOptions GetUseHydrogens OEPB::OEArea OEShape::OEBestOverlay OEShape::OEOverlap OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions GetUseInput3D OESz::OEFreeFormSolvOptions GetUseInputEnsemble OESz::OEFreeFormConfOptions OESz::OEFreeFormSolvOptions GetUseInternalCoord OESz::OETorsionScanOptions GetUseMaxHits OEShape::OEROCSOptions GetUseMMFF94s OEFF::OEMMFFIEFFOptions GetUseOptimalLambdas OEShape::OEHermiteOptions GetUsePackingResidues OESpruce::OELoopBuilderOptions GetUseProperty OEBioisostere::OEBroodScoreOptions GetUseProxyGrid OEShape::OEAnalyticOptions GetUserDefinedAngles OESz::OETorsionScanOptions GetUserStarts OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay GetUserStartsScaleFactor OESiteHopper::OESiteHopperPatchOptions GetUseSinglePointPB OESz::OETorsionScanOptions GetUseSolventCorr OESz::OEFreeFormConfOptions GetUseThompson OEConfGen::OETorDriveOptions GetUseVdW OEMolPotential::OENonBondIntcsOptions GetValence OEChem::OEAtomBase GetValenceCorrection OEChem::OELibraryGen GetValidateKekule OEChem::OELibraryGen OEChem::OEUniMolecularRxn OEChem::OEUniMolecularRxnOptions GetValidRMSD OESpruce::OESuperposeOptions GetValidSeqScore OESpruce::OESuperposeOptions GetValidTanimoto OESpruce::OESuperposeOptions GetValue OEChem::OEMolParameter OEChem::OEPredicateParameter OEChem::OESDDataPair OEGrapheme::OEColorGradientLabel OEMolProp::OEXLogPResult OEPlatform::OEHalfFloat OEPlatform::OEOnce OESystem::OEColorStop OESystem::OEMultiParameter OESystem::OETypedParameter GetValues OEChem::OEMolStyleColorer OEMolPotential::OEInteraction OESystem::OEFixedGrid OESystem::OEFixedMultiGrid OESystem::OESkewGrid OESystem::OETypedParameter GetValuesVector OESystem::OEPODParameter GetVar OEFF::OEComplexFF OEMolPotential::OEInterMolFunc1 OEOpt::OEAdaptor GetVariogram OEGraphSim::OEFastFPDatabase OEGraphSim::OEFPVariogram GetVdwParams OEMolPotential::OEFFParams GetVdwRadius OEMolPotential::OEFFParams GetVeber OEBioisostere::OEBroodHit OEBioisostere::OEMolPropertyOptions 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 GetVibrationalRotationalEntropy OESz::OEEntropyResults GetVisibility OESystem::OEParameter GetVolume OEMath::OEBox OEMath::OESphere GetWarnings OESz::OEFreeFormSolvResults GetWarnNoLigand OEBio::OESplitMolComplexOptions GetWarts OEConfGen::OEFlipperClassicOptions 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 GetXLogP OEBioisostere::OEBroodHit 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 HasAdjTypeAtNeutralpH OEProton::OEMultistatepKaModel HasAlphaBetaUnsat OEChem::OEAtomBase HasAltLoc OEBio::OEDesignUnit HasAtom OEBio::OEInteractionHintFragment OEChem::OEAtomBondSet OEChem::OEGroupBase HasAtomColorer OEChem::OE3DMolStyle HasAtomLabelColorer OEChem::OE3DMolStyle HasAtomLabelDataTag OEChem::OE3DMolStyle HasAtomLabelText OEChem::OE3DMolStyle HasAtomLabelType OEChem::OE3DMolStyle HasAtomStyle OEChem::OE3DMolStyle 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 HasConstraintMol OESpruce::OESuperpose HasContourStyle OEChem::OE3DMolStyle HasCoulomb OEMolPotential::OEForceField 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 HasGridContourColorer OEChem::OE3DMolStyle HasGridType OEChem::OE3DMolStyle HasHeader OEDepict::OEImageTableOptions HasHydrogenVisibility OEChem::OE3DMolStyle HasHyperlink OEDepict::OEFont HasIndexableFragmentHeavyAtomRange OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions HasInnerContourLevel OEBio::OEReceptor HasInteraction OEBio::OEInteractionHintContainer HasInteractionStyle OEChem::OE3DMolStyle HasInternalCharges OEMolPotential::OEForceField 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 HasPDBMetaData OEBio::OEDesignUnit HasPerceived OEChem::OEMolBase HaspKaRange OEProton::OEMultistatepKaModel HasProperties OEChem::OEMolPropertyList HasProperty OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay HasProtectiveGroupStyle OEDepict::OE2DMolDisplayOptions HasProtein OEBio::OEDesignUnit OEBioisostere::OEBroodQuery HasProteinColorer OEChem::OE3DMolStyle HasProteinConstraints OEBio::OEReceptor HasProteinStyle OEChem::OE3DMolStyle HasReceptor OEBio::OEDesignUnit HasRef OESpruce::OESuperpose HasRMSD OESpruce::OESuperposeResults HasRole OESystem::OERoleSet HasSDData OEMedChem::OEMatchedPair HasSeqScore OESpruce::OESuperposeResults 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 HasSurfaceAlpha OEChem::OE3DMolStyle HasSurfaceColorer OEChem::OE3DMolStyle HasSurfaceStyle OEChem::OE3DMolStyle HasSurfaceType OEChem::OE3DMolStyle HasTanimoto OESpruce::OESuperposeResults 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 in-memory InChI InChIKey IncrementCount OESystem::OEErrorHandlerImplBase IncrementReadFailureCt OEChem::oemolistream inertialatheavyatomstartsexample.java Example Code, [1] Info OESystem::OEErrorHandler Init OEBioisostere::OEBroodQuery OEBioisostere::OEDBReader OEBioisostere::OEDBWriter OEBioisostere::OEFragConfReader OEChem::OECliqueSearch OEChem::OELibraryGen OEChem::OELingoSim OEChem::OEMCSSearch OEChem::OESubSearch OEChem::OEUniMolecularRxn OEProton::OEMultistatepKaModel OEShape::OEColorForceField Initialize OEDocking::OEDock OEDocking::OEPosit OEDocking::OEScore installation integer atom type integer bond type Invert OEMedChem::OEMatchedPairTransform Iridium is_cacheable OEDataFlow::OEFieldTypeHandler 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::OEMatchedPairAnalyzer OEMedChem::OEMCSFragDatabase

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 isPOD OEDataFlow::OEFieldTypeHandler 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::OEHalogenBondInteractionHint OEBio::OEHBondInteractionHint OEBio::OEInteractionHint OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintContainer OEBio::OEInteractionHintTypeBase OEBio::OELigandInteractionHintComponent OEBio::OEPlaceHydrogensDetails OEBio::OEProteinInteractionHintComponent OEBio::OEReceptor OEBio::OESaltBridgeInteractionHint OEBio::OEStackingInteractionHint OEBioisostere::OEBroodDBPacket OEChem::OE3DMolStyle OEChem::OEConfRMSD OEChem::OECSVHeader OEChem::OELingoSim OEChem::OEMatchBase OEChem::OESubSearchDatabase OEChem::OESubSearchResult OEChem::OESubSearchScreen OEDepict::OE2DMolDisplay OEDepict::OE2DPath OEDepict::OEAlignmentResult OEDepict::OENearestAtom OEDepict::OENearestBond OEGrapheme::OE2DActiveSiteDisplay OEGrapheme::OENearestResidue OEGrapheme::OEShapeOverlapDisplay OEGrapheme::OEShapeQueryDisplay OEGraphSim::OEFastFPDatabase OEGraphSim::OEFastFPDatabaseParams OEGraphSim::OEFPTypeParams OEGraphSim::OESimSearchResult OEMolPotential::OEBendParams OEMolPotential::OEOutOfPlaneParams OEMolPotential::OEStretchParams OEMolPotential::OETorsionParams OEMolPotential::OEVdwParams OEProton::OEChargeEngineBase OEProton::OEDesignUnitCharges OESpruce::OESuperposeResults 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

JSON

K

Kekule form

Kekule SMILES kekulization

L

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

LINGO Linux Load OEBioisostere::OEBroodDBPacket OEBioisostere::OEBroodScore OEEon::OEEonHit OEFF::OEFF14SBSmirnoffParams OEMolSmirnoff::OESmirnoffParams OESystem::OEParameter LoadDefault OESystem::OEParameter LoadPotentialGrid OESz::OESzybki LoadValue OESystem::OEParameter

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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, [1] 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 MaxLocalStrain OEDocking::OEShapeFitOptions 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 memory-mapped MethodChoice OEDocking::OEPosit MinimizeRMSD OEChem::OEConfRMSD minpath.java Example Code MMCIF metadata ModifyOptions OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMatchedPairAnalyzerOptions module modules MOL 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 constructors OEBio::OEDesignUnit 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 Monte Carlo 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 nonterminal 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::OEFastFPDatabase OEGraphSim::OEFastFPDatabaseParams OEGraphSim::OEFPDatabase

NumFragments OEBio::OEInteractionHintContainer OEMedChem::OEMCSFragDatabase NumFrags OEBioisostere::OEDBBuilder 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 OEBioisostere::OEFragConfReader OEChem::OEMolDatabase OEMedChem::OEMatchedPairAnalyzer OEMedChem::OEMCSFragDatabase 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 OEB OEBio::OEAltGroup Constructors GetGroupCount GetGroupID GetLocationCount GetLocations operator bool operator= SetGroupID OEBio::OEAltLocation Constructors GetGroupID GetLocationCount GetLocationID operator bool operator= SetLocationID OEBio::OEAltLocationFactory Constructors GetAltAtoms GetAtomMapSize GetBondMapSize GetCurrentAtoms GetCurrentLocations GetGroup GetGroupCount GetGroups GetLocation GetLocationCodes GetSourceMol GetState MakeAltMol MakeCurrentAltMol MakePrimaryAltMol operator= SetAlt SetPrimaryAlt SetState OEBio::OEAltLocationState Constructors operator bool operator= ToHexString 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 ClearComponent ClearReceptor Constructors CreateCopy GetComponent GetComponentID GetComponents GetComponentsWithin GetComponentTag GetDataType GetIDs GetLigand GetMetal GetNucleicAcid GetPackingResidues GetPDBMetaData GetProtein GetReceptor GetSiteResidues GetSolvent GetStructureQuality GetTaggedComponents GetTags GetTarget GetTargetComponentID GetTargetComponentTag GetTitle GetTransform HasAltLoc HasComponent HasLigand HasMetal HasNucleicAcid HasPackingResidues HasPDBMetaData HasProtein HasReceptor HasSiteResidues HasSolvent HasStructureQuality HasTarget HasTitle HasTransform IsDataType Molecule constructors operator bool operator= SetTitle 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 operator= SetDetails SetWeight OEBio::OEInteractionHintComponentTypeBase Constructors CreateCopy GetName IsValid operator!= operator= operator== OEBio::OEInteractionHintContainer AddMolecule Constructors DeleteInteraction DeleteInteractions GetInteractions GetMolecule GetMolecules GetTitle HasInteraction IsValid NumFragments NumInteractions NumMolecules operator bool SetTitle 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 GetResolution GetRFree operator bool operator= SetAltConfs SetAsDensity SetCategory SetDPI SetExcipients SetHasMTZ SetIrrationalRFree SetLigandDensity SetPackingResidues SetPartOccupancyLigand SetPartOccupancyProtein SetPossibleCovalent SetResolution SetRFree 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::OEIsStandardAminoAcid Constructors CreateCopy operator() OEBio::OEIsStandardNucleicAcid 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 operator= SetMaxHeavyAtom OEBio::OEMakeAltMolOption OEBio::OEMakeAltMolOption::None OEBio::OEMakeAltMolOption::RemoveAltCodes OEBio::OEMolComplexCategorizer AddLigandName ClearLigandSubSearch Constructors CreateCopy GetBundleCofactors GetLigandSubSearch GetMaxLigAtoms GetMaxLigResidues GetMaxPeptideResidues GetMaxProteinAtoms GetMinLigAtoms GetResidueCategoryData operator() operator= SetBundleCofactors SetLigandSubSearch SetMaxLigAtoms SetMaxLigResidues SetMaxPeptideResidues SetMaxProteinAtoms SetMinLigAtoms SetResidueCategoryData UsingExplicitLigandName OEBio::OEMolComplexCategorizerBase CreateCopy GetBundleCofactors GetResidueCategoryData operator() UsingExplicitLigandName 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 GetMaxHalogenAngle GetMaxHalogenBondDistance GetMaxHBondDistance GetMaxMetalBondDistance GetMaxNonIdealAcceptorAngle GetMaxNonIdealDonorAngle GetMaxNonIdealHBondDistance GetMaxPiStackAngle GetMaxPiStackDistance GetMaxSaltBridgeDistance GetMaxTStackAngle GetMaxTStackDistance GetMaxUnpairedAngle GetMaxUnpairedDistance GetMinContactFraction GetMinCovalentFraction GetMinHBondContactFraction SetMaxAcceptorAngle SetMaxCationPiAngle SetMaxCationPiDistance SetMaxChargeAidedHBondDistance SetMaxContactFraction SetMaxCovalentFraction SetMaxDonorAngle SetMaxHalogenAngle SetMaxHalogenBondDistance SetMaxHBondDistance 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 operator= SetAddMetadata SetAltsMustBeCompatible SetBadClashOverlapDistance SetBypassPredicate SetFlipBiasScale SetFlipPredicate SetMaxSubstateCutoff SetNoFlipPredicate SetStandardizeBondLen SetWaterProcessing 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 GetInnerContourVolume GetNegativeImageGrid GetOuterContourLevel GetOuterContourVolume GetProteinConstraints GetTargetMask GetTargetPred HasCustomConstraints HasInnerContourLevel HasNegativeImageGrid HasOuterContourLevel HasProteinConstraints IsValid NumProteinConstraints operator= SetCustomConstraints SetInnerContourLevel SetOuterContourLevel OEBio::OEReceptorConstraintFeature AddNewSphere AddSmarts ClearSmarts ClearSpheres Constructor CreateCopy DeleteSmarts DeleteSphere GetEnabled GetFeatureName GetFeatureSpheres GetSmarts NumSmarts NumSpheres operator= SetEnabled SetFeatureName OEBio::OEReceptorCustomConstraints AddNewFeature Clear Constructors DeleteFeature GetConstraintFeatures NumFeatures operator= OEBio::OEReceptorProteinConstraint GetAtom GetEnabled GetName GetType SetAtom SetEnabled SetName SetType OEBio::OEResidueCategoryData AddToDB AllInDB ClearDBCategory Constructors FoundInDB GetEntries operator= RemoveFromDB Size 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 operator!= operator= operator== ResetFilters SetAddRGroup SetAdjustHCount SetAssumptions SetCategorizer SetCollectProteinByChain SetLigandFilter SetMaxBindingSiteDist SetMaxSurfaceWaterDist SetPromoteUnknowns SetProteinFilter SetSeparateResidues SetSplitCovalent SetSplitCovalentCofactors SetWarnNoLigand SetWaterFilter 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 operator bool operator= SetIridiumData OEBio::OESubsetDesignUnit OEBio::OESwapAIEResidueAtoms OEBio::OESymmetryCartesianToFractional OEBio::OESymmetryFractionalToCartesian OEBio::OETransformDesignUnit OEBio::OEUpdateDesignUnit OEBio::OEWriteAlignment OEBio::OEWriteDesignUnit OEBioisostere::OEBioisostereGetArch OEBioisostere::OEBioisostereGetLicensee OEBioisostere::OEBioisostereGetPlatform OEBioisostere::OEBioisostereGetRelease OEBioisostere::OEBioisostereGetSite OEBioisostere::OEBioisostereGetVersion OEBioisostere::OEBioisostereIsLicensed OEBioisostere::OEBroodBuildOptions Constructors GetBuildType GetCheckBond GetMaxLocalStrain GetNeutralPH GetTautomers operator= SetBuildType SetCheckBond SetMaxLocalStrain SetNeutralPH SetTautomers OEBioisostere::OEBroodBuildType OEBioisostere::OEBroodBuildType::NoOpt3D OEBioisostere::OEBroodBuildType::Optimize3D OEBioisostere::OEBroodBuildType::TwoD OEBioisostere::OEBroodDBFilter Constructors operator= Setup OEBioisostere::OEBroodDBPacket Constructors GetFragCount GetIdx IsValid Load operator= ToRecord OEBioisostere::OEBroodFragPrep Constructors Prep OEBioisostere::OEBroodGeneralOptions Constructors GetAttachScale GetBumpRadius GetScoreType operator= SetAttachScale SetBumpRadius SetScoreType OEBioisostere::OEBroodHit Constructors GetAbbottBioScore GetAromaticRingCount GetAttachScore GetBeliefScore GetColorScore GetComboScore GetComplexity GetEgan GetETAttachScore GetETComboScore GetETPBScore GetETShapeScore GetFragSmiles GetFrequency Getfsp3C GetHeavyCount GetIdeaGroup GetIdeaRank GetLipinskiAcc GetLipinskiDon GetLipinskiFail GetLocalStrain GetMol GetMolTanimotoCombo GetMolWt GetRingCount GetRingRatio GetRotorCount GetShapeScore GetSourceMolLabel GetSourceMolSmiles GetTPSA GetVeber GetXLogP operator= OEBioisostere::OEBroodHitlistOptions Constructors GetBuildOptions GetGenerateIdea GetMaxHits operator= SetBuildOptions SetGenerateIdea SetMaxHits OEBioisostere::OEBroodMolBuilder Build Constructors OEBioisostere::OEBroodOverlay Constructors Overlay SetupRef OEBioisostere::OEBroodOverlayBase Overlay Transform OEBioisostere::OEBroodQuery Constructors GetAttachCount GetHeavyCount HasProtein Init operator= OEBioisostere::OEBroodScore Constructors GetAttachCount GetAttachScore GetColorScore GetComboScore GetEnergy GetETAttachScore GetETComboScore GetETPBScore GetETShapeScore GetFrag GetFragMol GetShapeScore GetStatus Load operator= ToRecord OEBioisostere::OEBroodScoreOptions Constructors GetAttachCutoff GetCheckGeometry GetPropertyOptions GetRingOnly GetShapeCutoff GetUseBondOrder GetUseProperty operator= SetAttachCutoff SetCheckGeometry SetPropertyOptions SetRingOnly SetShapeCutoff SetUseBondOrder SetUseProperty OEBioisostere::OEBroodScoreType OEBioisostere::OEBroodScoreType::ET OEBioisostere::OEBroodScoreType::LinkOnly OEBioisostere::OEBroodScoreType::ROCS OEBioisostere::OEBroodStatusCode OEBioisostere::OEBroodStatusCode::BondOrderMismatch OEBioisostere::OEBroodStatusCode::ExcessStrain OEBioisostere::OEBroodStatusCode::Failed OEBioisostere::OEBroodStatusCode::Failed2DConstr OEBioisostere::OEBroodStatusCode::FailedAttachCut OEBioisostere::OEBroodStatusCode::FailedConstraints OEBioisostere::OEBroodStatusCode::FailedETAttach OEBioisostere::OEBroodStatusCode::FailedInit OEBioisostere::OEBroodStatusCode::FailedPropFilter OEBioisostere::OEBroodStatusCode::FailedProteinSelect OEBioisostere::OEBroodStatusCode::FailedQueryInit OEBioisostere::OEBroodStatusCode::FailedQueryMolRead OEBioisostere::OEBroodStatusCode::FailedRMSCut OEBioisostere::OEBroodStatusCode::FailedShapeCut OEBioisostere::OEBroodStatusCode::HasRingAtoms OEBioisostere::OEBroodStatusCode::InsuffRingAtoms OEBioisostere::OEBroodStatusCode::InvalidOptions OEBioisostere::OEBroodStatusCode::InvalidQuery3D OEBioisostere::OEBroodStatusCode::InvalidQueryAttach OEBioisostere::OEBroodStatusCode::InvalidQueryMol OEBioisostere::OEBroodStatusCode::InvalidQueryNoHeavyAtoms OEBioisostere::OEBroodStatusCode::InvalidQueryProtein OEBioisostere::OEBroodStatusCode::InvalidQueryRing OEBioisostere::OEBroodStatusCode::InvalidQuerySel OEBioisostere::OEBroodStatusCode::InvalidQuerySelProt OEBioisostere::OEBroodStatusCode::InvalidScore OEBioisostere::OEBroodStatusCode::MissingQueryFrag OEBioisostere::OEBroodStatusCode::NoAttachPt OEBioisostere::OEBroodStatusCode::NoConformers OEBioisostere::OEBroodStatusCode::NoRingAtoms OEBioisostere::OEBroodStatusCode::NoSelectionClash OEBioisostere::OEBroodStatusCode::ProteinBump OEBioisostere::OEBroodStatusCode::ReceptorClash OEBioisostere::OEBroodStatusCode::SelectFail OEBioisostere::OEBroodStatusCode::Success OEBioisostere::OEBroodStatusCode::UnequalAttachPt OEBioisostere::OEBroodStatusCode::UnstableBonds OEBioisostere::OECreateBroodQuery OEBioisostere::OEDBBuffer Add Constructors Finalize GetPackets OEBioisostere::OEDBBuilder Add AddCSV Constructors Expand Filter Generate GetFrag GetFrags GetFragSmiles GetFragSmilesCSV NumFrags Screen OEBioisostere::OEDBReader Constructors GetFragCount GetIndices GetNextPacket Init OEBioisostere::OEDBScreenOptions Constructors GetMinFreqHeavy GetMinFrequency operator= SetMinFreqHeavy SetMinFrequency OEBioisostere::OEDBWriter Constructors Finish Init Write OEBioisostere::OEExtrinsicPropOptions Constructors GetComplexity GetFrequency GetLipinski GetLipinskiAcc GetLipinskiDon GetLogP GetMartin operator= SetComplexity SetFrequency SetLipinski SetLipinskiAcc SetLipinskiDon SetLogP SetMartin OEBioisostere::OEFragConfReader Constructors Init NumMols ReadConformers OEBioisostere::OEFragmentOptions Constructors GetMaxChiral GetMaxDegree GetMaxHeavy GetMaxMolWt GetMinDegree GetMinHeavy GetSingleSourceMol GetSmarts operator= SetMaxChiral SetMaxDegree SetMaxHeavy SetMaxMolWt SetMinDegree SetMinHeavy SetSingleSourceMol SetSmarts SetSmartsFile OEBioisostere::OEFragOverlay Constructors GetRefFrag SetupRef OEBioisostere::OEGenerateConformers OEBioisostere::OEGetBroodStatus OEBioisostere::OEGetDBIndices OEBioisostere::OEHitlistBuilder AddScores Build Constructors GetAddCount GetBumpCount GetDeleteCount GetDuplicateCount GetHitCount GetHits GetInitHitCount GetMatchCount GetSecDuplicateCount GetStrainCount GetUnstableCount OEBioisostere::OEIntrinsicPropOptions Constructors GetAromaticJCT GetHeavyAtomCount GetMolWt GetRotorCount GetSp3CFrac GetTPSA operator= SetAromaticJCT SetHeavyAtomCount SetMolWt SetRotorCount SetSp3CFrac SetTPSA OEBioisostere::OEMolPropertyOptions Constructors GetEganEgg GetExtrinsicMaxOptions GetExtrinsicMinOptions GetIntrinsicMaxOptions GetIntrinsicMinOptions GetVeber operator= SetEganEgg SetExtrinsicMaxOptions SetExtrinsicMinOptions SetIntrinsicMaxOptions SetIntrinsicMinOptions SetVeber OEBioisostere::OEReadBroodQuery OEBioisostere::OEWriteBroodQuery OEBondBase OEBondIdxSelected OEBuildMDLQueryExpression OEBuildMDLQueryExpressions OEChem::OE2DRingDictionary AddRings Constructors NumRings OEChem::OE2DRingDictionaryCreatorOptions Constructors GetAddCarbonSkeleton GetAddCarbonSkeletonWithBondStereo GetRetainExistingBuiltInTemplates GetRetainExistingTemplates operator= SetAddCarbonSkeleton SetAddCarbonSkeletonWithBondStereo SetRetainExistingBuiltInTemplates SetRetainExistingTemplates OEChem::OE3DMolStyle ClearAtomColorer ClearAtomLabelColorer ClearAtomLabelDataTag ClearAtomLabelText ClearAtomLabelType ClearAtomStyle ClearContourStyle ClearGridContourColorer ClearGridType ClearHydrogenVisibility ClearInteractionStyle ClearProteinColorer ClearProteinStyle ClearSurfaceAlpha ClearSurfaceColorer ClearSurfaceStyle ClearSurfaceType Constructors FromString GetAtomColorer GetAtomLabelColorer GetAtomLabelDataTag GetAtomLabelPrecision GetAtomLabelText GetAtomLabelType GetAtomStyle GetContourStyle GetGridContourColorer GetGridType GetHydrogenVisibility GetInteractionStyle GetProteinColorer GetProteinStyle GetString GetSurfaceAlpha GetSurfaceColorer GetSurfaceStyle GetSurfaceType HasAtomColorer HasAtomLabelColorer HasAtomLabelDataTag HasAtomLabelText HasAtomLabelType HasAtomStyle HasContourStyle HasGridContourColorer HasGridType HasHydrogenVisibility HasInteractionStyle HasProteinColorer HasProteinStyle HasSurfaceAlpha HasSurfaceColorer HasSurfaceStyle HasSurfaceType IsValid operator< operator= operator== SetAtomColorer SetAtomLabelColorer SetAtomLabelDataTag SetAtomLabelText SetAtomLabelType SetAtomStyle SetContourStyle SetGridContourColorer SetGridType SetHydrogenVisibility SetInteractionStyle SetProteinColorer SetProteinStyle SetSurfaceAlpha SetSurfaceColorer SetSurfaceStyle SetSurfaceType OEChem::OE3DToAtomStereo OEChem::OE3DToBondStereo OEChem::OE3DToInternalStereo OEChem::OEAbsCanonicalConfTest CombineMols CompareMols CreateCopy OEChem::OEAbsoluteConfTest CombineMols CompareMols Constructors CreateCopy OEChem::OEAcyclicPath OEChem::OEAddCustomFASTAResidue OEChem::OEAddExplicitHydrogens OEChem::OEAddMMCIFData OEChem::OEAddMols OEChem::OEAddMolStyles OEChem::OEAddPDBData OEChem::OEAddSDData OEChem::OEAnisoUij Constructors GetU11 GetU12 GetU13 GetU22 GetU23 GetU33 SetU11 SetU12 SetU13 SetU22 SetU23 SetU33 OEChem::OEApplyStateFromRef OEChem::OEApplyStyleChange 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 operator= OrderBonds RemoveBond SetAromatic SetAtomicNum SetAxial SetChiral SetFormalCharge SetHyb SetImplicitHCount SetInRing SetIntType SetIsotope SetMapIdx SetName SetPartialCharge SetRadius SetRxnRole SetStereo SetSymmetryClass SetType Sweep OEChem::OEAtomBondSet Add AddAtom AddAtoms AddBond AddBonds Clear ClearAtoms ClearAtomsAndBonds ClearBonds Constructors CreateCopy GetAtoms GetBonds GetParent HasAtom HasBond IsEmpty NumAtoms NumBonds operator= Remove RemoveAtom RemoveAtoms RemoveBond RemoveBonds Sweep Translate OEChem::OEAtomColorScheme OEChem::OEAtomColorScheme::AltLocation OEChem::OEAtomColorScheme::Amino OEChem::OEAtomColorScheme::BEGIN OEChem::OEAtomColorScheme::BFactor OEChem::OEAtomColorScheme::Chain OEChem::OEAtomColorScheme::Element OEChem::OEAtomColorScheme::END OEChem::OEAtomColorScheme::FormalCharge OEChem::OEAtomColorScheme::GenericData OEChem::OEAtomColorScheme::Occupancy OEChem::OEAtomColorScheme::PartialCharge OEChem::OEAtomColorScheme::ProteinSequence OEChem::OEAtomColorScheme::Residue OEChem::OEAtomColorScheme::ResidueHydrophobicity OEChem::OEAtomColorScheme::SecondaryStructure OEChem::OEAtomColorScheme::Shapely OEChem::OEAtomColorScheme::Solid 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::OEAtomLabelScheme OEChem::OEAtomLabelScheme::AltLocation OEChem::OEAtomLabelScheme::BEGIN OEChem::OEAtomLabelScheme::BFactor OEChem::OEAtomLabelScheme::Chirality OEChem::OEAtomLabelScheme::Degree OEChem::OEAtomLabelScheme::Element OEChem::OEAtomLabelScheme::END OEChem::OEAtomLabelScheme::FormalCharge OEChem::OEAtomLabelScheme::GenericData OEChem::OEAtomLabelScheme::HasStereoSpecified OEChem::OEAtomLabelScheme::Hybridization OEChem::OEAtomLabelScheme::ImplicitHCount OEChem::OEAtomLabelScheme::Index OEChem::OEAtomLabelScheme::IntegerType OEChem::OEAtomLabelScheme::IsChiral OEChem::OEAtomLabelScheme::IsInRing OEChem::OEAtomLabelScheme::Isotope OEChem::OEAtomLabelScheme::MapIdx OEChem::OEAtomLabelScheme::MMFFType OEChem::OEAtomLabelScheme::Occupancy OEChem::OEAtomLabelScheme::OEChemIdx OEChem::OEAtomLabelScheme::Off OEChem::OEAtomLabelScheme::PartialCharge OEChem::OEAtomLabelScheme::Radius OEChem::OEAtomLabelScheme::ResidueInfo OEChem::OEAtomLabelScheme::ResidueInfoCA OEChem::OEAtomLabelScheme::Symmetry OEChem::OEAtomLabelScheme::Type OEChem::OEAtomLabelScheme::User 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::OEAtomStyle OEChem::OEAtomStyle::BallAndStick OEChem::OEAtomStyle::BEGIN OEChem::OEAtomStyle::CPK OEChem::OEAtomStyle::END OEChem::OEAtomStyle::Hidden OEChem::OEAtomStyle::Stars OEChem::OEAtomStyle::Stick OEChem::OEAtomStyle::Wireframe OEChem::OEBaseColorScheme OEChem::OEBaseColorScheme::BEGIN OEChem::OEBaseColorScheme::END OEChem::OEBaseColorScheme::GenericData OEChem::OEBaseColorScheme::Solid 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 operator= SetAromatic SetBgn SetChiral SetEnd SetInRing SetIntType SetOrder SetStereo SetType SwapEnds Sweep 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::OECalcPMI 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::OEClearMMCIFData OEChem::OEClearPartialCharges OEChem::OEClearPDBData OEChem::OEClearResidue OEChem::OEClearResidues OEChem::OEClearRotorCompressData OEChem::OEClearSDData OEChem::OEClearStyle OEChem::OECliqueSearch AddConstraint ClearConstraints Constructors GetMaxMatches GetMinAtoms GetPattern GetSaveRange Init Match operator bool operator= SetMaxMatches SetMCSFunc SetMinAtoms SetSaveRange OEChem::OEConfBase AddAtom AddBond ClearCoords Delete GetCoords GetCoordsPtr GetIdx GetMCMol GetTitle GetTorsion GetTransform HasTitle IsDeleted operator= RemoveAtom RemoveBond SetCoords SetTorsion Transform OEChem::OEConfRMSD CalculateRMSD Constructors GetOptions IsValid MinimizeRMSD NumAutomorphs OEChem::OEConfRMSDOptions Constructors GetIgnoreHydrogens GetIgnoreTerminalHeavy GetMaxMatches operator= SetIgnoreHydrogens SetIgnoreTerminalHeavy SetMaxMatches OEChem::OEConfTestBase CombineMols CompareMols CreateCopy HasCompareMols OEChem::OEConstCoords Constructors GetPtr operator const T * OEChem::OEContourStyle OEChem::OEContourStyle::BEGIN OEChem::OEContourStyle::Cloud OEChem::OEContourStyle::END OEChem::OEContourStyle::Hidden OEChem::OEContourStyle::Mesh OEChem::OEContourStyle::Solid 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::OECopyMMCIFData OEChem::OECopyMol OEChem::OECopyPDBData OEChem::OECopySDData OEChem::OECorrectAcidProtonGeometry OEChem::OECount OEChem::OECreateAbsSmiString OEChem::OECreateAtomSmartsString OEChem::OECreateBondSmartsString OEChem::OECreateCanSmiString OEChem::OECreateCSVHeader OEChem::OECreateInChI OEChem::OECreateInChIKey OEChem::OECreateIsoSmiString OEChem::OECreateMolDatabaseIdx OEChem::OECreateSlnString OEChem::OECreateSmartsString 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::OECXSMILESToMol 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 operator= SetPhi SetPsi SetTheta 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::AtomParityChange OEChem::OEExprType::BondOrder OEChem::OEExprType::BondParityChange 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::FormalChargeChange OEChem::OEExprType::Halogen OEChem::OEExprType::HCount OEChem::OEExprType::HCountChange 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 operator= SetRetainBondStereo SetRetainExistingTemplates OEChem::OEExtractRingTemplates OEChem::OEFastaToMol OEChem::OEFileStringParameter Constructors operator= OEChem::OEFileStringType OEChem::OEFileStringType::BroodQMol OEChem::OEFileStringType::DU OEChem::OEFileStringType::Mol OEChem::OEFileStringType::Mol3D OEChem::OEFileStringType::MolReceptor OEChem::OEFileStringTypeFlavor OEChem::OEFileStringTypeFlavor::DEFAULT OEChem::OEFileStringTypeFlavor::Default OEChem::OEFileStringTypeFlavor::Dim2D OEChem::OEFileStringTypeFlavor::Dim2D3D OEChem::OEFileStringTypeFlavor::Dim3D OEChem::OEFileStringTypeFlavor::FileList OEChem::OEFileStringTypeFlavor::Input OEChem::OEFileStringTypeFlavor::InputDefault OEChem::OEFileStringTypeFlavor::MolOnly OEChem::OEFileStringTypeFlavor::NoListDefault OEChem::OEFileStringTypeFlavor::Output OEChem::OEFileStringTypeFlavor::OutputDefault OEChem::OEFileStringTypeFlavor::Pretty OEChem::OEFileStringTypeFlavor::RxnOnly OEChem::OEFindRingAtomsAndBonds OEChem::OEFormalPartialCharges OEChem::OEFormat OEChem::OEFormat::CAN OEChem::OEFormat::CDX OEChem::OEFormat::CIF OEChem::OEFormat::CSV OEChem::OEFormat::CXSMILES 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::OEGetAtomColor OEChem::OEGetAtomComment OEChem::OEGetAtomicNum OEChem::OEGetAtomicSymbol OEChem::OEGetAtomLabelColor OEChem::OEGetAtomLabelText OEChem::OEGetAutomorphs OEChem::OEGetAverageWeight OEChem::OEGetBondiVdWRadius OEChem::OEGetCenterAndExtents OEChem::OEGetCenterOfMass OEChem::OEGetColorSchemeName 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::OEGetMMCIFData 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::OEGetRadiusOfGyration 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::OEGetStyle OEChem::OEGetStyleChange OEChem::OEGetStyleIndex OEChem::OEGetSubSearchScreenType OEChem::OEGetSubtree OEChem::OEGetTokenizer OEChem::OEGetTorsion OEChem::OEGetTorsions OEChem::OEGetTripleBondNeighbor OEChem::OEGetUniMolecularRxnIter OEChem::OEGraphMol Constructors operator OEMolBase & operator= SCMol 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() OEChem::OEHasHvyDegree Constructors CreateCopy operator() OEChem::OEHasIdx Constructors CreateCopy operator() OEChem::OEHasImplicitHydrogenExpression OEChem::OEHasImplicitHydrogens OEChem::OEHasMapIdx Constructors CreateCopy operator() OEChem::OEHasMMCIFData OEChem::OEHasMolDBIdx OEChem::OEHasMultipleBond OEChem::OEHasOrder Constructors CreateCopy operator() OEChem::OEHasPartialCharges OEChem::OEHasPDBData OEChem::OEHasResidue OEChem::OEHasResidueNumber Constructors CreateCopy operator() OEChem::OEHasResidues OEChem::OEHasSDData OEChem::OEHasSingleBond OEChem::OEHasStereoHydrogens OEChem::OEHasStyle OEChem::OEHasTokenizer OEChem::OEHasTripleBond OEChem::OEHistogramFormula OEChem::OEHybridization OEChem::OEHybridization::sp OEChem::OEHybridization::sp2 OEChem::OEHybridization::sp3 OEChem::OEHybridization::sp3d OEChem::OEHybridization::sp3d2 OEChem::OEHybridization::Unknown OEChem::OEHydrogenCounter Constructors operator= OEChem::OEHydrogenVisibility OEChem::OEHydrogenVisibility::All OEChem::OEHydrogenVisibility::BEGIN OEChem::OEHydrogenVisibility::END OEChem::OEHydrogenVisibility::Off OEChem::OEHydrogenVisibility::Polar OEChem::OEIdxSelected Constructors CreateCopy operator() OEChem::OEIFlavor OEChem::OEIFlavor::CAN OEChem::OEIFlavor::CAN::Default OEChem::OEIFlavor::CDX OEChem::OEIFlavor::CDX::Default OEChem::OEIFlavor::CIF OEChem::OEIFlavor::CIF::BondHydToClosest OEChem::OEIFlavor::CIF::BondOrder OEChem::OEIFlavor::CIF::Default OEChem::OEIFlavor::CIF::FormalCrg OEChem::OEIFlavor::CIF::ImplicitH OEChem::OEIFlavor::CIF::NormalizeHydPos OEChem::OEIFlavor::CIF::OccFilterOneHalf OEChem::OEIFlavor::CIF::RemovePBCImages OEChem::OEIFlavor::CIF::RemoveQuestionMarkInLabel OEChem::OEIFlavor::CIF::Rings OEChem::OEIFlavor::CSV OEChem::OEIFlavor::CSV::DEFAULT OEChem::OEIFlavor::CSV::Default OEChem::OEIFlavor::CSV::Header OEChem::OEIFlavor::CXSMILES OEChem::OEIFlavor::CXSMILES::Canon OEChem::OEIFlavor::CXSMILES::DEFAULT OEChem::OEIFlavor::CXSMILES::Default OEChem::OEIFlavor::CXSMILES::Strict OEChem::OEIFlavor::FASTA OEChem::OEIFlavor::FASTA::CustomResidues OEChem::OEIFlavor::FASTA::Default OEChem::OEIFlavor::FASTA::EmbeddedSMILES OEChem::OEIFlavor::Generic OEChem::OEIFlavor::Generic::AroMask OEChem::OEIFlavor::Generic::DEFAULT OEChem::OEIFlavor::Generic::Default OEChem::OEIFlavor::Generic::GenericMask OEChem::OEIFlavor::Generic::OEAroModelDaylight OEChem::OEIFlavor::Generic::OEAroModelMDL OEChem::OEIFlavor::Generic::OEAroModelMMFF OEChem::OEIFlavor::Generic::OEAroModelOpenEye OEChem::OEIFlavor::Generic::OEAroModelTripos OEChem::OEIFlavor::Generic::Rings OEChem::OEIFlavor::Generic::SpecificMask OEChem::OEIFlavor::ISM OEChem::OEIFlavor::ISM::Default OEChem::OEIFlavor::MDL OEChem::OEIFlavor::MDL::Default OEChem::OEIFlavor::MDL::FixBondMarks OEChem::OEIFlavor::MDL::ForceImp2ExpENHSTE OEChem::OEIFlavor::MDL::SuppressEmptyMolSkip OEChem::OEIFlavor::MDL::SuppressImp2ExpENHSTE OEChem::OEIFlavor::MMCIF OEChem::OEIFlavor::MMCIF::ALTLOC OEChem::OEIFlavor::MMCIF::DEFAULT OEChem::OEIFlavor::MMCIF::NoAltLoc OEChem::OEIFlavor::MMCIF::SpruceDefault OEChem::OEIFlavor::MMOD OEChem::OEIFlavor::MMOD::Default OEChem::OEIFlavor::MMOD::FormalCrg OEChem::OEIFlavor::MOL2 OEChem::OEIFlavor::MOL2::AllMask OEChem::OEIFlavor::MOL2::DEFAULT OEChem::OEIFlavor::MOL2::Default OEChem::OEIFlavor::MOL2::Forcefield OEChem::OEIFlavor::MOL2::M2H OEChem::OEIFlavor::MOL2H OEChem::OEIFlavor::MOL2H::AllMask OEChem::OEIFlavor::MOL2H::DEFAULT OEChem::OEIFlavor::MOL2H::Default OEChem::OEIFlavor::MOL2H::M2H OEChem::OEIFlavor::OEB OEChem::OEIFlavor::OEB::Default OEChem::OEIFlavor::OEZ OEChem::OEIFlavor::OEZ::Default OEChem::OEIFlavor::PDB OEChem::OEIFlavor::PDB::ALL OEChem::OEIFlavor::PDB::AllMask OEChem::OEIFlavor::PDB::ALTLOC OEChem::OEIFlavor::PDB::BasicMask OEChem::OEIFlavor::PDB::BondOrder OEChem::OEIFlavor::PDB::CHARGE OEChem::OEIFlavor::PDB::Connect OEChem::OEIFlavor::PDB::DATA OEChem::OEIFlavor::PDB::DEFAULT OEChem::OEIFlavor::PDB::Default OEChem::OEIFlavor::PDB::DELPHI OEChem::OEIFlavor::PDB::END OEChem::OEIFlavor::PDB::ENDM OEChem::OEIFlavor::PDB::ExtraMask OEChem::OEIFlavor::PDB::FORMALCHARGE OEChem::OEIFlavor::PDB::FormalCrg OEChem::OEIFlavor::PDB::ImplicitH OEChem::OEIFlavor::PDB::RADIUS OEChem::OEIFlavor::PDB::Rings OEChem::OEIFlavor::PDB::SecStruct OEChem::OEIFlavor::PDB::SpruceDefault OEChem::OEIFlavor::PDB::TER OEChem::OEIFlavor::PDB::TerMask OEChem::OEIFlavor::RDF OEChem::OEIFlavor::RDF::Default OEChem::OEIFlavor::RDF::FixBondMarks OEChem::OEIFlavor::RDF::ForceImp2ExpENHSTE OEChem::OEIFlavor::RDF::SuppressEmptyMolSkip OEChem::OEIFlavor::RDF::SuppressImp2ExpENHSTE OEChem::OEIFlavor::SDF OEChem::OEIFlavor::SDF::Default OEChem::OEIFlavor::SDF::FixBondMarks OEChem::OEIFlavor::SDF::ForceImp2ExpENHSTE OEChem::OEIFlavor::SDF::SuppressEmptyMolSkip OEChem::OEIFlavor::SDF::SuppressImp2ExpENHSTE OEChem::OEIFlavor::SKC OEChem::OEIFlavor::SKC::Default OEChem::OEIFlavor::SMI OEChem::OEIFlavor::SMI::Canon OEChem::OEIFlavor::SMI::DEFAULT OEChem::OEIFlavor::SMI::Default OEChem::OEIFlavor::SMI::Strict OEChem::OEIFlavor::USM OEChem::OEIFlavor::USM::Default OEChem::OEIFlavor::XYZ OEChem::OEIFlavor::XYZ::BondOrder OEChem::OEIFlavor::XYZ::Connect OEChem::OEIFlavor::XYZ::Default OEChem::OEIFlavor::XYZ::ExtraMask OEChem::OEIFlavor::XYZ::FormalCrg OEChem::OEIFlavor::XYZ::ImplicitH OEChem::OEIFlavor::XYZ::Rings OEChem::OEInChIOptions Constructors GetChiral GetFixedHLayer GetHydrogens GetNonPolymerPseudoAtoms GetRacemicStereo GetReconnectedMetals GetRelativeStereo GetStereo GetTimeout GetUndefinedStereo operator= SetChiral SetFixedHLayer SetHydrogens SetNonPolymerPseudoAtoms SetRacemicStereo SetReconnectedMetals SetRelativeStereo SetStereo SetTimeout SetUndefinedStereo OEChem::OEInChIToMol OEChem::OEInit2DRingDictionary OEChem::OEInitDefaultHandler OEChem::OEInitHandler OEChem::OEInSamePart Constructors CreateCopy operator() operator= OEChem::OEInteractionStyle OEChem::OEInteractionStyle::BEGIN OEChem::OEInteractionStyle::Bumps OEChem::OEInteractionStyle::END OEChem::OEInteractionStyle::IntermolecularHBonds OEChem::OEInteractionStyle::IntramolecularHBonds OEChem::OEInteractionStyle::Off OEChem::OEInteractionStyle::UnsatisfiedHBonds OEChem::OEInvertCenter OEChem::OEIs2DFormat OEChem::OEIs3DFormat OEChem::OEIsAromaticAtom CreateCopy operator() OEChem::OEIsAromaticBond CreateCopy operator() OEChem::OEIsAtomHybridization Constructors CreateCopy operator() OEChem::OEIsBinary OEChem::OEIsBridgeHead CreateCopy operator() OEChem::OEIsCAlpha CreateCopy operator() OEChem::OEIsCarbon CreateCopy operator() OEChem::OEIsChiralAtom CreateCopy operator() OEChem::OEIsChiralBond CreateCopy operator() OEChem::OEIsCommonIsotope OEChem::OEIsComplementaryScreenType OEChem::OEIsExtension OEChem::OEIsGZip OEChem::OEIsHalide CreateCopy operator() OEChem::OEIsHalogen CreateCopy operator() OEChem::OEIsHeavy CreateCopy operator() OEChem::OEIsHetero CreateCopy operator() OEChem::OEIsHydrogen CreateCopy operator() OEChem::OEIsInvertibleNitrogen CreateCopy operator() OEChem::OEIsMDLStereoGroup Constructors CreateCopy operator() OEChem::OEIsMember Add Constructors CreateCopy operator() operator= Set OEChem::OEIsMemberPtr Add Constructors CreateCopy operator() operator= Set OEChem::OEIsMetal CreateCopy operator() OEChem::OEIsNitrogen CreateCopy operator() OEChem::OEIsNonRingAtomDoubleBondedToRing CreateCopy operator() OEChem::OEIsomericConfTest CombineMols CompareMols Constructors CreateCopy OEChem::OEIsOxygen CreateCopy operator() OEChem::OEIsPhosphorus CreateCopy operator() OEChem::OEIsPolar CreateCopy operator() OEChem::OEIsPolarHydrogen CreateCopy operator() OEChem::OEIsProductGroup Constructors CreateCopy operator() OEChem::OEIsReactantGroup Constructors CreateCopy operator() OEChem::OEIsReadable OEChem::OEIsRGroup Constructors CreateCopy operator() OEChem::OEIsRotor Constructors CreateCopy operator() OEChem::OEIsRxnComponentGroup Constructors CreateCopy operator() OEChem::OEIsSDDataFormat OEChem::OEIsSulfur CreateCopy operator() OEChem::OEIsTermHeavyAtom CreateCopy operator() OEChem::OEIsTerminalOxygen OEChem::OEIsTerminalSulfur OEChem::OEIsValid2DRingDictionary OEChem::OEIsValidAtomValence CreateCopy operator() OEChem::OEIsValidMDLAtomValence CreateCopy operator() OEChem::OEIsValidSubSearchDatabase OEChem::OEIsValidSubSearchScreenString OEChem::OEIsWriteable OEChem::OEKekulize OEChem::OELibraryGen AddStartingMaterial ClearStartingMaterial Constructors GetAssignMapIdx GetClearCoordinates GetExplicitHydrogens GetProducts GetRemoveUnmappedFragments GetStartingMaterial GetTitleSeparator GetValenceCorrection GetValidateKekule Init NumPossibleProducts NumReactants operator bool operator() operator= SetAssignMapIdx SetClearCoordinates SetExplicitHydrogens SetRemoveUnmappedFragments SetStartingMaterial SetTitleSeparator SetValenceCorrection SetValidateKekule OEChem::OELingoSim Constructors GetType Init IsValid operator= SetImpl Similarity OEChem::OELingoType OEChem::OELingoType::Default OEChem::OELingoType::IsoSmiMap OEChem::OELingoType::Undefined OEChem::OEMacroModelAtomTypeNames OEChem::OEMacroModelAtomTypes OEChem::OEMacroModelTypeElement OEChem::OEMacroModelTypeName OEChem::OEMacroModelTypeNames OEChem::OEMakeSubSearchQueryScreen OEChem::OEMakeSubSearchTargetScreen OEChem::OEMatch AddPair Clear Constructors CreateCopy GetAtoms GetBonds NumAtoms NumBonds operator= OEChem::OEMatchBase Clear CreateCopy GetAtoms GetBonds GetPatternAtoms GetPatternBonds GetTargetAtoms GetTargetBonds IsValid NumAtoms NumBonds operator bool OEChem::OEMatchFunc Constructors CreateCopy operator bool operator() OEChem::OEMatchPair Constructors operator= OEChem::OEMCMolBase ClearBase ClearMCMol ClearMolBase DeleteConf DeleteConfs GetActive GetConf GetConfList GetConfs GetMaxConfIdx GetMCMolTitle IsDeleted NewConf NumConfs operator= OrderConfs PopActive PushActive SetActive SweepConfs OEChem::OEMCMolType OEChem::OEMCMolType::Cartesian OEChem::OEMCMolType::DoubleCartesian OEChem::OEMCMolType::FloatCartesian OEChem::OEMCMolType::HalfFloatCartesian OEChem::OEMCMolType::LongDoubleCartesian OEChem::OEMCMolType::MaxType OEChem::OEMCMolType::OEDBMCMol OEChem::OEMCMolType::OEDefault OEChem::OEMCMolType::Undefined OEChem::OEMCSFunc CreateCopy operator() OEChem::OEMCSFuncParameter Constructors operator= OEChem::OEMCSMaxAtoms CreateCopy operator() OEChem::OEMCSMaxAtomsCompleteCycles Constructors CreateCopy operator() OEChem::OEMCSMaxBonds CreateCopy operator() OEChem::OEMCSMaxBondsCompleteCycles Constructors CreateCopy operator() OEChem::OEMCSSearch AddConstraint ClearConstraints Constructors GetMaxMatches GetMinAtoms GetPattern Init Match operator bool operator= SetMaxMatches SetMCSFunc SetMinAtoms OEChem::OEMCSType OEChem::OEMCSType::Approximate OEChem::OEMCSType::Default OEChem::OEMCSType::Exhaustive OEChem::OEMDLClearBondStereo OEChem::OEMDLClearParity OEChem::OEMDLCorrectBondStereo OEChem::OEMDLGetParity OEChem::OEMDLGetValence OEChem::OEMDLHasIncorrectBondStereo OEChem::OEMDLHasParity OEChem::OEMDLPerceiveBondStereo OEChem::OEMDLPerceiveParity OEChem::OEMDLQueryOpts OEChem::OEMDLQueryOpts::AddBondAliphaticConstraint OEChem::OEMDLQueryOpts::AddBondTopologyConstraint OEChem::OEMDLQueryOpts::Default OEChem::OEMDLQueryOpts::ExactMatchStarAtoms OEChem::OEMDLQueryOpts::MatchAtomStereo OEChem::OEMDLQueryOpts::MatchIsotope OEChem::OEMDLQueryOpts::Optimize OEChem::OEMDLQueryOpts::ReactionQuery OEChem::OEMDLQueryOpts::SuppressExplicitH OEChem::OEMDLSetParity OEChem::OEMDLStereoFromBondStereo OEChem::OEMDLStereoFromParity OEChem::OEMMFF94InitialCharges OEChem::OEMMFF94PartialCharges OEChem::OEMMFFAtomType OEChem::OEMMFFAtomTypeNames OEChem::OEMMFFAtomTypes OEChem::OEMMFFClearRemappedElements OEChem::OEMMFFRemapElement OEChem::OEMMFFType OEChem::OEMMFFType::B OEChem::OEMMFFType::BR OEChem::OEMMFFType::Br OEChem::OEMMFFType::BR_ OEChem::OEMMFFType::C OEChem::OEMMFFType::C5 OEChem::OEMMFFType::C5A OEChem::OEMMFFType::C5B OEChem::OEMMFFType::C__ OEChem::OEMMFFType::CA2 OEChem::OEMMFFType::CB OEChem::OEMMFFType::CC OEChem::OEMMFFType::CGD OEChem::OEMMFFType::CGD_ OEChem::OEMMFFType::CIM OEChem::OEMMFFType::CION OEChem::OEMMFFType::CL OEChem::OEMMFFType::Cl OEChem::OEMMFFType::CL_ OEChem::OEMMFFType::CLO4 OEChem::OEMMFFType::CN OEChem::OEMMFFType::CNN_ OEChem::OEMMFFType::CO OEChem::OEMMFFType::CO2M OEChem::OEMMFFType::CON OEChem::OEMMFFType::CONN OEChem::OEMMFFType::COO OEChem::OEMMFFType::COON OEChem::OEMMFFType::COOO OEChem::OEMMFFType::COR OEChem::OEMMFFType::COS OEChem::OEMMFFType::CP OEChem::OEMMFFType::CR OEChem::OEMMFFType::CR3R OEChem::OEMMFFType::CR4E OEChem::OEMMFFType::CR4R OEChem::OEMMFFType::CS OEChem::OEMMFFType::CS2M OEChem::OEMMFFType::CSN OEChem::OEMMFFType::CSO OEChem::OEMMFFType::CSO2 OEChem::OEMMFFType::CSP OEChem::OEMMFFType::CSP2 OEChem::OEMMFFType::CSS OEChem::OEMMFFType::CU1 OEChem::OEMMFFType::CU2 OEChem::OEMMFFType::DUMMY OEChem::OEMMFFType::F OEChem::OEMMFFType::F_ OEChem::OEMMFFType::FE2 OEChem::OEMMFFType::FE3 OEChem::OEMMFFType::H3N OEChem::OEMMFFType::HC OEChem::OEMMFFType::HGD_ OEChem::OEMMFFType::HIM OEChem::OEMMFFType::HN5_ OEChem::OEMMFFType::HNC OEChem::OEMMFFType::HNC_ OEChem::OEMMFFType::HNC__ OEChem::OEMMFFType::HNCC OEChem::OEMMFFType::HNCN OEChem::OEMMFFType::HNCO OEChem::OEMMFFType::HNCS OEChem::OEMMFFType::HNM OEChem::OEMMFFType::HNN OEChem::OEMMFFType::HNN_ OEChem::OEMMFFType::HNNC OEChem::OEMMFFType::HNNN OEChem::OEMMFFType::HNO OEChem::OEMMFFType::HNO2 OEChem::OEMMFFType::HNOX OEChem::OEMMFFType::HNPO OEChem::OEMMFFType::HNR OEChem::OEMMFFType::HNR_ OEChem::OEMMFFType::HNSO OEChem::OEMMFFType::HO OEChem::OEMMFFType::HO_ OEChem::OEMMFFType::HO__ OEChem::OEMMFFType::HOCC OEChem::OEMMFFType::HOCN OEChem::OEMMFFType::HOCO OEChem::OEMMFFType::HOCS OEChem::OEMMFFType::HOH OEChem::OEMMFFType::HOM OEChem::OEMMFFType::HON OEChem::OEMMFFType::HOP OEChem::OEMMFFType::HOR OEChem::OEMMFFType::HOS OEChem::OEMMFFType::HP OEChem::OEMMFFType::HPD_ OEChem::OEMMFFType::HPYL OEChem::OEMMFFType::HS OEChem::OEMMFFType::HSE OEChem::OEMMFFType::HSe OEChem::OEMMFFType::HSI OEChem::OEMMFFType::HSN OEChem::OEMMFFType::HSP2 OEChem::OEMMFFType::HX OEChem::OEMMFFType::I OEChem::OEMMFFType::K OEChem::OEMMFFType::LI OEChem::OEMMFFType::MAXTYPE OEChem::OEMMFFType::MG2 OEChem::OEMMFFType::N2OX OEChem::OEMMFFType::N3OX OEChem::OEMMFFType::N5 OEChem::OEMMFFType::N5_ OEChem::OEMMFFType::N5A OEChem::OEMMFFType::N5A_ OEChem::OEMMFFType::N5AX OEChem::OEMMFFType::N5B OEChem::OEMMFFType::N5B_ OEChem::OEMMFFType::N5BX OEChem::OEMMFFType::N5M OEChem::OEMMFFType::N5OX OEChem::OEMMFFType::N_ OEChem::OEMMFFType::NA OEChem::OEMMFFType::NAZT OEChem::OEMMFFType::NC OEChem::OEMMFFType::NC_ OEChem::OEMMFFType::NCC OEChem::OEMMFFType::NCC_ OEChem::OEMMFFType::NCN OEChem::OEMMFFType::NCN_ OEChem::OEMMFFType::NCN__ OEChem::OEMMFFType::NCO OEChem::OEMMFFType::NCP OEChem::OEMMFFType::NCS OEChem::OEMMFFType::NGD_ OEChem::OEMMFFType::NIM OEChem::OEMMFFType::NM OEChem::OEMMFFType::NN OEChem::OEMMFFType::NN_ OEChem::OEMMFFType::NNC OEChem::OEMMFFType::NNN OEChem::OEMMFFType::NO OEChem::OEMMFFType::NO2 OEChem::OEMMFFType::NO3 OEChem::OEMMFFType::NPD_ OEChem::OEMMFFType::NPO2 OEChem::OEMMFFType::NPO3 OEChem::OEMMFFType::NPOX OEChem::OEMMFFType::NPYD OEChem::OEMMFFType::NPYL OEChem::OEMMFFType::NR OEChem::OEMMFFType::NR_ OEChem::OEMMFFType::NR__ OEChem::OEMMFFType::NSO OEChem::OEMMFFType::NSO2 OEChem::OEMMFFType::NSO3 OEChem::OEMMFFType::NSP OEChem::OEMMFFType::O OEChem::OEMMFFType::O2CM OEChem::OEMMFFType::O2N OEChem::OEMMFFType::O2NO OEChem::OEMMFFType::O2P OEChem::OEMMFFType::O2S OEChem::OEMMFFType::O3N OEChem::OEMMFFType::O3P OEChem::OEMMFFType::O3S OEChem::OEMMFFType::O4CL OEChem::OEMMFFType::O4Cl OEChem::OEMMFFType::O4P OEChem::OEMMFFType::O4S OEChem::OEMMFFType::O_ OEChem::OEMMFFType::O__ OEChem::OEMMFFType::OC OEChem::OEMMFFType::OCC OEChem::OEMMFFType::OCN OEChem::OEMMFFType::OCN_ OEChem::OEMMFFType::OCO OEChem::OEMMFFType::OCO_ OEChem::OEMMFFType::OCR OEChem::OEMMFFType::OCS OEChem::OEMMFFType::OFUR OEChem::OEMMFFType::OH2 OEChem::OEMMFFType::OM OEChem::OEMMFFType::OM2 OEChem::OEMMFFType::ON OEChem::OEMMFFType::ON_ OEChem::OEMMFFType::ONO OEChem::OEMMFFType::ONO2 OEChem::OEMMFFType::OP OEChem::OEMMFFType::OP_ OEChem::OEMMFFType::OPO OEChem::OEMMFFType::OPO2 OEChem::OEMMFFType::OPO3 OEChem::OEMMFFType::OR OEChem::OEMMFFType::OS OEChem::OEMMFFType::OS_ OEChem::OEMMFFType::OS__ OEChem::OEMMFFType::OS___ OEChem::OEMMFFType::OSMS OEChem::OEMMFFType::OSO OEChem::OEMMFFType::OSO2 OEChem::OEMMFFType::OSO3 OEChem::OEMMFFType::OSO_ OEChem::OEMMFFType::OXN OEChem::OEMMFFType::P OEChem::OEMMFFType::PC OEChem::OEMMFFType::PO OEChem::OEMMFFType::PO2 OEChem::OEMMFFType::PO3 OEChem::OEMMFFType::PO4 OEChem::OEMMFFType::PTET OEChem::OEMMFFType::S OEChem::OEMMFFType::S2CM OEChem::OEMMFFType::SC OEChem::OEMMFFType::SE OEChem::OEMMFFType::Se OEChem::OEMMFFType::SI OEChem::OEMMFFType::SM OEChem::OEMMFFType::SN OEChem::OEMMFFType::SNO OEChem::OEMMFFType::SO OEChem::OEMMFFType::SO2 OEChem::OEMMFFType::SO2_ OEChem::OEMMFFType::SO2M OEChem::OEMMFFType::SO2N OEChem::OEMMFFType::SO3 OEChem::OEMMFFType::SO4 OEChem::OEMMFFType::SO_ OEChem::OEMMFFType::SP OEChem::OEMMFFType::SSMO OEChem::OEMMFFType::SSOM OEChem::OEMMFFType::STHI OEChem::OEMMFFType::UNK OEChem::OEMMFFType::ZN2 OEChem::OEMMFFTypeIndex OEChem::OEMMFFTypeName OEChem::OEMMFFTypeNames OEChem::OEMMFFTypeResult Constructors GetFailed GetMMFFType OEChem::OEMModType OEChem::OEMModType::B2 OEChem::OEMModType::B3 OEChem::OEMModType::Ba OEChem::OEMModType::Br OEChem::OEMModType::C0 OEChem::OEMModType::C1 OEChem::OEMModType::c1 OEChem::OEMModType::C2 OEChem::OEMModType::c2 OEChem::OEMModType::C3 OEChem::OEMModType::CA OEChem::OEMModType::Ca OEChem::OEMModType::CB OEChem::OEMModType::CC OEChem::OEMModType::CD OEChem::OEMModType::CE OEChem::OEMModType::CF OEChem::OEMModType::Cl OEChem::OEMModType::CM OEChem::OEMModType::Cm OEChem::OEMModType::CP OEChem::OEMModType::CR OEChem::OEMModType::Cs OEChem::OEMModType::Du OEChem::OEMModType::F0 OEChem::OEMModType::f2 OEChem::OEMModType::f3 OEChem::OEMModType::H0 OEChem::OEMModType::H1 OEChem::OEMModType::H2 OEChem::OEMModType::H3 OEChem::OEMModType::H4 OEChem::OEMModType::H5 OEChem::OEMModType::I0 OEChem::OEMModType::K0 OEChem::OEMModType::Li OEChem::OEMModType::Lp OEChem::OEMModType::M2 OEChem::OEMModType::M3 OEChem::OEMModType::m3 OEChem::OEMModType::M4 OEChem::OEMModType::m4 OEChem::OEMModType::M5 OEChem::OEMModType::m5 OEChem::OEMModType::M6 OEChem::OEMModType::m6 OEChem::OEMModType::M7 OEChem::OEMModType::MAXTYPE OEChem::OEMModType::Mg OEChem::OEMModType::N0 OEChem::OEMModType::N1 OEChem::OEMModType::N2 OEChem::OEMModType::n2 OEChem::OEMModType::N3 OEChem::OEMModType::n3 OEChem::OEMModType::N4 OEChem::OEMModType::N5 OEChem::OEMModType::NA OEChem::OEMModType::Na OEChem::OEMModType::NB OEChem::OEMModType::NC OEChem::OEMModType::ND OEChem::OEMModType::NE OEChem::OEMModType::NF OEChem::OEMModType::NG OEChem::OEMModType::NH OEChem::OEMModType::NI OEChem::OEMModType::NM OEChem::OEMModType::NP OEChem::OEMModType::O0 OEChem::OEMModType::O2 OEChem::OEMModType::o2 OEChem::OEMModType::O3 OEChem::OEMModType::o3 OEChem::OEMModType::OA OEChem::OEMModType::OM OEChem::OEMModType::OP OEChem::OEMModType::OQ OEChem::OEMModType::OW OEChem::OEMModType::P0 OEChem::OEMModType::Rb OEChem::OEMModType::S0 OEChem::OEMModType::S1 OEChem::OEMModType::S2 OEChem::OEMModType::SA OEChem::OEMModType::Si OEChem::OEMModType::SM OEChem::OEMModType::SP OEChem::OEMModType::Z0 OEChem::OEMModType::Zn OEChem::OEMol ClearBase ClearMCMol ClearMolBase Constructors GetConfList MCMol operator OEMCMolBase & operator= SCMol OEChem::OEMolBase Clear ClearBase ClearCoords Compress Count CreateCopy DeleteAtom DeleteBond DeleteGroup GetAtom GetAtomList GetAtoms GetBond GetBondList GetBonds GetCoords GetDimension GetEnergy GetGroup GetGroupList GetGroups GetMaxAtomIdx GetMaxBondIdx GetTitle HasPerceived IsDataType IsDeleted IsRxn NewAtom NewBond NewGroup NumAtoms NumBonds NumGroups operator bool operator= OrderAtoms OrderBonds ResetPerceived SetCoords SetDimension SetEnergy SetPerceived SetRxn SetTitle Sweep UnCompress OEChem::OEMolBaseType OEChem::OEMolBaseType::MaxType OEChem::OEMolBaseType::OEDBMol OEChem::OEMolBaseType::OEDefault OEChem::OEMolBaseType::OEMiniMol OEChem::OEMolBaseType::Undefined OEChem::OEMolDatabase Clear Constructors CreateCopy Delete GetDataType GetFlavor GetFormat GetIdx GetIdxs GetMaxMolIdx GetMolecule GetMoleculeString GetRow GetTitle GetTitles IsDataType IsDeleted NumMols Open Order Save WriteMolecule OEChem::OEMolDatabaseSaveOptions Constructors GetFlavor GetFormat GetIdxFileName GetWriteIdx SetFlavor SetFormat SetIdxFileName SetWriteIdx OEChem::OEMolDBException Constructors what OEChem::OEMolecularFormula OEChem::OEMolGDPropertyFxn Constructors operator= OEChem::oemolistream close Constructors eof getbyte GetConfTest getline GetMCMolBases GetMolBases GetReadFailureCt IncrementReadFailureCt openByteArray operator bool operator OEPlatform::oeistream & peekbyte read ResetReadFailureCt rewind seek SetConfTest SetFlavor SetFormat Setgz SetTracer size skip skipbyte skipline tell OEChem::oemolithread close Constructors GetIStream GetMolStream openstring SetFlavor SetFormat OEChem::oemolostream close Constructors flush getByteArray openstring operator bool operator OEPlatform::oeostream & put SetFlavor SetFormat Setgz SetString tell write OEChem::oemolothread close Constructors GetMolStream GetOStream GetString openstring SetFlavor SetFormat OEChem::OEMolParameter Constructors GetSetting GetValue operator= SetValue OEChem::OEMolPropertyFxn CreateCopy Get Has OEChem::OEMolPropertyList Add Clear Constructors CreateCopy GetProperty GetSize HasProperties operator= OEChem::OEMolReaderParameter Constructors operator= OEChem::OEMolSDPropertyFxn Constructors operator= OEChem::oemolstreambase ClearCSVHeader close GetBinaryIOHandler GetCSVHeader GetFileName GetFlavor GetFormat Getgz open SetFlavor SetFormat OEChem::OEMolStyleColorer AddColor ClearColors Constructors GetColor GetColorScheme GetDataTypes GetDefaultColor GetNumColors GetPropertyName GetValues operator< operator= operator== SetDefaultColor OEChem::OEMolTaggedPropertyFxn Constructors operator= OEChem::oemolthreadbase GetMol operator bool PeekMol PutMol OEChem::OEMolToCXSMILES OEChem::OEMolToInChI OEChem::OEMolToInChIKey OEChem::OEMolToSmiles OEChem::OEMolToSTDInChI OEChem::OEMolToSTDInChIKey OEChem::OEMolWriterParameter Constructors operator= OEChem::OEMultipleBondCount OEChem::OEMutableCoords Constructors GetPtr operator T * OEChem::OENbrs Constructors GetBgn GetDist GetDist2 GetEnd OEChem::OENearestNbrs Constructors GetNbrs OEChem::OENearestNbrsMethod OEChem::OENearestNbrsMethod::AllByAll OEChem::OENearestNbrsMethod::Auto OEChem::OENearestNbrsMethod::Default OEChem::OENearestNbrsMethod::LocalHash OEChem::OENearestNbrsMethod::ZCoordSort OEChem::OENetCharge OEChem::OENewMCMolBase OEChem::OENewMolBase OEChem::OENewQMolBase OEChem::OENormalize OEChem::OENthAtom Constructors CreateCopy operator() OEChem::OEOFlavor OEChem::OEOFlavor::CAN OEChem::OEOFlavor::CAN::AllBonds OEChem::OEOFlavor::CAN::AtomMaps OEChem::OEOFlavor::CAN::AtomStereo OEChem::OEOFlavor::CAN::BondStereo OEChem::OEOFlavor::CAN::Canonical OEChem::OEOFlavor::CAN::DEFAULT OEChem::OEOFlavor::CAN::Default OEChem::OEOFlavor::CAN::EnhStereo OEChem::OEOFlavor::CAN::ExtBonds OEChem::OEOFlavor::CAN::Hydrogens OEChem::OEOFlavor::CAN::ImpHCount OEChem::OEOFlavor::CAN::Isotopes OEChem::OEOFlavor::CAN::Kekule OEChem::OEOFlavor::CAN::RGroups OEChem::OEOFlavor::CAN::SmiMask OEChem::OEOFlavor::CAN::SuperAtoms OEChem::OEOFlavor::CDX OEChem::OEOFlavor::CDX::Add2D OEChem::OEOFlavor::CDX::Default OEChem::OEOFlavor::CDX::UnsetBad2DStereo OEChem::OEOFlavor::CIF OEChem::OEOFlavor::CIF::Default OEChem::OEOFlavor::CSV OEChem::OEOFlavor::CSV::DEFAULT OEChem::OEOFlavor::CSV::Default OEChem::OEOFlavor::CSV::Header OEChem::OEOFlavor::CXSMILES OEChem::OEOFlavor::CXSMILES::AllBonds OEChem::OEOFlavor::CXSMILES::AtomMaps OEChem::OEOFlavor::CXSMILES::AtomStereo OEChem::OEOFlavor::CXSMILES::BondStereo OEChem::OEOFlavor::CXSMILES::Canonical OEChem::OEOFlavor::CXSMILES::DEFAULT OEChem::OEOFlavor::CXSMILES::Default OEChem::OEOFlavor::CXSMILES::EnhStereo OEChem::OEOFlavor::CXSMILES::ExtBonds OEChem::OEOFlavor::CXSMILES::Hydrogens OEChem::OEOFlavor::CXSMILES::ImpHCount OEChem::OEOFlavor::CXSMILES::Isotopes OEChem::OEOFlavor::CXSMILES::Kekule OEChem::OEOFlavor::CXSMILES::RGroups OEChem::OEOFlavor::CXSMILES::SmiMask OEChem::OEOFlavor::CXSMILES::SuperAtoms OEChem::OEOFlavor::FASTA OEChem::OEOFlavor::FASTA::Default OEChem::OEOFlavor::Generic OEChem::OEOFlavor::Generic::AroMask OEChem::OEOFlavor::Generic::DEFAULT OEChem::OEOFlavor::Generic::Default OEChem::OEOFlavor::Generic::GenericMask OEChem::OEOFlavor::Generic::OEAroModelDaylight OEChem::OEOFlavor::Generic::OEAroModelMDL OEChem::OEOFlavor::Generic::OEAroModelMMFF OEChem::OEOFlavor::Generic::OEAroModelOpenEye OEChem::OEOFlavor::Generic::OEAroModelTripos OEChem::OEOFlavor::Generic::Rings OEChem::OEOFlavor::Generic::SpecificMask OEChem::OEOFlavor::INCHI OEChem::OEOFlavor::INCHI::Chiral OEChem::OEOFlavor::INCHI::Default OEChem::OEOFlavor::INCHI::FixedHLayer OEChem::OEOFlavor::INCHI::Hydrogens OEChem::OEOFlavor::INCHI::RacemicStereo OEChem::OEOFlavor::INCHI::ReconnectedMetals OEChem::OEOFlavor::INCHI::RelativeStereo OEChem::OEOFlavor::INCHI::Stereo OEChem::OEOFlavor::INCHI::Title OEChem::OEOFlavor::INCHIKEY OEChem::OEOFlavor::INCHIKEY::Chiral OEChem::OEOFlavor::INCHIKEY::Default OEChem::OEOFlavor::INCHIKEY::FixedHLayer OEChem::OEOFlavor::INCHIKEY::Hydrogens OEChem::OEOFlavor::INCHIKEY::RacemicStereo OEChem::OEOFlavor::INCHIKEY::ReconnectedMetals OEChem::OEOFlavor::INCHIKEY::RelativeStereo OEChem::OEOFlavor::INCHIKEY::Stereo OEChem::OEOFlavor::INCHIKEY::Title OEChem::OEOFlavor::ISM OEChem::OEOFlavor::ISM::AllBonds OEChem::OEOFlavor::ISM::AtomMaps OEChem::OEOFlavor::ISM::AtomStereo OEChem::OEOFlavor::ISM::BondStereo OEChem::OEOFlavor::ISM::Canonical OEChem::OEOFlavor::ISM::DEFAULT OEChem::OEOFlavor::ISM::Default OEChem::OEOFlavor::ISM::EnhStereo OEChem::OEOFlavor::ISM::ExtBonds OEChem::OEOFlavor::ISM::Hydrogens OEChem::OEOFlavor::ISM::ImpHCount OEChem::OEOFlavor::ISM::Isotopes OEChem::OEOFlavor::ISM::Kekule OEChem::OEOFlavor::ISM::RGroups OEChem::OEOFlavor::ISM::SmiMask OEChem::OEOFlavor::ISM::SuperAtoms OEChem::OEOFlavor::MDL OEChem::OEOFlavor::MDL::Add2D OEChem::OEOFlavor::MDL::CurrentParity OEChem::OEOFlavor::MDL::DEFAULT OEChem::OEOFlavor::MDL::Default OEChem::OEOFlavor::MDL::MCHG OEChem::OEOFlavor::MDL::MDLParity OEChem::OEOFlavor::MDL::MISO OEChem::OEOFlavor::MDL::MMask OEChem::OEOFlavor::MDL::MRGP OEChem::OEOFlavor::MDL::MV30 OEChem::OEOFlavor::MDL::NoParity OEChem::OEOFlavor::MDL::PMask OEChem::OEOFlavor::MDL::SuppressImp2ExpENHSTE OEChem::OEOFlavor::MDL::SuppressTimestamps OEChem::OEOFlavor::MDL::UnsetBad2DStereo OEChem::OEOFlavor::MF OEChem::OEOFlavor::MF::DEFAULT OEChem::OEOFlavor::MF::Default OEChem::OEOFlavor::MF::Title OEChem::OEOFlavor::MMCIF OEChem::OEOFlavor::MMCIF::Default OEChem::OEOFlavor::MMOD OEChem::OEOFlavor::MMOD::AtomTypes OEChem::OEOFlavor::MMOD::DEFAULT OEChem::OEOFlavor::MMOD::Default OEChem::OEOFlavor::MOL2 OEChem::OEOFlavor::MOL2::AllMask OEChem::OEOFlavor::MOL2::AtomNames OEChem::OEOFlavor::MOL2::AtomTypeNames OEChem::OEOFlavor::MOL2::BondTypeNames OEChem::OEOFlavor::MOL2::ChargePrecision OEChem::OEOFlavor::MOL2::DEFAULT OEChem::OEOFlavor::MOL2::Default OEChem::OEOFlavor::MOL2::Forcefield OEChem::OEOFlavor::MOL2::GeneralFFFormat OEChem::OEOFlavor::MOL2::Hydrogens OEChem::OEOFlavor::MOL2::NameMask OEChem::OEOFlavor::MOL2::OrderAtoms OEChem::OEOFlavor::MOL2::Substructure OEChem::OEOFlavor::MOL2H OEChem::OEOFlavor::MOL2H::AllMask OEChem::OEOFlavor::MOL2H::AtomNames OEChem::OEOFlavor::MOL2H::AtomTypeNames OEChem::OEOFlavor::MOL2H::BondTypeNames OEChem::OEOFlavor::MOL2H::DEFAULT OEChem::OEOFlavor::MOL2H::Default OEChem::OEOFlavor::MOL2H::Hydrogens OEChem::OEOFlavor::MOL2H::NameMask OEChem::OEOFlavor::MOL2H::OrderAtoms OEChem::OEOFlavor::MOL2H::Substructure OEChem::OEOFlavor::MOPAC OEChem::OEOFlavor::MOPAC::AllMask OEChem::OEOFlavor::MOPAC::CHARGES OEChem::OEOFlavor::MOPAC::DEFAULT OEChem::OEOFlavor::MOPAC::Default OEChem::OEOFlavor::MOPAC::XYZ OEChem::OEOFlavor::OEB OEChem::OEOFlavor::OEB::Default OEChem::OEOFlavor::OEZ OEChem::OEOFlavor::OEZ::Default OEChem::OEOFlavor::PDB OEChem::OEOFlavor::PDB::AllMask OEChem::OEOFlavor::PDB::BasicMask OEChem::OEOFlavor::PDB::BONDS OEChem::OEOFlavor::PDB::BOTH OEChem::OEOFlavor::PDB::CHARGE OEChem::OEOFlavor::PDB::CurrentResidues OEChem::OEOFlavor::PDB::DEFAULT OEChem::OEOFlavor::PDB::Default OEChem::OEOFlavor::PDB::DELPHI OEChem::OEOFlavor::PDB::ELEMENT OEChem::OEOFlavor::PDB::FORMALCHARGE OEChem::OEOFlavor::PDB::HETBONDS OEChem::OEOFlavor::PDB::NoResidues OEChem::OEOFlavor::PDB::OEResidues OEChem::OEOFlavor::PDB::OrderAtoms OEChem::OEOFlavor::PDB::ORDERS OEChem::OEOFlavor::PDB::RADIUS OEChem::OEOFlavor::PDB::TER OEChem::OEOFlavor::SDF OEChem::OEOFlavor::SDF::Add2D OEChem::OEOFlavor::SDF::CurrentParity OEChem::OEOFlavor::SDF::DEFAULT OEChem::OEOFlavor::SDF::Default OEChem::OEOFlavor::SDF::MCHG OEChem::OEOFlavor::SDF::MDLParity OEChem::OEOFlavor::SDF::MISO OEChem::OEOFlavor::SDF::MMask OEChem::OEOFlavor::SDF::MRGP OEChem::OEOFlavor::SDF::MV30 OEChem::OEOFlavor::SDF::NoParity OEChem::OEOFlavor::SDF::PMask OEChem::OEOFlavor::SDF::SuppressImp2ExpENHSTE OEChem::OEOFlavor::SDF::SuppressTimestamps OEChem::OEOFlavor::SDF::UnsetBad2DStereo OEChem::OEOFlavor::SLN OEChem::OEOFlavor::SLN::Default OEChem::OEOFlavor::SMI OEChem::OEOFlavor::SMI::AllBonds OEChem::OEOFlavor::SMI::AtomMaps OEChem::OEOFlavor::SMI::AtomStereo OEChem::OEOFlavor::SMI::BondStereo OEChem::OEOFlavor::SMI::Canonical OEChem::OEOFlavor::SMI::DEFAULT OEChem::OEOFlavor::SMI::Default OEChem::OEOFlavor::SMI::EnhStereo OEChem::OEOFlavor::SMI::ExtBonds OEChem::OEOFlavor::SMI::Hydrogens OEChem::OEOFlavor::SMI::ImpHCount OEChem::OEOFlavor::SMI::Isotopes OEChem::OEOFlavor::SMI::Kekule OEChem::OEOFlavor::SMI::RGroups OEChem::OEOFlavor::SMI::SmiMask OEChem::OEOFlavor::SMI::SuperAtoms OEChem::OEOFlavor::USM OEChem::OEOFlavor::USM::AllBonds OEChem::OEOFlavor::USM::AtomMaps OEChem::OEOFlavor::USM::AtomStereo OEChem::OEOFlavor::USM::BondStereo OEChem::OEOFlavor::USM::Canonical OEChem::OEOFlavor::USM::DEFAULT OEChem::OEOFlavor::USM::Default OEChem::OEOFlavor::USM::EnhStereo OEChem::OEOFlavor::USM::ExtBonds OEChem::OEOFlavor::USM::Hydrogens OEChem::OEOFlavor::USM::ImpHCount OEChem::OEOFlavor::USM::Isotopes OEChem::OEOFlavor::USM::Kekule OEChem::OEOFlavor::USM::RGroups OEChem::OEOFlavor::USM::SmiMask OEChem::OEOFlavor::USM::SuperAtoms OEChem::OEOFlavor::XYZ OEChem::OEOFlavor::XYZ::Charges OEChem::OEOFlavor::XYZ::Default OEChem::OEOFlavor::XYZ::DoublePrecision OEChem::OEOFlavor::XYZ::SinglePrecision OEChem::OEOFlavor::XYZ::Symbols OEChem::OEOmegaConfTest CombineMols CompareMols Constructors CreateCopy OEChem::OEOutFileStringParameter Constructors operator= OEChem::OEOverlayConfsByRMSD OEChem::OEParseInChI OEChem::OEParseSmarts OEChem::OEParseSmiles OEChem::OEParseSmilesOptions Constructors GetCanon GetCXSMILES GetQuiet GetStrict SetCanon SetCXSMILES SetQuiet SetStrict OEChem::OEParseSmirks OEChem::OEPartPredT Constructors CreateCopy operator() operator= SelectPart OEChem::OEPDBAtomName OEChem::OEPDBAtomName::C OEChem::OEPDBAtomName::C10 OEChem::OEPDBAtomName::C11 OEChem::OEPDBAtomName::C12 OEChem::OEPDBAtomName::C13 OEChem::OEPDBAtomName::C14 OEChem::OEPDBAtomName::C15 OEChem::OEPDBAtomName::C16 OEChem::OEPDBAtomName::C19 OEChem::OEPDBAtomName::C1_ OEChem::OEPDBAtomName::C2 OEChem::OEPDBAtomName::C21 OEChem::OEPDBAtomName::C24 OEChem::OEPDBAtomName::C2_ OEChem::OEPDBAtomName::C2A OEChem::OEPDBAtomName::C3 OEChem::OEPDBAtomName::C3_ OEChem::OEPDBAtomName::C4 OEChem::OEPDBAtomName::C4_ OEChem::OEPDBAtomName::C5 OEChem::OEPDBAtomName::C5_ OEChem::OEPDBAtomName::C5M OEChem::OEPDBAtomName::C6 OEChem::OEPDBAtomName::C8 OEChem::OEPDBAtomName::CA OEChem::OEPDBAtomName::CAnext OEChem::OEPDBAtomName::CB OEChem::OEPDBAtomName::CD OEChem::OEPDBAtomName::CD1 OEChem::OEPDBAtomName::CD2 OEChem::OEPDBAtomName::CE OEChem::OEPDBAtomName::CE1 OEChem::OEPDBAtomName::CE2 OEChem::OEPDBAtomName::CE3 OEChem::OEPDBAtomName::CG OEChem::OEPDBAtomName::CG1 OEChem::OEPDBAtomName::CG2 OEChem::OEPDBAtomName::CH1 OEChem::OEPDBAtomName::CH2 OEChem::OEPDBAtomName::CH3 OEChem::OEPDBAtomName::CM1 OEChem::OEPDBAtomName::CM2 OEChem::OEPDBAtomName::CM5 OEChem::OEPDBAtomName::CM7 OEChem::OEPDBAtomName::Cprev OEChem::OEPDBAtomName::CZ OEChem::OEPDBAtomName::CZ2 OEChem::OEPDBAtomName::CZ3 OEChem::OEPDBAtomName::N OEChem::OEPDBAtomName::N1 OEChem::OEPDBAtomName::N2 OEChem::OEPDBAtomName::N20 OEChem::OEPDBAtomName::N3 OEChem::OEPDBAtomName::N4 OEChem::OEPDBAtomName::N6 OEChem::OEPDBAtomName::N7 OEChem::OEPDBAtomName::N9 OEChem::OEPDBAtomName::ND1 OEChem::OEPDBAtomName::ND2 OEChem::OEPDBAtomName::NE OEChem::OEPDBAtomName::NE1 OEChem::OEPDBAtomName::NE2 OEChem::OEPDBAtomName::NH1 OEChem::OEPDBAtomName::NH2 OEChem::OEPDBAtomName::Nnext OEChem::OEPDBAtomName::NZ OEChem::OEPDBAtomName::O OEChem::OEPDBAtomName::O17 OEChem::OEPDBAtomName::O18 OEChem::OEPDBAtomName::O1P OEChem::OEPDBAtomName::O2 OEChem::OEPDBAtomName::O22 OEChem::OEPDBAtomName::O23 OEChem::OEPDBAtomName::O2_ OEChem::OEPDBAtomName::O2P OEChem::OEPDBAtomName::O3_ OEChem::OEPDBAtomName::O3P OEChem::OEPDBAtomName::O4 OEChem::OEPDBAtomName::O4_ OEChem::OEPDBAtomName::O5_ OEChem::OEPDBAtomName::O6 OEChem::OEPDBAtomName::OD OEChem::OEPDBAtomName::OD1 OEChem::OEPDBAtomName::OD2 OEChem::OEPDBAtomName::OE OEChem::OEPDBAtomName::OE1 OEChem::OEPDBAtomName::OE2 OEChem::OEPDBAtomName::OE3 OEChem::OEPDBAtomName::OE4 OEChem::OEPDBAtomName::OG OEChem::OEPDBAtomName::OG1 OEChem::OEPDBAtomName::OH OEChem::OEPDBAtomName::OXT OEChem::OEPDBAtomName::P OEChem::OEPDBAtomName::SD OEChem::OEPDBAtomName::SE_ OEChem::OEPDBAtomName::SG OEChem::OEPDBAtomName::UNK OEChem::OEPDBOrderAtoms OEChem::OEPerceiveBondOrders OEChem::OEPerceiveChiral OEChem::OEPerceiveCIPStereo OEChem::OEPerceived OEChem::OEPerceived::Aromaticity OEChem::OEPerceived::AtomStereo OEChem::OEPerceived::BondStereo OEChem::OEPerceived::Chains OEChem::OEPerceived::Chiral OEChem::OEPerceived::Energy OEChem::OEPerceived::Hybridization OEChem::OEPerceived::PartialCharges OEChem::OEPerceived::RingAtomsAndBonds OEChem::OEPerceived::SecondaryStructure OEChem::OEPerceiveResidues OEChem::OEPerceiveSymmetry OEChem::OEPRECompress OEChem::OEPredicateParameter Constructors GetDefault GetSetting GetValue operator= SetDefault SetValue OEChem::OEPrepareSearch OEChem::OEPreserveResInfo OEChem::OEPreserveResInfo::All OEChem::OEPreserveResInfo::AlternateLocation OEChem::OEPreserveResInfo::AtomName OEChem::OEPreserveResInfo::BFactor OEChem::OEPreserveResInfo::ChainID OEChem::OEPreserveResInfo::Default OEChem::OEPreserveResInfo::FragmentNumber OEChem::OEPreserveResInfo::HetAtom OEChem::OEPreserveResInfo::InsertCode OEChem::OEPreserveResInfo::None OEChem::OEPreserveResInfo::Occupancy OEChem::OEPreserveResInfo::ResidueName OEChem::OEPreserveResInfo::ResidueNumber OEChem::OEPreserveResInfo::SerialNumber OEChem::OEPreserveRotCompress OEChem::OEProperty OEChem::OEProperty::Acceptor OEChem::OEProperty::All OEChem::OEProperty::Anisou OEChem::OEProperty::Aromatic OEChem::OEProperty::AroModel OEChem::OEProperty::AtomMemberPred OEChem::OEProperty::AtomName OEChem::OEProperty::AtomTypeInt OEChem::OEProperty::AtomTypes OEChem::OEProperty::AtomTypeString OEChem::OEProperty::BondMemberPred OEChem::OEProperty::BondOrders OEChem::OEProperty::BondStereo OEChem::OEProperty::BondTypeString OEChem::OEProperty::Both OEChem::OEProperty::Chiral OEChem::OEProperty::Chirality OEChem::OEProperty::Closure OEChem::OEProperty::ClosureBonds OEChem::OEProperty::Component OEChem::OEProperty::Degree OEChem::OEProperty::Deleted OEChem::OEProperty::DeletedAtoms OEChem::OEProperty::DeletedBonds OEChem::OEProperty::Dimension OEChem::OEProperty::Donor OEChem::OEProperty::Double OEChem::OEProperty::Endo OEChem::OEProperty::Exo OEChem::OEProperty::Hybridization OEChem::OEProperty::HydrogenMode OEChem::OEProperty::Isotope OEChem::OEProperty::Kekule OEChem::OEProperty::MapIdx OEChem::OEProperty::MatchOrder OEChem::OEProperty::OEBase OEChem::OEProperty::PartialCharge OEChem::OEProperty::PartialChargeModel OEChem::OEProperty::Perceived OEChem::OEProperty::PhCorrected OEChem::OEProperty::Radius OEChem::OEProperty::Residue OEChem::OEProperty::Ring OEChem::OEProperty::RingAtomsAndBonds OEChem::OEProperty::Rotor OEChem::OEProperty::Rxn OEChem::OEProperty::RxnRole OEChem::OEProperty::Single OEChem::OEProperty::StereoDefined OEChem::OEProperty::SymClass OEChem::OEProperty::Triple OEChem::OEProperty::Undefined OEChem::OEProperty::Valence OEChem::OEProperty::Visit OEChem::OEProperty::X OEChem::OEProperty::Y OEChem::OEProperty::Z OEChem::OEProteinColorScheme OEChem::OEProteinColorScheme::AtomColor OEChem::OEProteinColorScheme::BEGIN OEChem::OEProteinColorScheme::END OEChem::OEProteinStyle OEChem::OEProteinStyle::Backbone OEChem::OEProteinStyle::BEGIN OEChem::OEProteinStyle::CAlpha OEChem::OEProteinStyle::END OEChem::OEProteinStyle::Off OEChem::OEProteinStyle::Ribbons OEChem::OEQAtomBase GetParentAtom GetQAtoms GetQBonds IsDataType OEChem::OEQBase GetExpr SetExpr OEChem::OEQBondBase GetParentBond IsDataType OEChem::OEQMol BuildExpressions Constructors GetQAtoms GetQBonds operator OEMolBase & operator OEQMolBase & operator= QMol SCMol OEChem::OEQMolBase BuildExpressions Constructors CreateCopy GetQAtoms GetQBonds IsDataType operator= OEChem::OEQMolType OEChem::OEQMolType::MaxType OEChem::OEQMolType::OEDefault OEChem::OEQMolType::Undefined OEChem::OEQuaternion Constructors CreateCopy Extract GetInverse GetQuaternion operator= OEChem::OERadiiType OEChem::OERadiiType::BondiHVdw OEChem::OERadiiType::BondiVdw OEChem::OERadiiType::Covalent OEChem::OERadiiType::Default OEChem::OERadiiType::Delphi OEChem::OERadiiType::Delphi_Robust OEChem::OERadiiType::HonigIonicCavity OEChem::OERadiiType::HonigIonicCavity_Robust OEChem::OERadiiType::Max OEChem::OERadiiType::None OEChem::OERadiiType::PaulingVdw OEChem::OERadiiType::PaulingVdw_Robust OEChem::OERadiiType::Zap7 OEChem::OERadiiType::Zap7_CarbonylOxygen OEChem::OERadiiType::Zap7_DoublyBondedOxygen OEChem::OERadiiType::Zap9 OEChem::OERadiiType::Zap9_JCAMD2010 OEChem::OERadiiType::Zap9_JMC2008 OEChem::OERandomizeTorsions OEChem::OEReadCDXFile OEChem::OEReadCIFFile OEChem::OEReadCSVFile OEChem::OEReadCSVHeader OEChem::OEReadFASTAFile OEChem::OEReadMacroModelFile OEChem::OEReadMDLFile OEChem::OEReadMDLQueryFile OEChem::OEReadMDLReactionQueryFile OEChem::OEReadMol2File OEChem::OEReadMolecule OEChem::OEReadMolFromByteArray OEChem::OEReadMOPACFile OEChem::OEReadOEBFile OEChem::OEReadPDBFile OEChem::OEReadRxnFile OEChem::OEReadSketchFile OEChem::OEReadXYZFile OEChem::OERefInputAppOptions Constructors GetInFile GetOutFile GetRefFile operator= SetInFile SetOutFile SetRefFile OEChem::OEResidue Constructors GetAlternateLocation GetBFactor GetChainID GetEntityID GetExtChainID GetFragmentNumber GetInsertCode GetModelNumber GetName GetOccupancy GetResidueNumber GetSecondaryStructure GetSequenceID GetSerialNumber GetSubChainID IsHetAtom operator bool operator= SetAlternateLocation SetBFactor SetChainID SetEntityID SetExtChainID SetFragmentNumber SetHetAtom SetInsertCode SetModelNumber SetName SetOccupancy SetResidueNumber SetSecondaryStructure SetSequenceID SetSerialNumber SetSubChainID OEChem::OEResidueHydrogens OEChem::OEResidueIndex OEChem::OEResidueIndex::_1MA OEChem::OEResidueIndex::_2MG OEChem::OEResidueIndex::_3NI OEChem::OEResidueIndex::_4MO OEChem::OEResidueIndex::_4TI OEChem::OEResidueIndex::_5MC OEChem::OEResidueIndex::_5MU OEChem::OEResidueIndex::_6MO OEChem::OEResidueIndex::_7MG OEChem::OEResidueIndex::A OEChem::OEResidueIndex::ABA OEChem::OEResidueIndex::ACE OEChem::OEResidueIndex::ADP OEChem::OEResidueIndex::AF3 OEChem::OEResidueIndex::ALA OEChem::OEResidueIndex::ALF OEChem::OEResidueIndex::ARG OEChem::OEResidueIndex::ASH OEChem::OEResidueIndex::ASN OEChem::OEResidueIndex::ASP OEChem::OEResidueIndex::ASX OEChem::OEResidueIndex::ATP OEChem::OEResidueIndex::AU OEChem::OEResidueIndex::AU3 OEChem::OEResidueIndex::BME OEChem::OEResidueIndex::BR OEChem::OEResidueIndex::C OEChem::OEResidueIndex::CGU OEChem::OEResidueIndex::CIM OEChem::OEResidueIndex::CIP OEChem::OEResidueIndex::CL OEChem::OEResidueIndex::CME OEChem::OEResidueIndex::CO OEChem::OEResidueIndex::CO3 OEChem::OEResidueIndex::CSD OEChem::OEResidueIndex::CU OEChem::OEResidueIndex::CU1 OEChem::OEResidueIndex::CYH OEChem::OEResidueIndex::CYM OEChem::OEResidueIndex::CYS OEChem::OEResidueIndex::CYX OEChem::OEResidueIndex::DA OEChem::OEResidueIndex::DC OEChem::OEResidueIndex::DG OEChem::OEResidueIndex::DI OEChem::OEResidueIndex::DMS OEChem::OEResidueIndex::DU OEChem::OEResidueIndex::EDO OEChem::OEResidueIndex::EOH OEChem::OEResidueIndex::EU OEChem::OEResidueIndex::EU3 OEChem::OEResidueIndex::FAD OEChem::OEResidueIndex::FE OEChem::OEResidueIndex::FE2 OEChem::OEResidueIndex::FOR OEChem::OEResidueIndex::G OEChem::OEResidueIndex::GLH OEChem::OEResidueIndex::GLN OEChem::OEResidueIndex::GLU OEChem::OEResidueIndex::GLX OEChem::OEResidueIndex::GLY OEChem::OEResidueIndex::GOL OEChem::OEResidueIndex::H2U OEChem::OEResidueIndex::HEM OEChem::OEResidueIndex::HID OEChem::OEResidueIndex::HIE OEChem::OEResidueIndex::HIP OEChem::OEResidueIndex::HIS OEChem::OEResidueIndex::HOH OEChem::OEResidueIndex::HSE OEChem::OEResidueIndex::HYL OEChem::OEResidueIndex::HYP OEChem::OEResidueIndex::I OEChem::OEResidueIndex::ILE OEChem::OEResidueIndex::IOD OEChem::OEResidueIndex::IR OEChem::OEResidueIndex::IR3 OEChem::OEResidueIndex::LEU OEChem::OEResidueIndex::LIG OEChem::OEResidueIndex::LYN OEChem::OEResidueIndex::LYS OEChem::OEResidueIndex::LYZ OEChem::OEResidueIndex::M2G OEChem::OEResidueIndex::MEN OEChem::OEResidueIndex::MET OEChem::OEResidueIndex::MLE OEChem::OEResidueIndex::MLY OEChem::OEResidueIndex::MN OEChem::OEResidueIndex::MN3 OEChem::OEResidueIndex::MOH OEChem::OEResidueIndex::MOL OEChem::OEResidueIndex::MSE OEChem::OEResidueIndex::NAD OEChem::OEResidueIndex::NAG OEChem::OEResidueIndex::NHE OEChem::OEResidueIndex::NI OEChem::OEResidueIndex::NME OEChem::OEResidueIndex::OMC OEChem::OEResidueIndex::OMG OEChem::OEResidueIndex::ORN OEChem::OEResidueIndex::OS OEChem::OEResidueIndex::OS4 OEChem::OEResidueIndex::PCA OEChem::OEResidueIndex::PEO OEChem::OEResidueIndex::PER OEChem::OEResidueIndex::PHE OEChem::OEResidueIndex::PO2 OEChem::OEResidueIndex::PO4 OEChem::OEResidueIndex::PRO OEChem::OEResidueIndex::PSU OEChem::OEResidueIndex::PT OEChem::OEResidueIndex::PT4 OEChem::OEResidueIndex::PTR OEChem::OEResidueIndex::RU OEChem::OEResidueIndex::SAR OEChem::OEResidueIndex::SB OEChem::OEResidueIndex::SEP OEChem::OEResidueIndex::SER OEChem::OEResidueIndex::SO2 OEChem::OEResidueIndex::SO4 OEChem::OEResidueIndex::SX OEChem::OEResidueIndex::T OEChem::OEResidueIndex::TAU OEChem::OEResidueIndex::THR OEChem::OEResidueIndex::TPO OEChem::OEResidueIndex::TRP OEChem::OEResidueIndex::TYM OEChem::OEResidueIndex::TYR OEChem::OEResidueIndex::U OEChem::OEResidueIndex::UNK OEChem::OEResidueIndex::UNL OEChem::OEResidueIndex::V OEChem::OEResidueIndex::VAL OEChem::OEResidueIndex::Y1 OEChem::OEResidueIndex::YB OEChem::OEResidueIndex::YB2 OEChem::OEResidueIndex::YG OEChem::OEResidueIndex::YT3 OEChem::OEResidueToString OEChem::OERGroupsToHydrogens OEChem::OERingBondCount OEChem::OERMSD OEChem::OERotate OEChem::OERotMatrix Constructors CreateCopy Extract GetInverse GetRotMatrix operator= OEChem::OERxnAutomapMethod OEChem::OERxnAutomapMethod::DEFAULT OEChem::OERxnAutomapMethod::MCSMapping OEChem::OERxnAutomapper AutoMapRxn Constructors GetOptions operator= OEChem::OERxnAutomapperOptions Constructors GetClearMapping GetExtendMappedRegions GetMappingMethod GetMCSExhaustiveMode GetStrictMapping operator= SetClearMapping SetExtendMappedRegions SetMappingMethod SetMCSExhaustiveMode SetStrictMapping OEChem::OERxnAutomapStatus OEChem::OERxnAutomapStatus::Failure OEChem::OERxnAutomapStatus::InvalidComponents OEChem::OERxnAutomapStatus::InvalidMethod OEChem::OERxnAutomapStatus::NonReactionInput OEChem::OERxnAutomapStatus::Success OEChem::OERxnRole OEChem::OERxnRole::Agent OEChem::OERxnRole::Catalyst OEChem::OERxnRole::None OEChem::OERxnRole::Product OEChem::OERxnRole::Reactant OEChem::OESameChain OEChem::OESameResidue OEChem::OESameSubSearchScreenTypes OEChem::OEScrambleMolecule OEChem::OEScreen OEChem::OESDDataPair Constructors GetTag GetValue SetTag SetValue OEChem::OESet2DHydrogenGeom OEChem::OESet3DHydrogenGeom OEChem::OESetAngle OEChem::OESetAnisou OEChem::OESetAtomComment OEChem::OESetCIPStereo OEChem::OESetComment OEChem::OESetDefaultFlavors OEChem::OESetDefaultIFlavors OEChem::OESetDefaultOFlavors OEChem::OESetDimensionFromCoords OEChem::OESetDistance OEChem::OESetMCSExhaustiveSearchTruncationLimit OEChem::OESetMDLDimensionFromCoords OEChem::OESetMMCIFData OEChem::OESetOEGraphMol OEChem::OESetOEMol OEChem::OESetOEQMol OEChem::OESetPackedCoords OEChem::OESetPDBData OEChem::OESetSDData OEChem::OESetStyle OEChem::OESetStyleIndex OEChem::OESetTorsion OEChem::OEShortestPath OEChem::OESimilarByRMSD Constructors CreateCopy operator() operator= OEChem::OESimpleAppOptions Constructors GetInFile GetOutFile operator= SetInFile SetOutFile OEChem::OESingleBondCount OEChem::OESLNFlag OEChem::OESLNFlag::Canonical OEChem::OESLNFlag::Coords2D OEChem::OESLNFlag::Coords3D OEChem::OESLNFlag::DEFAULT OEChem::OESLNFlag::FCharge OEChem::OESLNFlag::Hydrogens OEChem::OESLNFlag::Isotopes OEChem::OESLNFlag::Kekule OEChem::OESLNFlag::Name OEChem::OESMARTSAtomFlag OEChem::OESMARTSAtomFlag::AAmap OEChem::OESMARTSAtomFlag::AnyAtomType OEChem::OESMARTSAtomFlag::AtomAll OEChem::OESMARTSAtomFlag::AtomDefault OEChem::OESMARTSAtomFlag::AtomExact OEChem::OESMARTSAtomFlag::AtomType OEChem::OESMARTSAtomFlag::Charge OEChem::OESMARTSAtomFlag::Charge0 OEChem::OESMARTSAtomFlag::Chirality OEChem::OESMARTSAtomFlag::Connectivity OEChem::OESMARTSAtomFlag::DEFAULT OEChem::OESMARTSAtomFlag::DegreeCount OEChem::OESMARTSAtomFlag::HCount OEChem::OESMARTSAtomFlag::HCount0 OEChem::OESMARTSAtomFlag::Hybridization OEChem::OESMARTSAtomFlag::IgnoreArom OEChem::OESMARTSAtomFlag::ImplicitHCount OEChem::OESMARTSAtomFlag::ImplicitHCount0 OEChem::OESMARTSAtomFlag::Isotope OEChem::OESMARTSAtomFlag::LeavingGroup OEChem::OESMARTSAtomFlag::RingBondCount OEChem::OESMARTSAtomFlag::Valence OEChem::OESMARTSBondFlag OEChem::OESMARTSBondFlag::AnyBondType OEChem::OESMARTSBondFlag::AromBondType OEChem::OESMARTSBondFlag::BondAll OEChem::OESMARTSBondFlag::BondDefault OEChem::OESMARTSBondFlag::BondExact OEChem::OESMARTSBondFlag::BondTopo OEChem::OESMARTSBondFlag::BondType OEChem::OESMARTSBondFlag::Chirality OEChem::OESMARTSBondFlag::DEFAULT OEChem::OESmartsLexReplace OEChem::OESmartsParseOpts OEChem::OESmartsParseOpts::Default OEChem::OESmartsParseOpts::None OEChem::OESmartsParseOpts::Optimize OEChem::OESmartsParseOpts::RingConstraint OEChem::OESmilesAtomCount OEChem::OESMILESFlag OEChem::OESMILESFlag::AllBonds OEChem::OESMILESFlag::AtomMaps OEChem::OESMILESFlag::AtomStereo OEChem::OESMILESFlag::BondStereo OEChem::OESMILESFlag::Canonical OEChem::OESMILESFlag::DEFAULT OEChem::OESMILESFlag::EnhStereo OEChem::OESMILESFlag::ExtBonds OEChem::OESMILESFlag::Hydrogens OEChem::OESMILESFlag::ImpHCount OEChem::OESMILESFlag::ISOMERIC OEChem::OESMILESFlag::Isotopes OEChem::OESMILESFlag::Kekule OEChem::OESMILESFlag::RGroups OEChem::OESMILESFlag::SuperAtoms OEChem::OESmilesToMol OEChem::OESortConfsBySDTag OEChem::OESortConfsByTag OEChem::OEString2OEAtomExpr OEChem::OEString2OEBondExpr OEChem::OEStyleGridType OEChem::OEStyleGridType::BEGIN OEChem::OEStyleGridType::Electrostatic OEChem::OEStyleGridType::END OEChem::OESubSearch AddConstraint AtomMatch ClearConstraints Constructors GetMaxMatches GetPattern Init Match operator bool operator= SetMaxMatches SingleMatch OEChem::OESubSearchDatabase Constructors GetDatabaseType GetMatchIndices GetMatchTitles GetMolecule GetScreenType GetTitle IsValid NumMatches NumMolecules NumProcessors Open Search OEChem::OESubSearchDatabaseType OEChem::OESubSearchDatabaseType::Default OEChem::OESubSearchDatabaseType::InMemoryMultiThreaded OEChem::OESubSearchDatabaseType::MolDatabaseMultiThreaded OEChem::OESubSearchQuery Constructors GetMaxMatches SetFilter SetMaxMatches OEChem::OESubSearchResult Cancel Constructors GetMatchIndices GetSearchStatus IsValid NumMatches NumScreened NumSearched NumTargets NumTotalMatches OEChem::OESubSearchScreen Constructors GetScreenType IsValid operator= OEChem::OESubSearchScreenType OEChem::OESubSearchScreenType::Default OEChem::OESubSearchScreenType::MDL OEChem::OESubSearchScreenType::Molecule OEChem::OESubSearchScreenType::SMARTS OEChem::OESubSearchScreenTypeBase GetName GetScreenType GetScreenTypeString GetSize GetVersion GetVersionString OEChem::OESubSearchStatus OEChem::OESubSearchStatus::Canceled OEChem::OESubSearchStatus::Finished OEChem::OESubSearchStatus::InProgress OEChem::OESubSearchStatus::Uninitialized OEChem::OESubSearchStatusToName OEChem::OESubsetMol OEChem::OESuppressHydrogens OEChem::OESurfaceColorScheme OEChem::OESurfaceColorScheme::AtomColor OEChem::OESurfaceColorScheme::BEGIN OEChem::OESurfaceColorScheme::Concavity OEChem::OESurfaceColorScheme::Curvature OEChem::OESurfaceColorScheme::Distance OEChem::OESurfaceColorScheme::Electrostatic OEChem::OESurfaceColorScheme::END OEChem::OESurfaceColorScheme::GenericData OEChem::OESurfaceColorScheme::Grid OEChem::OESurfaceColorScheme::HBondPotential OEChem::OESurfaceColorScheme::Hydrophobicity OEChem::OESurfaceColorScheme::Solid OEChem::OESurfaceColorScheme::SurfacePotential OEChem::OESurfaceStyle OEChem::OESurfaceStyle::BEGIN OEChem::OESurfaceStyle::END OEChem::OESurfaceStyle::Mesh OEChem::OESurfaceStyle::Points OEChem::OESurfaceStyle::Solid OEChem::OESurfaceType OEChem::OESurfaceType::Accessible OEChem::OESurfaceType::BEGIN OEChem::OESurfaceType::END OEChem::OESurfaceType::Molecular OEChem::OESurfaceType::Off OEChem::OESurfaceType::VDW OEChem::OESweepRotorCompressHydrogens OEChem::OESweepStyles OEChem::OESymmetryNumber OEChem::OETerminalOCount OEChem::OETerminalSCount OEChem::OETheFunctionFormerlyKnownAsStripSalts OEChem::OETokenizerBase GetNextToken ParseTitle OEChem::OETorsion Constructors OEChem::OETrans Clear Compress Constructors Extract GetInverse GetTransforms operator bool operator+= operator= PushBack PushFront Transform OEChem::OETransBase CreateCopy Extract GetInverse Transform OEChem::OETranslate OEChem::OETranslation Constructors CreateCopy Extract GetInverse GetTranslation operator+= operator= OEChem::OETrimConformers OEChem::OETripleBondCount OEChem::OETriposAtomNames OEChem::OETriposAtomType OEChem::OETriposAtomTypeNames OEChem::OETriposAtomTypes OEChem::OETriposBondTypeNames OEChem::OETriposOrderAtoms OEChem::OETriposResonantTypeNames OEChem::OETriposType OEChem::OETriposType::Al OEChem::OETriposType::Br OEChem::OETriposType::C1 OEChem::OETriposType::C2 OEChem::OETriposType::C3 OEChem::OETriposType::Ca OEChem::OETriposType::Car OEChem::OETriposType::Ccat OEChem::OETriposType::Cl OEChem::OETriposType::Cooh OEChem::OETriposType::Croh OEChem::OETriposType::Crth OEChem::OETriposType::Cu OEChem::OETriposType::Du OEChem::OETriposType::F OEChem::OETriposType::Fe OEChem::OETriposType::H OEChem::OETriposType::I OEChem::OETriposType::K OEChem::OETriposType::Li OEChem::OETriposType::Lp OEChem::OETriposType::MAXTYPE OEChem::OETriposType::Mg OEChem::OETriposType::Mn OEChem::OETriposType::Mo OEChem::OETriposType::N1 OEChem::OETriposType::N2 OEChem::OETriposType::N3 OEChem::OETriposType::N4 OEChem::OETriposType::Na OEChem::OETriposType::Nam OEChem::OETriposType::Nar OEChem::OETriposType::Npl3 OEChem::OETriposType::O2 OEChem::OETriposType::O3 OEChem::OETriposType::Oco2 OEChem::OETriposType::P3 OEChem::OETriposType::S2 OEChem::OETriposType::S3 OEChem::OETriposType::Se OEChem::OETriposType::Si OEChem::OETriposType::Sn OEChem::OETriposType::So OEChem::OETriposType::So2 OEChem::OETriposType::Zn OEChem::OETriposTypeElement OEChem::OETriposTypeIndex OEChem::OETriposTypeName OEChem::OETriposTypeNames OEChem::OEUnaryToBinaryAnd Constructors CreateCopy operator() OEChem::OEUnaryToBinaryOr Constructors CreateCopy operator() OEChem::OEUnAtomPredParameter Constructors operator= OEChem::OEUnBondPredParameter Constructors operator= OEChem::OEUncolorMol OEChem::OEUncolorStrategy OEChem::OEUncolorStrategy::BemisMurcko OEChem::OEUncolorStrategy::ConvertAtomTypeToC OEChem::OEUncolorStrategy::ConvertBondTypeToSingle OEChem::OEUncolorStrategy::Default OEChem::OEUncolorStrategy::RemoveAtomProperties OEChem::OEUncolorStrategy::RemoveAtomStereo OEChem::OEUncolorStrategy::RemoveBondStereo OEChem::OEUncolorStrategy::RemoveDimension OEChem::OEUncolorStrategy::RemoveGroupStereo OEChem::OEUncolorStrategy::UncolorNone OEChem::OEUniMolecularRxn Constructors GetClearCoordinates GetOptions GetValidateKekule Init operator bool operator() operator= SetClearCoordinates SetValidateKekule OEChem::OEUniMolecularRxnFixValence OEChem::OEUniMolecularRxnFixValence::All OEChem::OEUniMolecularRxnFixValence::Altered OEChem::OEUniMolecularRxnFixValence::DEFAULT OEChem::OEUniMolecularRxnFixValence::Default OEChem::OEUniMolecularRxnFixValence::Explicit OEChem::OEUniMolecularRxnOptions Constructors GetAlteredTag GetClearCoordinates GetFixValence GetMaxMatches GetStrictSmirks GetValidateKekule operator= SetAlteredTag SetClearCoordinates SetFixValence SetMaxMatches SetStrictSmirks SetValidateKekule OEChem::OEVectorBindings Add Constructors Get operator= OEChem::OEWeightedRMSD OEChem::OEWrite2DRingDictionary OEChem::OEWriteCDXFile OEChem::OEWriteCIFFile OEChem::OEWriteConstMolecule OEChem::OEWriteCSVFile OEChem::OEWriteCSVHeader OEChem::OEWriteFASTAFile OEChem::OEWriteMacroModelFile OEChem::OEWriteMDLFile OEChem::OEWriteMol2File OEChem::OEWriteMolecule OEChem::OEWriteMolReturnCode OEChem::OEWriteMolReturnCode::FormatNotWritable OEChem::OEWriteMolReturnCode::InvalidSDData OEChem::OEWriteMolReturnCode::MolInvalidForFileFormatSpec OEChem::OEWriteMolReturnCode::NoConformer OEChem::OEWriteMolReturnCode::OEBWriteFailure OEChem::OEWriteMolReturnCode::Success OEChem::OEWriteMolReturnCode::TooManyAtoms OEChem::OEWriteMolToByteArray OEChem::OEWriteMOPACInputFile OEChem::OEWritePDBFile OEChem::OEWriteXYZFile OEChem::OEZap7Version OEChem::OEZap7Version::CarbonylOxygen OEChem::OEZap7Version::Default OEChem::OEZap7Version::DoublyBondedOxygen OEChem::OEZap7Version::Undefined OEChem::OEZap9Version OEChem::OEZap9Version::Default OEChem::OEZap9Version::JCAMD2010 OEChem::OEZap9Version::JMC2008 OEChem::OEZap9Version::Undefined oecheminfo.java Example Code OECombineMolComplexFragments OEConfGen::OEAddGlobalFragLib OEConfGen::OEBuilderBase AddFragLib ClearFragLibs OEConfGen::OEClearGlobalFragLib OEConfGen::OEConfFixOptions Constructors GetAtomExpr GetBondExpr GetFixDeleteH GetFixMaxMatch GetFixMCS GetFixMol GetFixPredicate GetFixRMS GetFixSmarts GetFixSubSearch GetFixUniqueMatch GetMCSFunc GetMCSMinAtoms GetMCSType HasFixPattern operator= SetAtomExpr SetBondExpr SetFixDeleteH SetFixMaxMatch SetFixMCS SetFixMol SetFixPredicate SetFixRMS SetFixSmarts SetFixSubSearch SetFixUniqueMatch SetMCSFunc SetMCSMinAtoms SetMCSType OEConfGen::OEConformerBuilder Build Constructors operator= OEConfGen::OEConfSlicer Constructors operator= Slice OEConfGen::OEFlipper OEConfGen::OEFlipperClassicOptions Constructors GetAtomPredicate GetBondPredicate GetEnhancedStereo GetEnumBridgehead GetEnumEZ GetEnumNitrogen GetEnumRS GetEnumSpecifiedStereo GetMaxCenters GetWarts operator= SetAtomPredicate SetBondPredicate SetEnhancedStereo SetEnumBridgehead SetEnumEZ SetEnumNitrogen SetEnumRS SetEnumSpecifiedStereo SetMaxCenters SetWarts OEConfGen::OEFlipperOptions Constructors GetAtomPredicate GetBondPredicate GetEnhancedStereo GetEnumAtoms GetEnumAtomSpecifiedStereo GetEnumBonds GetEnumBondSpecifiedStereo GetEnumBridgehead GetEnumEZ GetEnumNitrogen GetEnumRelativeAtomStereo GetEnumRS GetEnumSpecifiedStereo GetMaxCenters GetWarts operator= SetAtomPredicate SetBondPredicate SetEnhancedStereo SetEnumAtoms SetEnumAtomSpecifiedStereo SetEnumBonds SetEnumBondSpecifiedStereo SetEnumBridgehead SetEnumEZ SetEnumNitrogen SetEnumRelativeAtomStereo SetEnumRS SetEnumSpecifiedStereo SetMaxCenters SetWarts OEConfGen::OEFlipperStereoCenters OEConfGen::OEFragBuilder Build Constructors GetOptions operator= SetOptions OEConfGen::OEFragBuilderMode OEConfGen::OEFragBuilderMode::Default OEConfGen::OEFragBuilderMode::Dense OEConfGen::OEFragBuilderMode::Fast OEConfGen::OEFragBuilderMode::Strict OEConfGen::OEFragBuilderOptions Constructors GetForceField GetMacroCycOptions GetNonRingOptions GetRingOptions operator= SetForceField SetMacroCycOptions SetNonRingOptions SetRingOptions OEConfGen::OEFragOptions Constructors GetEnergyWindow GetFragGen GetFragKeep GetRMS GetTimeLimit operator= SetEnergyWindow SetFragGen SetFragKeep SetRMS SetTimeLimit OEConfGen::OEGetOmegaError OEConfGen::OEGetTorValues OEConfGen::OEIsMacrocycle OEConfGen::OEMacrocycleBuilder Build Constructors GetOptions operator= SetOptions OEConfGen::OEMacrocycleBuilderOptions Constructors GetDielectricConst GetRandomSeed GetRefTolerance GetSkipRefinement operator= SetDielectricConst SetRandomSeed SetRefTolerance SetSkipRefinement OEConfGen::OEMacrocycleOmega Build Constructors GetOptions operator= SetOptions OEConfGen::OEMacrocycleOmegaOptions Constructors GetEnergyWindow GetIterCycleSize GetMacrocycleBuilderOptions GetMaxConfs GetMaxIter GetSliceEnsembleOptions operator= SetEnergyWindow SetIterCycleSize SetMacrocycleBuilderOptions SetMaxConfs SetMaxIter SetSliceEnsembleOptions OEConfGen::OEMakeFragLib AddFrag Constructors GenerateMissingFrags GetMissingFrags operator= OEConfGen::OEMolBuilder Build Constructors GetOptions operator= Prep SetOptions OEConfGen::OEMolBuilderOptions Constructors GetCanonOrder GetEnumNitrogen GetEnumRing GetFragBuilderOptions GetFromCT GetIgnoreStereo GetMaxEnumConfs GetSampleHydrogens GetStrictAtomTypes operator= SetCanonOrder SetEnumNitrogen SetEnumRing SetFragBuilderMode SetFragBuilderOptions SetFromCT SetIgnoreStereo SetMaxEnumConfs SetSampleHydrogens SetStrictAtomTypes OEConfGen::OENitrogenEnumeration OEConfGen::OENitrogenEnumeration::All OEConfGen::OENitrogenEnumeration::Default OEConfGen::OENitrogenEnumeration::Off OEConfGen::OENitrogenEnumeration::Unspecified OEConfGen::OEOmega AddFragLib Build ClearFragLibs Constructors GetOptions operator= SetOptions OEConfGen::OEOmegaForceFieldType OEConfGen::OEOmegaForceFieldType::Invalid OEConfGen::OEOmegaForceFieldType::MMFF OEConfGen::OEOmegaForceFieldType::MMFF94S OEConfGen::OEOmegaForceFieldType::MMFF94S_NOESTAT OEConfGen::OEOmegaForceFieldType::MMFF94S_SHEFF OEConfGen::OEOmegaForceFieldType::MMFF94S_TRUNC OEConfGen::OEOmegaForceFieldType::MMFF94Smod OEConfGen::OEOmegaForceFieldType::MMFF94Smod_NOESTAT OEConfGen::OEOmegaForceFieldType::MMFF94Smod_SHEFF OEConfGen::OEOmegaForceFieldType::MMFF94Smod_TRUNC OEConfGen::OEOmegaForceFieldType::MMFF_NOESTAT OEConfGen::OEOmegaForceFieldType::MMFF_SHEFF OEConfGen::OEOmegaForceFieldType::MMFF_TRUNC OEConfGen::OEOmegaForceFieldType::SAGE OEConfGen::OEOmegaForceFieldType::SAGE_NOESTAT OEConfGen::OEOmegaForceFieldType::SAGE_SHEFF OEConfGen::OEOmegaGetArch OEConfGen::OEOmegaGetLibraryRelease OEConfGen::OEOmegaGetLibraryVersion OEConfGen::OEOmegaGetLicensee OEConfGen::OEOmegaGetPlatform OEConfGen::OEOmegaGetRelease OEConfGen::OEOmegaGetSite OEConfGen::OEOmegaGetVersion OEConfGen::OEOmegaIsGPUReady OEConfGen::OEOmegaIsLicensed OEConfGen::OEOmegaOptions Constructors GetConfFixOptions GetEnergyWindow GetIncludeInput GetMaxConfs GetMolBuilderOptions GetSliceEnsembleOptions GetStrictStereo GetTorDriveOptions GetTorsionDrive GetWarts operator= SetConfFixOptions SetEnergyWindow SetIncludeInput SetMaxConfs SetMolBuilderOptions SetSliceEnsembleOptions SetStrictStereo SetTorDriveOptions SetTorsionDrive SetWarts OEConfGen::OEOmegaReturnCode OEConfGen::OEOmegaReturnCode::ExceedsAtomDegree4 OEConfGen::OEOmegaReturnCode::ExplicitHydrogens OEConfGen::OEOmegaReturnCode::Failed OEConfGen::OEOmegaReturnCode::FailedCharges OEConfGen::OEOmegaReturnCode::FailedCTBuild OEConfGen::OEOmegaReturnCode::FailedDGConfGen OEConfGen::OEOmegaReturnCode::FailedDupSetup OEConfGen::OEOmegaReturnCode::FailedFixMatch OEConfGen::OEOmegaReturnCode::FailedSmartMatch OEConfGen::OEOmegaReturnCode::FailedTorAssign OEConfGen::OEOmegaReturnCode::FailedTorDrive OEConfGen::OEOmegaReturnCode::InvalidOptions OEConfGen::OEOmegaReturnCode::MissingFFParams OEConfGen::OEOmegaReturnCode::No3DFromCT OEConfGen::OEOmegaReturnCode::No3DTorDrive OEConfGen::OEOmegaReturnCode::NoFixedFragment OEConfGen::OEOmegaReturnCode::NoValidConfs OEConfGen::OEOmegaReturnCode::Success OEConfGen::OEOmegaReturnCode::TooManyRotors OEConfGen::OEOmegaReturnCode::UnspecifiedStereo OEConfGen::OEOmegaSampling OEConfGen::OEOmegaSampling::Classic OEConfGen::OEOmegaSampling::Dense OEConfGen::OEOmegaSampling::FastROCS OEConfGen::OEOmegaSampling::Pose OEConfGen::OEOmegaSampling::ROCS OEConfGen::OEOmegaSystemHasGPU OEConfGen::OERingFragOptions Constructors GetStartFactor operator= SetStartFactor OEConfGen::OESliceEnsemble OEConfGen::OESliceEnsembleDefaults OEConfGen::OESliceEnsembleDefaults::EWindow OEConfGen::OESliceEnsembleDefaults::MaxConfs OEConfGen::OESliceEnsembleDefaults::RMS OEConfGen::OESliceEnsembleOptions Constructors GetEnergyRange GetEnergyWindow GetMaxConfRange GetMaxConfs GetMaxTerminalHeavy GetRangeIncrement GetRMSRange GetRMSThreshold operator= SetEnergyRange SetEnergyWindow SetMaxConfRange SetMaxConfs SetMaxTerminalHeavy SetRangeIncrement SetRMSRange SetRMSThreshold OEConfGen::OEThompsonOptions Constructors GetBatchMaxRotors GetMaxTrials GetMaxTrialsRange GetPriorTemperature GetTrialsRangeIncrement operator= SetBatchMaxRotors SetMaxTrials SetMaxTrialsRange SetPriorTemperature SetTrialsRangeIncrement OEConfGen::OETorDriveOptions Constructors ExceedsMaxRotors GetCommentEnergy GetForceField GetMaxRotors GetMaxSearchTime GetRotorOffset GetRotorPredicate GetSDEnergy GetThompsonOptions GetTorLib GetUseGPU GetUseThompson operator= SetCommentEnergy SetForceField SetMaxRotors SetMaxSearchTime SetRotorOffset SetRotorPredicate SetSDEnergy SetThompsonOptions SetTorLib SetUseGPU SetUseThompson OEConfGen::OETorDriver Constructors GenerateConfs GetForceField GetSliceEnsembleOptions GetTorDriveOptions operator= SetForceField SetSliceEnsembleOptions SetTorDriveOptions OEConfGen::OETorLib AddTorsionLibrary AddTorsionRule ClearTorsionLibrary Constructors GetTorRule GetTorRules HasTorRule operator bool ResetTorsionLibrary SetTorsionLibrary OEConfGen::OETorLibParameter Constructors operator= OEConfGen::OETorLibType OEConfGen::OETorLibType::Default OEConfGen::OETorLibType::GubaV21 OEConfGen::OETorLibType::Original OEConfGen::Suboption Parameter Defaults OEConfIdxSelected OEConstr::OEDihedralQuadPenalty Constructors GetPenaltyConstant GetSpecifiedAngle operator= OEConstr::OEHarmonicPotential Constructors Get_dc Get_kc operator= Set Set_dc Set_kc OEDataFlow::OEBytes OEDataFlow::OEFieldMeta OEDataFlow::OEFieldTypeHandler get_name is_cacheable isPOD OEDataFlow::OEMakeMatchField OEDataFlow::OEMatchField OEDataFlow::OEMolRecord OEDataFlow::OERange OEDataFlow::OEReadRecord OEDataFlow::OERecord OEDataFlow::OERecordReturnCode OEDataFlow::OERecordReturnCode::MetadataMismatch OEDataFlow::OERecordReturnCode::NoValue OEDataFlow::OERecordReturnCode::NullValue OEDataFlow::OERecordReturnCode::OK OEDataFlow::OERecordReturnCode::TypeMismatch OEDataFlow::Types OEDepict::OE2DAtomDisplay Constructors CreateCopy GetCharge GetCoords GetHCount GetHPosition GetLabel GetLabelFont GetMass GetProperty GetPropertyFont GetPropertyOffset GetRadical HasLabel HasProperty operator= SetCharge SetCoords SetHCount SetHPosition SetLabel SetLabelFont SetMass SetProperty SetPropertyFont SetPropertyOffset SetRadical OEDepict::OE2DBondDisplay Constructors CreateCopy GetBgnPen GetDisplayPos GetDisplayType GetEndPen GetProperty GetPropertyFont GetPropertyOffset HasProperty operator= SetBgnPen SetDisplayPos SetDisplayType SetEndPen SetProperty SetPropertyFont SetPropertyOffset OEDepict::OE2DMolDisplay Constructors CreateCopy GetAtomDisplay GetAtomDisplays GetBondDisplay GetBondDisplays GetDataType GetHeight GetLayer GetOptions GetScale GetWidth IsDataType IsValid operator= OEDepict::OE2DMolDisplayOptions Constructors GetAromaticStyle GetAtomColor GetAtomColorStyle GetAtomLabelFont GetAtomLabelFontScale GetAtomPropertyFunctor GetAtomPropLabelFont GetAtomPropLabelFontScale GetAtomStereoStyle GetAtomSVGMarkupFunctor GetAtomVisibilityFunctor GetBackgroundColor GetBondColorStyle GetBondLineAtomLabelGapScale GetBondLineGapScale GetBondPropertyFunctor GetBondPropLabelFont GetBondPropLabelFontScale GetBondStereoStyle GetBondSVGMarkupFunctor GetBondWidthScaling GetDefaultBondPen GetExplicitAtomLabelAngle GetHeight GetHydrogenStyle GetMargin GetProtectiveGroupLabelFont GetProtectiveGroupStyle GetScale GetSuperAtomLabelFont GetSuperAtomStyle GetTitleFont GetTitleFontScale GetTitleHeight GetTitleLocation GetWidth HasProtectiveGroupStyle operator= SetAromaticStyle SetAtomColor SetAtomColorStyle SetAtomLabelFont SetAtomLabelFontScale SetAtomPropertyFunctor SetAtomPropLabelFont SetAtomPropLabelFontScale SetAtomStereoStyle SetAtomSVGMarkupFunctor SetAtomVisibilityFunctor SetBackgroundColor SetBondColorStyle SetBondLineAtomLabelGapScale SetBondLineGapScale SetBondPropertyFunctor SetBondPropLabelFont SetBondPropLabelFontScale SetBondStereoStyle SetBondSVGMarkupFunctor SetBondWidthScaling SetDefaultBondPen SetDimensions SetExplicitAtomLabelAngle SetHeight SetHydrogenStyle SetMargin SetMargins SetProtectiveGroupLabelFont SetProtectiveGroupStyle SetScale SetSuperAtomLabelFont SetSuperAtomStyle SetTitleFont SetTitleFontScale SetTitleHeight SetTitleLocation SetWidth OEDepict::OE2DMolDisplaySetup OEDepict::OE2DMolDisplaySetup::All OEDepict::OE2DMolDisplaySetup::AromaticStyle OEDepict::OE2DMolDisplaySetup::AtomColorStyle OEDepict::OE2DMolDisplaySetup::AtomPropDisplay OEDepict::OE2DMolDisplaySetup::AtomStereoStyle OEDepict::OE2DMolDisplaySetup::BondColorStyle OEDepict::OE2DMolDisplaySetup::BondPropDisplay OEDepict::OE2DMolDisplaySetup::BondStereoStyle OEDepict::OE2DMolDisplaySetup::DefaultLineWidth OEDepict::OE2DMolDisplaySetup::HydrogenStyle OEDepict::OE2DMolDisplaySetup::ProtectiveGroupStyle OEDepict::OE2DMolDisplaySetup::Scale OEDepict::OE2DMolDisplaySetup::SuperAtomStyle OEDepict::OE2DMolDisplaySetup::TitleLocation OEDepict::OE2DPath AddCurveSegment AddLineSegment AddStartPoint Constructors GetEnd GetPoints GetStart IsClosed IsValid operator= SetClosed OEDepict::OE2DPathPoint Constructors GetPoint GetPointType operator= OEDepict::OE2DPathPointType OEDepict::OE2DPathPointType::CurveC1 OEDepict::OE2DPathPointType::CurveC2 OEDepict::OE2DPathPointType::CurveEnd OEDepict::OE2DPathPointType::LineEnd OEDepict::OE2DPathPointType::Start OEDepict::OE2DPoint Constructors GetX GetY operator * operator*= operator+ operator+= operator- operator-= operator/ operator/= operator= SetX SetY OEDepict::OEAddBuiltInHiddenSVGClass OEDepict::OEAddBuiltInVisibleSVGClass OEDepict::OEAddDepictionHydrogens OEDepict::OEAddHighlighting OEDepict::OEAddHighlightOverlay OEDepict::OEAddInteractiveIcon OEDepict::OEAddLabel OEDepict::OEAddOpenEyeIcon OEDepict::OEAddSVGClickEvent OEDepict::OEAddSVGHover OEDepict::OEAddSVGToggle OEDepict::OEAddWatermark OEDepict::OEAlignment OEDepict::OEAlignment::Center OEDepict::OEAlignment::Default OEDepict::OEAlignment::Left OEDepict::OEAlignment::Right OEDepict::OEAlignmentOptions Constructors GetAddDepictionHydrogens GetClearCoords GetFixedCoords GetMaxAllowedAtomPairClashes GetMaxBondRotations GetMaxPatternMatches GetRMSDCutoff GetRotateAroundBonds GetSuppressHydrogens operator= SetAddDepictionHydrogens SetClearCoords SetFixedCoords SetMaxAllowedAtomPairClashes SetMaxBondRotations SetMaxPatternMatches SetRMSDCutoff SetRotateAroundBonds SetSuppressHydrogens OEDepict::OEAlignmentResult Clear Constructors CreateCopy GetAtoms GetBonds GetRMSD IsValid NumAtoms NumBonds operator= OEDepict::OEAnnotateDepictionProblems OEDepict::OEAnnotateValenceProblems OEDepict::OEAromaticStyle OEDepict::OEAromaticStyle::Circle OEDepict::OEAromaticStyle::Dash OEDepict::OEAromaticStyle::Default OEDepict::OEAromaticStyle::Kekule OEDepict::OEAtomColorStyle OEDepict::OEAtomColorStyle::BlackCPK OEDepict::OEAtomColorStyle::BlackMonochrome OEDepict::OEAtomColorStyle::Default OEDepict::OEAtomColorStyle::WhiteCPK OEDepict::OEAtomColorStyle::WhiteMonochrome OEDepict::OEAtomDisplayBase GetAtom GetDataType IsDataType IsVisible SetVisible OEDepict::OEAtomStereoStyle OEDepict::OEAtomStereoStyle::Default OEDepict::OEAtomStereoStyle::Display OEDepict::OEAtomStereoStyle::Display::All OEDepict::OEAtomStereoStyle::Display::AtomStereo OEDepict::OEAtomStereoStyle::Display::CIPAtomStereo OEDepict::OEAtomStereoStyle::Display::Default OEDepict::OEAtomStereoStyle::Display::MDLStereoCenter OEDepict::OEAtomStereoStyle::HashWedgeStyle OEDepict::OEAtomStereoStyle::HashWedgeStyle::Default OEDepict::OEAtomStereoStyle::HashWedgeStyle::Fancy OEDepict::OEAtomStereoStyle::HashWedgeStyle::Standard OEDepict::OEAtomStereoStyle::Hidden OEDepict::OEAtomSVGAtomIdxMarkup Constructors CreateCopy GetClassName GetGroupId OEDepict::OEAtomSVGMarkupBase CreateCopy GetClassName GetGroupId OEDepict::OEAtomSVGNoMarkup Constructors CreateCopy GetClassName GetGroupId OEDepict::OEAtomSVGResidueMarkup Constructors CreateCopy GetClassName GetGroupId OEDepict::OEBondColorStyle OEDepict::OEBondColorStyle::ByElement OEDepict::OEBondColorStyle::Default OEDepict::OEBondColorStyle::Monochrome OEDepict::OEBondDisplayBase GetBond GetDataType IsDataType IsVisible SetVisible OEDepict::OEBondDisplayPosition OEDepict::OEBondDisplayPosition::Center OEDepict::OEBondDisplayPosition::Left OEDepict::OEBondDisplayPosition::Right OEDepict::OEBondDisplayType OEDepict::OEBondDisplayType::Any OEDepict::OEBondDisplayType::Aromatic OEDepict::OEBondDisplayType::AromaticDash OEDepict::OEBondDisplayType::Double OEDepict::OEBondDisplayType::DoubleArom OEDepict::OEBondDisplayType::DoubleBowTie OEDepict::OEBondDisplayType::Hash OEDepict::OEBondDisplayType::Hidden OEDepict::OEBondDisplayType::Quadruple OEDepict::OEBondDisplayType::Single OEDepict::OEBondDisplayType::SingleArom OEDepict::OEBondDisplayType::SingleDouble OEDepict::OEBondDisplayType::Triple OEDepict::OEBondDisplayType::Wavy OEDepict::OEBondDisplayType::Wedge OEDepict::OEBondStereoStyle OEDepict::OEBondStereoStyle::Default OEDepict::OEBondStereoStyle::Display OEDepict::OEBondStereoStyle::Display::All OEDepict::OEBondStereoStyle::Display::BondStereo OEDepict::OEBondStereoStyle::Display::CIPBondStereo OEDepict::OEBondStereoStyle::Display::Default OEDepict::OEBondStereoStyle::Hidden OEDepict::OEBondSVGBondIdxMarkup Constructors CreateCopy GetClassName GetGroupId OEDepict::OEBondSVGMarkupBase CreateCopy GetClassName GetGroupId OEDepict::OEBondSVGNoMarkup Constructors CreateCopy GetClassName GetGroupId OEDepict::OEConfigure2DMolDisplayOptions OEDepict::OEConfigureColor OEDepict::OEConfigureHighlightColor OEDepict::OEConfigureHighlightParams OEDepict::OEConfigureHighlightStyle OEDepict::OEConfigureImageGridNumColumns OEDepict::OEConfigureImageGridNumRows OEDepict::OEConfigureImageGridParams OEDepict::OEConfigureImageHeight OEDepict::OEConfigureImageOptions OEDepict::OEConfigureImageWidth OEDepict::OEConfigureMultiPageOrientation OEDepict::OEConfigureMultiPageParams OEDepict::OEConfigureMultiPageSize OEDepict::OEConfigurePrepareDepictionOptions OEDepict::OEConfigureReportOptions OEDepict::OECreateWin32GraphicsImage OEDepict::OEDepict OEDepict::OEDepict::OEBlackBoxPen OEDepict::OEDepict::OEBlackPen OEDepict::OEDepict::OEBlueBoxPen OEDepict::OEDepict::OEBluePen OEDepict::OEDepict::OEDarkBackgroundColor OEDepict::OEDepict::OEDefaultFont OEDepict::OEDepict::OEGreenBoxPen OEDepict::OEDepict::OEGreenPen OEDepict::OEDepict::OELightBackgroundColor OEDepict::OEDepict::OELightGreyBoxPen OEDepict::OEDepict::OELightGreyPen OEDepict::OEDepict::OERedBoxPen OEDepict::OEDepict::OERedPen OEDepict::OEDepict::OESVGAreaPen OEDepict::OEDepict::OETransparentPen OEDepict::OEDepict::OEWhiteBoxPen OEDepict::OEDepict::OEWhitePen OEDepict::OEDepictCoordinates OEDepict::OEDepictGetArch OEDepict::OEDepictGetLicensee OEDepict::OEDepictGetPlatform OEDepict::OEDepictGetRelease OEDepict::OEDepictGetSite OEDepict::OEDepictGetVersion OEDepict::OEDepictIsLicensed OEDepict::OEDepictOrientation OEDepict::OEDepictOrientation::Default OEDepict::OEDepictOrientation::Horizontal OEDepict::OEDepictOrientation::Original OEDepict::OEDepictOrientation::Square OEDepict::OEDepictOrientation::Vertical OEDepict::OEDisplayAtomIdx Constructors CreateCopy operator() OEDepict::OEDisplayAtomMapIdx Constructors CreateCopy operator() OEDepict::OEDisplayAtomPropBase CreateCopy operator() OEDepict::OEDisplayBondIdx Constructors CreateCopy operator() OEDepict::OEDisplayBondPropBase CreateCopy operator() OEDepict::OEDisplayNoAtomProp Constructors CreateCopy operator() OEDepict::OEDisplayNoBondProp Constructors CreateCopy operator() OEDepict::OEDrawBorder OEDepict::OEDrawChevronArrow OEDepict::OEDrawCurvedArrow OEDepict::OEDrawCurvedBorder OEDepict::OEDrawCurvedRectangle OEDepict::OEDrawEquilibriumArrow OEDepict::OEDrawHighlighting OEDepict::OEDrawLegendLayout OEDepict::OEDrawReactionArrow OEDepict::OEDrawResonanceArrow OEDepict::OEDrawSVGHoverText OEDepict::OEDrawSVGToggleText OEDepict::OEDrawText OEDepict::OEDrawTextToCenter OEDepict::OEEstimateTextWidth OEDepict::OEFill OEDepict::OEFill::Default OEDepict::OEFill::Off OEDepict::OEFill::On OEDepict::OEFont Constructors GetAlignment GetColor GetFamily GetHyperlink GetRotationAngle GetSize GetStyle HasHyperlink operator!= operator= operator== SetAlignment SetColor SetFamily SetHyperlink SetRotationAngle SetSize SetStyle OEDepict::OEFontFamily OEDepict::OEFontFamily::Arial OEDepict::OEFontFamily::Courier OEDepict::OEFontFamily::Default OEDepict::OEFontFamily::Helvetica OEDepict::OEFontFamily::Times OEDepict::OEFontStyle OEDepict::OEFontStyle::Bold OEDepict::OEFontStyle::Default OEDepict::OEFontStyle::Italic OEDepict::OEFontStyle::Normal OEDepict::OEGetAverageBondLengthInDispCoords OEDepict::OEGetBuiltInHiddenSVGClass OEDepict::OEGetBuiltInVisibleSVGClass OEDepict::OEGetCenter OEDepict::OEGetColor OEDepict::OEGetDefaultAtomColor OEDepict::OEGetDisplayCoords OEDepict::OEGetHighlightColor OEDepict::OEGetHighlightStyle OEDepict::OEGetImageGridNumColumns OEDepict::OEGetImageGridNumRows OEDepict::OEGetImageHeight OEDepict::OEGetImageWidth OEDepict::OEGetLabelPosition OEDepict::OEGetMoleculeCoords OEDepict::OEGetMoleculeScale OEDepict::OEGetMultiPageOrientation OEDepict::OEGetMultiPageSize OEDepict::OEGetNearbyAtom OEDepict::OEGetNearbyBond OEDepict::OEGetNearestAtom OEDepict::OEGetNearestBond OEDepict::OEGetPageHeight OEDepict::OEGetPageWidth OEDepict::OEGetSupportedImageFileExtensions OEDepict::OEGetSupportedMultiPageImageFileExtensions OEDepict::OEHasDepictionHydrogens OEDepict::OEHighlightBase Constructors CreateCopy OEDepict::OEHighlightByBallAndStick Constructors CreateCopy GetAtomLabelMonochrome GetBallRadiusScale GetColor GetStickWidthScale operator= SetAtomLabelMonochrome SetBallRadiusScale SetColor SetStickWidthScale OEDepict::OEHighlightByCogwheel Constructors CreateCopy GetAtomLabelMonochrome GetBallRadiusScale GetColor GetInnerContour GetLineWidthScale GetStickWidthScale operator= SetAtomLabelMonochrome SetBallRadiusScale SetColor SetInnerContour SetLineWidthScale SetStickWidthScale OEDepict::OEHighlightByColor Constructors CreateCopy GetAtomExternalHighlight GetColor GetLineWidthScale operator= SetAtomExternalHighlight SetColor SetLineWidthScale OEDepict::OEHighlightByLasso Constructors CreateCopy GetAtomLabelMonochrome GetColor GetConsiderAtomLabelBoundingBox GetLassoScale GetLineWidthScale GetPen GetPosition operator= SetAtomLabelMonochrome SetColor SetConsiderAtomLabelBoundingBox SetLassoScale SetLineWidthScale SetPen SetPosition OEDepict::OEHighlightByStick Constructors CreateCopy GetAtomExternalHighlightRatio GetAtomLabelMonochrome GetColor GetStickWidthScale operator= SetAtomExternalHighlightRatio SetAtomLabelMonochrome SetColor SetStickWidthScale OEDepict::OEHighlightLabel Constructors GetBoundingBoxPen GetFont GetFontScale GetText SetBoundingBoxPen SetFont SetFontScale OEDepict::OEHighlightOverlayBase Constructors GetColors SetColors OEDepict::OEHighlightOverlayByBallAndStick Constructors GetAtomLabelMonochrome GetBallRadiusScale GetStickWidthScale operator= SetAtomLabelMonochrome SetBallRadiusScale SetStickWidthScale OEDepict::OEHighlightOverlayStyle OEDepict::OEHighlightOverlayStyle::BallAndStick OEDepict::OEHighlightOverlayStyle::Default OEDepict::OEHighlightParamName OEDepict::OEHighlightParamName::Color OEDepict::OEHighlightParamName::Style OEDepict::OEHighlightSetup OEDepict::OEHighlightSetup::All OEDepict::OEHighlightSetup::Color OEDepict::OEHighlightSetup::Style OEDepict::OEHighlightStyle OEDepict::OEHighlightStyle::BallAndStick OEDepict::OEHighlightStyle::Cogwheel OEDepict::OEHighlightStyle::Color OEDepict::OEHighlightStyle::Default OEDepict::OEHighlightStyle::Lasso OEDepict::OEHighlightStyle::Stick OEDepict::OEHydrogenPos OEDepict::OEHydrogenPos::East OEDepict::OEHydrogenPos::North OEDepict::OEHydrogenPos::South OEDepict::OEHydrogenPos::Undefined OEDepict::OEHydrogenPos::West OEDepict::OEHydrogenStyle OEDepict::OEHydrogenStyle::Default OEDepict::OEHydrogenStyle::ExplicitAll OEDepict::OEHydrogenStyle::ExplicitHetero OEDepict::OEHydrogenStyle::ExplicitTerminal OEDepict::OEHydrogenStyle::Hidden OEDepict::OEHydrogenStyle::ImplicitAll OEDepict::OEHydrogenStyle::ImplicitHetero OEDepict::OEHydrogenStyle::ImplicitTerminal OEDepict::OEIconLocation OEDepict::OEIconLocation::BottomLeft OEDepict::OEIconLocation::BottomRight OEDepict::OEIconLocation::Default OEDepict::OEIconLocation::TopLeft OEDepict::OEIconLocation::TopRight OEDepict::OEImage Clear Constructors DrawArc DrawCircle DrawCubicBezier DrawLine DrawPath DrawPie DrawPoint DrawPolygon DrawQuadraticBezier DrawRectangle DrawText DrawTriangle GetHeight GetWidth IsEmpty Render OEDepict::OEImageBase Clear Constructors DrawArc DrawCircle DrawCubicBezier DrawLine DrawPath DrawPie DrawPoint DrawPolygon DrawQuadraticBezier DrawRectangle DrawText DrawTriangle GetGlobalOffset GetHeight GetMinFontSize GetSVGClass GetSVGGroup GetSVGGroups GetWidth NewSVGClass NewSVGGroup PopGroup PushGroup SetMinFontSize OEDepict::OEImageFileBase Constructors GetExtension IsVisible PopGroup PushGroup Write OEDepict::OEImageFileCreatorBase Constructors CreateCopy CreateImage GetExtension IsMultiPage OEDepict::OEImageFrame Clear Constructors DrawArc DrawCircle DrawCubicBezier DrawLine DrawPath DrawPie DrawPoint DrawPolygon DrawQuadraticBezier DrawRectangle DrawText DrawTriangle GetHeight GetOffset GetWidth OEDepict::OEImageGrid Constructors GetCell GetCellGap GetCellHeight GetCells GetCellWidth GetMargin NumCols NumRows SetCellGap SetMargin SetMargins OEDepict::OEImageGridParamName OEDepict::OEImageGridParamName::NumColumns OEDepict::OEImageGridParamName::NumRows OEDepict::OEImageGridSetup OEDepict::OEImageGridSetup::All OEDepict::OEImageGridSetup::NumColumns OEDepict::OEImageGridSetup::NumRows OEDepict::OEImageParamName OEDepict::OEImageParamName::Height OEDepict::OEImageParamName::Width OEDepict::OEImageSetup OEDepict::OEImageSetup::All OEDepict::OEImageSetup::Height OEDepict::OEImageSetup::Width OEDepict::OEImageTable Constructors DrawText GetBodyCell GetBodyCells GetCell GetCells GetHeaderCell GetHeaderCells GetOptions GetStubColumnCell GetStubColumnCells NumColumns NumRows OEDepict::OEImageTableOptions Constructors GetCellBorderPen GetCellColor GetCellFont GetHeaderColor GetHeaderFont GetMargin GetStubColumnColor GetStubColumnFont HasHeader HasStubColumn NumColumns NumRows operator= SetBaseFontSize SetCellBorderPen SetCellColor SetCellFont SetColumnWidths SetHeader SetHeaderColor SetHeaderFont SetMargin SetMargins SetRowHeights SetStubColumn SetStubColumnColor SetStubColumnFont OEDepict::OEImageTableStyle OEDepict::OEImageTableStyle::Default OEDepict::OEImageTableStyle::LightBlue OEDepict::OEImageTableStyle::LightGreen OEDepict::OEImageTableStyle::LightGrey OEDepict::OEImageTableStyle::MediumBlue OEDepict::OEImageTableStyle::MediumGreen OEDepict::OEImageTableStyle::MediumGrey OEDepict::OEImageTableStyle::NoStyle OEDepict::OEImageTableStyle::SantaFe OEDepict::OEIsRegisteredImageFile OEDepict::OEIsRegisteredMultiPageImageFile OEDepict::OEIsValidSVGClassName OEDepict::OEIsValidSVGGroupId OEDepict::OEJavaImageBase Constructors GetAntiAliasing GetGraphics SetAntiAliasing OEDepict::OELayerPosition OEDepict::OELayerPosition::Above OEDepict::OELayerPosition::Below OEDepict::OELayerPosition::SVG OEDepict::OELegendColorStyle OEDepict::OELegendColorStyle::Default OEDepict::OELegendColorStyle::LightBlue OEDepict::OELegendColorStyle::LightGreen OEDepict::OELegendColorStyle::LightGrey OEDepict::OELegendColorStyle::NoStyle OEDepict::OELegendInteractiveStyle OEDepict::OELegendInteractiveStyle::Default OEDepict::OELegendInteractiveStyle::Hover OEDepict::OELegendInteractiveStyle::Permanent OEDepict::OELegendInteractiveStyle::Toggle OEDepict::OELegendLayout Constructors GetLegendArea GetOptions OEDepict::OELegendLayoutOptions Constructors GetButtonFont GetButtonHeightScale GetButtonPen GetButtonWidthScale GetColorStyle GetInteractiveStyle GetLayoutStyle GetLegendBoxPen GetMargin operator= SetButtonFont SetButtonHeightScale SetButtonPen SetButtonWidthScale SetLegendBoxPen SetMargin SetMargins OEDepict::OELegendLayoutStyle OEDepict::OELegendLayoutStyle::Default OEDepict::OELegendLayoutStyle::HorizontalBottomLeft OEDepict::OELegendLayoutStyle::HorizontalBottomRight OEDepict::OELegendLayoutStyle::HorizontalTopLeft OEDepict::OELegendLayoutStyle::HorizontalTopRight OEDepict::OELegendLayoutStyle::VerticalBottomLeft OEDepict::OELegendLayoutStyle::VerticalBottomRight OEDepict::OELegendLayoutStyle::VerticalTopLeft OEDepict::OELegendLayoutStyle::VerticalTopRight OEDepict::OELengthenVector OEDepict::OELineCap OEDepict::OELineCap::Butt OEDepict::OELineCap::Default OEDepict::OELineCap::Round OEDepict::OELineCap::Square OEDepict::OELineJoin OEDepict::OELineJoin::Bevel OEDepict::OELineJoin::Default OEDepict::OELineJoin::Miter OEDepict::OELineJoin::Round OEDepict::OEMargin OEDepict::OEMargin::Bottom OEDepict::OEMargin::Left OEDepict::OEMargin::Right OEDepict::OEMargin::Top OEDepict::OEMolDisplayBase GetDataType GetMolecule IsDataType OEDepict::OEMultiPageImageFile Constructors GetOrientation GetPage GetPageHeight GetPages GetPageWidth NewPage NumPages OEDepict::OEMultiPageParamName OEDepict::OEMultiPageParamName::PageOrientation OEDepict::OEMultiPageParamName::PageSize OEDepict::OEMultiPageSetup OEDepict::OEMultiPageSetup::All OEDepict::OEMultiPageSetup::PageOrientation OEDepict::OEMultiPageSetup::PageSize OEDepict::OENearestAtom Constructors GetAtom GetDisplayPosition GetDist IsValid OEDepict::OENearestBond Constructors GetBond GetDisplayPosition GetDist IsValid OEDepict::OEOffsetMolDisplay OEDepict::OEPageOrientation OEDepict::OEPageOrientation::Default OEDepict::OEPageOrientation::Landscape OEDepict::OEPageOrientation::Portrait OEDepict::OEPageSize OEDepict::OEPageSize::Custom OEDepict::OEPageSize::Default OEDepict::OEPageSize::ISO_A4 OEDepict::OEPageSize::US_Legal OEDepict::OEPageSize::US_Letter OEDepict::OEPen Constructors GetBackColor GetFill GetForeColor GetLineCap GetLineJoin GetLineStipple GetLineWidth GetStippleFactor operator!= operator= operator== SetBackColor SetFill SetForeColor SetLineCap SetLineJoin SetLineStipple SetLineWidth SetStippleFactor OEDepict::OEPrepareAlignedDepiction OEDepict::OEPrepareDepiction OEDepict::OEPrepareDepictionOptions Constructors GetAddDepictionHydrogens GetClearCoords GetDepictOrientation GetPerceiveBondStereo GetSuppressHydrogens operator= SetAddDepictionHydrogens SetClearCoords SetDepictOrientation SetPerceiveBondStereo SetSuppressHydrogens OEDepict::OEPrepareDepictionSetup OEDepict::OEPrepareDepictionSetup::All OEDepict::OEPrepareDepictionSetup::ClearCoords OEDepict::OEPrepareDepictionSetup::DepictOrientation OEDepict::OEPrepareDepictionSetup::SuppressHydrogens OEDepict::OEPrepareMultiAlignedDepiction OEDepict::OEProtectiveGroupStyle OEDepict::OEProtectiveGroupStyle::Ac OEDepict::OEProtectiveGroupStyle::Ad OEDepict::OEProtectiveGroupStyle::All OEDepict::OEProtectiveGroupStyle::Alloc OEDepict::OEProtectiveGroupStyle::Benzoyl OEDepict::OEProtectiveGroupStyle::Benzyl OEDepict::OEProtectiveGroupStyle::Bn OEDepict::OEProtectiveGroupStyle::Boc OEDepict::OEProtectiveGroupStyle::Bom OEDepict::OEProtectiveGroupStyle::Bpoc OEDepict::OEProtectiveGroupStyle::Bs OEDepict::OEProtectiveGroupStyle::Bt OEDepict::OEProtectiveGroupStyle::Btm OEDepict::OEProtectiveGroupStyle::Bz OEDepict::OEProtectiveGroupStyle::Bzh OEDepict::OEProtectiveGroupStyle::Bzl OEDepict::OEProtectiveGroupStyle::BzOM OEDepict::OEProtectiveGroupStyle::Cbz OEDepict::OEProtectiveGroupStyle::cHx OEDepict::OEProtectiveGroupStyle::Dan OEDepict::OEProtectiveGroupStyle::Dansyl OEDepict::OEProtectiveGroupStyle::DCB OEDepict::OEProtectiveGroupStyle::DDE OEDepict::OEProtectiveGroupStyle::DDIV OEDepict::OEProtectiveGroupStyle::Default OEDepict::OEProtectiveGroupStyle::DEIPS OEDepict::OEProtectiveGroupStyle::DMAB OEDepict::OEProtectiveGroupStyle::DMIPS OEDepict::OEProtectiveGroupStyle::DMPM OEDepict::OEProtectiveGroupStyle::DMPS OEDepict::OEProtectiveGroupStyle::DMTr OEDepict::OEProtectiveGroupStyle::DNBZ OEDepict::OEProtectiveGroupStyle::DNP OEDepict::OEProtectiveGroupStyle::DOC OEDepict::OEProtectiveGroupStyle::DPIPS OEDepict::OEProtectiveGroupStyle::Dpp OEDepict::OEProtectiveGroupStyle::DTBMS OEDepict::OEProtectiveGroupStyle::EE OEDepict::OEProtectiveGroupStyle::ESC OEDepict::OEProtectiveGroupStyle::Fmoc OEDepict::OEProtectiveGroupStyle::FourOMeBz OEDepict::OEProtectiveGroupStyle::FPMP OEDepict::OEProtectiveGroupStyle::Im OEDepict::OEProtectiveGroupStyle::Lev OEDepict::OEProtectiveGroupStyle::MDIPS OEDepict::OEProtectiveGroupStyle::MDPS OEDepict::OEProtectiveGroupStyle::MEM OEDepict::OEProtectiveGroupStyle::Mes OEDepict::OEProtectiveGroupStyle::MMTR OEDepict::OEProtectiveGroupStyle::MOM OEDepict::OEProtectiveGroupStyle::Moz OEDepict::OEProtectiveGroupStyle::MPC OEDepict::OEProtectiveGroupStyle::MPM OEDepict::OEProtectiveGroupStyle::MS OEDepict::OEProtectiveGroupStyle::MTHP OEDepict::OEProtectiveGroupStyle::MTM OEDepict::OEProtectiveGroupStyle::MTr OEDepict::OEProtectiveGroupStyle::Np OEDepict::OEProtectiveGroupStyle::NPE OEDepict::OEProtectiveGroupStyle::NPEOC OEDepict::OEProtectiveGroupStyle::NPES OEDepict::OEProtectiveGroupStyle::NPS OEDepict::OEProtectiveGroupStyle::NVOC OEDepict::OEProtectiveGroupStyle::OBzl OEDepict::OEProtectiveGroupStyle::Off OEDepict::OEProtectiveGroupStyle::ONOS OEDepict::OEProtectiveGroupStyle::OtBu OEDepict::OEProtectiveGroupStyle::PAC OEDepict::OEProtectiveGroupStyle::PBF OEDepict::OEProtectiveGroupStyle::PCB OEDepict::OEProtectiveGroupStyle::PHF OEDepict::OEProtectiveGroupStyle::Pht OEDepict::OEProtectiveGroupStyle::Piv OEDepict::OEProtectiveGroupStyle::PMB OEDepict::OEProtectiveGroupStyle::PMBM OEDepict::OEProtectiveGroupStyle::Poc OEDepict::OEProtectiveGroupStyle::PPi OEDepict::OEProtectiveGroupStyle::SEM OEDepict::OEProtectiveGroupStyle::SES OEDepict::OEProtectiveGroupStyle::StBu OEDepict::OEProtectiveGroupStyle::TBDMS OEDepict::OEProtectiveGroupStyle::TBDPS OEDepict::OEProtectiveGroupStyle::TBMPS OEDepict::OEProtectiveGroupStyle::TBS OEDepict::OEProtectiveGroupStyle::TCP OEDepict::OEProtectiveGroupStyle::Teoc OEDepict::OEProtectiveGroupStyle::TES OEDepict::OEProtectiveGroupStyle::Tf OEDepict::OEProtectiveGroupStyle::TFA OEDepict::OEProtectiveGroupStyle::Thexyl OEDepict::OEProtectiveGroupStyle::THF OEDepict::OEProtectiveGroupStyle::THP OEDepict::OEProtectiveGroupStyle::TIPS OEDepict::OEProtectiveGroupStyle::TMOB OEDepict::OEProtectiveGroupStyle::TMS OEDepict::OEProtectiveGroupStyle::Tos OEDepict::OEProtectiveGroupStyle::transCinnamyl OEDepict::OEProtectiveGroupStyle::Trisyl OEDepict::OEProtectiveGroupStyle::Troc OEDepict::OEProtectiveGroupStyle::TRT OEDepict::OEProtectiveGroupStyle::TS OEDepict::OEProtectiveGroupStyle::Xyl OEDepict::OEProtectiveGroupStyle::Z OEDepict::OERadicalDisplayType OEDepict::OERadicalDisplayType::Diradical OEDepict::OERadicalDisplayType::Monoradical OEDepict::OERadicalDisplayType::Off OEDepict::OEReduceFontSizeToFit OEDepict::OERegisterImageFile OEDepict::OERenderMolecule OEDepict::OERenderMoleculeToBytes OEDepict::OERenderMoleculeToString OEDepict::OEReport Constructors GetBodies GetBody GetCell GetCellHeight GetCells GetCellWidth GetFooter GetFooterHeight GetFooters GetFooterWidth GetHeader GetHeaderHeight GetHeaders GetHeaderWidth GetOptions GetPage GetPageHeight GetPages GetPageWidth IsBodyPage IsGridPage NewBody NewCell NumBodyPages NumColsPerPage NumGridPages NumPages NumRowsPerPage OEDepict::OEReportOptions Constructors GetCellGap GetCellHeight GetCellWidth GetFooterHeight GetFooterWidth GetHeaderHeight GetHeaderWidth GetPageHeight GetPageMargin GetPageWidth NumColsPerPage NumRowsPerPage operator= SetCellGap SetFooterHeight SetHeaderHeight SetPageHeight SetPageMargin SetPageMargins SetPageOrientation SetPageSize SetPageWidth OEDepict::OEReportSetup OEDepict::OEReportSetup::All OEDepict::OEReportSetup::NumColsPerPage OEDepict::OEReportSetup::NumRowsPerPage OEDepict::OEReportSetup::PageHeight OEDepict::OEReportSetup::PageOrientation OEDepict::OEReportSetup::PageSize OEDepict::OEReportSetup::PageWidth OEDepict::OERotateVector OEDepict::OEScale OEDepict::OEScale::AutoScale OEDepict::OEScale::Default OEDepict::OESetup2DMolDisplayOptions OEDepict::OESetupPrepareDepictionOptions OEDepict::OESetupReportOptions OEDepict::OEStipple OEDepict::OEStipple::Default OEDepict::OEStipple::Dot OEDepict::OEStipple::DotDash OEDepict::OEStipple::DotDashDash OEDepict::OEStipple::LongDash OEDepict::OEStipple::NoLine OEDepict::OEStipple::ShortDash OEDepict::OEStipple::Solid OEDepict::OESuperAtomStyle OEDepict::OESuperAtomStyle::All OEDepict::OESuperAtomStyle::Bu OEDepict::OESuperAtomStyle::Carbon OEDepict::OESuperAtomStyle::CCl3 OEDepict::OESuperAtomStyle::CF3 OEDepict::OESuperAtomStyle::CHO OEDepict::OESuperAtomStyle::CN OEDepict::OESuperAtomStyle::CNO OEDepict::OESuperAtomStyle::COO_ OEDepict::OESuperAtomStyle::COOH OEDepict::OESuperAtomStyle::Default OEDepict::OESuperAtomStyle::Et OEDepict::OESuperAtomStyle::Ether OEDepict::OESuperAtomStyle::Halide OEDepict::OESuperAtomStyle::iBu OEDepict::OESuperAtomStyle::Me OEDepict::OESuperAtomStyle::N2 OEDepict::OESuperAtomStyle::N3 OEDepict::OESuperAtomStyle::NC OEDepict::OESuperAtomStyle::NCO OEDepict::OESuperAtomStyle::Nitrogen OEDepict::OESuperAtomStyle::NO2 OEDepict::OESuperAtomStyle::OBu OEDepict::OESuperAtomStyle::OEt OEDepict::OESuperAtomStyle::Off OEDepict::OESuperAtomStyle::OMe OEDepict::OESuperAtomStyle::ONO OEDepict::OESuperAtomStyle::OPr OEDepict::OESuperAtomStyle::Oxygen OEDepict::OESuperAtomStyle::OxygenAndNitrogen OEDepict::OESuperAtomStyle::Phosphorus OEDepict::OESuperAtomStyle::PO3H2 OEDepict::OESuperAtomStyle::Pr OEDepict::OESuperAtomStyle::sBu OEDepict::OESuperAtomStyle::SO3_ OEDepict::OESuperAtomStyle::SO3H OEDepict::OESuperAtomStyle::Sulfur OEDepict::OESuperAtomStyle::tBu OEDepict::OESuppressNonDepictionHydrogens OEDepict::OESVGClass Constructors GetName OEDepict::OESVGGroup AddSVGClass Constructors GetId IsVisible OEDepict::OETitleLocation OEDepict::OETitleLocation::Bottom OEDepict::OETitleLocation::Default OEDepict::OETitleLocation::Hidden OEDepict::OETitleLocation::Top OEDepict::OEWrite2DRingDictionaryReport OEDepict::OEWriteImage OEDepict::OEWriteImageToBytes OEDepict::OEWriteImageToString OEDepict::OEWriteMultiPageImage OEDepict::OEWriteReport OEDepict::OEWriteReportPageByPage OEDepict::OEWriteReportToBytes OEDepict::OEWriteReportToString OEDocking::OEAddDockingInteractions OEDocking::OEAlignReceptorFunction CreateCopy operator() SetupTarget OEDocking::OEAlignReceptors OEDocking::OEAllowedClashType OEDocking::OEAllowedClashType::ANY OEDocking::OEAllowedClashType::HYDROGEN OEDocking::OEAllowedClashType::NONE OEDocking::OEBox Constructors GetXMax GetXMin GetYMax GetYMin GetZMax GetZMin operator= Setup OEDocking::OEBoxArea OEDocking::OEBoxBase Destructor GetXMax GetXMin GetYMax GetYMin GetZMax GetZMin operator= Setup OEDocking::OEBoxExtend OEDocking::OEBoxTranslate OEDocking::OEBoxVolume OEDocking::OEBoxXDim OEDocking::OEBoxXMid OEDocking::OEBoxYDim OEDocking::OEBoxYMid OEDocking::OEBoxZDim OEDocking::OEBoxZMid OEDocking::OECreateDUFromReceptorMol OEDocking::OECustomConstraints AddFeature Clear Constructors DeleteFeature GetFeatures NumFeatures operator= OEDocking::OEDock AnnotatePose CacheScoringSetup Constructor DockMultiConformerMolecule GetComponentNames GetHighScoresAreBetter GetName Initialize IsInitialized ScoreAtom ScoreAtomComponent ScoreLigand ScoreLigandComponent OEDocking::OEDockingGetArch OEDocking::OEDockingGetLicensee OEDocking::OEDockingGetPlatform OEDocking::OEDockingGetRelease OEDocking::OEDockingGetSite OEDocking::OEDockingGetVersion OEDocking::OEDockingReturnCode OEDocking::OEDockingReturnCode::Aborted OEDocking::OEDockingReturnCode::ConformerGenError OEDocking::OEDockingReturnCode::CoordError OEDocking::OEDockingReturnCode::EmptyLigand OEDocking::OEDockingReturnCode::EmptyProtein OEDocking::OEDockingReturnCode::Failure OEDocking::OEDockingReturnCode::GridSetupError OEDocking::OEDockingReturnCode::InvalidScore OEDocking::OEDockingReturnCode::NoConstraintMatch OEDocking::OEDockingReturnCode::NotInitialized OEDocking::OEDockingReturnCode::NoValidNonClashPoses OEDocking::OEDockingReturnCode::NoValidPoses OEDocking::OEDockingReturnCode::OptimizationError OEDocking::OEDockingReturnCode::OutsideGrid OEDocking::OEDockingReturnCode::ScoreError OEDocking::OEDockingReturnCode::Success OEDocking::OEDockingReturnCode::TypingError OEDocking::OEDockingReturnCodeGetName OEDocking::OEDockMethod OEDocking::OEDockMethod::Chemgauss OEDocking::OEDockMethod::Chemgauss3 OEDocking::OEDockMethod::Chemgauss4 OEDocking::OEDockMethod::Chemscore OEDocking::OEDockMethod::Default OEDocking::OEDockMethod::Hybrid OEDocking::OEDockMethod::Hybrid1 OEDocking::OEDockMethod::Hybrid2 OEDocking::OEDockMethod::INVALID OEDocking::OEDockMethod::PLP OEDocking::OEDockMethod::Shapegauss OEDocking::OEDockMethodConfigure OEDocking::OEDockMethodGetName OEDocking::OEDockMethodGetValue OEDocking::OEDockOptions Constructor GetResolution GetScoreMethod operator= SetResolution SetScoreMethod OEDocking::OEFeature AddSmarts AddSphere ClearSmarts ClearSpheres CreateCopy DeleteSmarts DeleteSphere Destructor GetEnabled GetFeatureName GetSmarts GetSpheres NumSmarts NumSpheres operator= SetEnabled SetFeatureName OEDocking::OEGetEstimatedPositProbability OEDocking::OEGetPositMethod OEDocking::OEHasClash OEDocking::OEHybrid Constructor OEDocking::OEInBox OEDocking::OEInSphere OEDocking::OEIsReceptor OEDocking::OEMakeBoxMolecule OEDocking::OEMakeReceptor OEDocking::OEMakeReceptorDeprecated OEDocking::OEMakeReceptorOptions Constructor GetAutoConstraints GetBoxExtension GetBoxMol GetNegativeImageType GetTargetMask GetTargetPred operator= SetAutoConstraints SetBoxExtension SetBoxMol SetNegativeImageType SetTargetMask SetTargetPred OEDocking::OENegativeImageType OEDocking::OENegativeImageType::Default OEDocking::OENegativeImageType::INVALID OEDocking::OENegativeImageType::LargeShape OEDocking::OENegativeImageType::SmallShape OEDocking::OENegativeImageType::StandardShape OEDocking::OENegativeImageTypeConfigure OEDocking::OENegativeImageTypeGetName OEDocking::OENegativeImageTypeGetValue OEDocking::OEPoseOptimizer Constructor operator= Optimize OEDocking::OEPoseOptimizerOptions Constructor GetFlexRange GetForceField GetNonBondCutoff operator= SetFlexRange SetForceField SetNonBondCutoff OEDocking::OEPoseRelaxMode OEDocking::OEPoseRelaxMode::ALL OEDocking::OEPoseRelaxMode::CLASHED OEDocking::OEPoseRelaxMode::NONE OEDocking::OEPosit AddReceptor ClearReceptors Constructor Dock DockMultiConformerMolecule GetHighScoresAreBetter GetInvalidScore GetName Initialize IsInitialized MethodChoice operator= RankDesignUnits RankReceptors ScoreLigand OEDocking::OEPositMethod OEDocking::OEPositMethod::ALL OEDocking::OEPositMethod::FRED OEDocking::OEPositMethod::HYBRID OEDocking::OEPositMethod::SHAPEFIT OEDocking::OEPositMethod::UNKNOWN OEDocking::OEPositMethodGetName OEDocking::OEPositOptions Constructor GetAllowedClashType GetBestReceptorPoseOnly GetExcludeSelf GetFlexiOverlayOptions GetFullConformationSearch GetIgnoreNitrogenStereo GetMinProbability GetPoserCacheCount GetPoseRelaxMode GetPoseRelaxOptions GetPositMethods GetTorLib operator= SetAllowedClashType SetBestReceptorPoseOnly SetExcludeSelf SetFlexiOverlayOptions SetFullConformationSearch SetIgnoreNitrogenStereo SetMinProbability SetPoserCacheCount SetPoseRelaxMode SetPoseRelaxOptions SetPositMethods SetTorLib OEDocking::OEPositProbability Constructor Estimate operator= PoseEstimate SetupRef OEDocking::OEPositResults Constructors GetNumPoses GetReturnCode GetSinglePoseResults operator= OEDocking::OEProteinConstraint GetAtom GetEnabled GetName GetType SetAtom SetEnabled SetName SetType OEDocking::OEProteinConstraintType OEDocking::OEProteinConstraintType::Acceptor OEDocking::OEProteinConstraintType::Chelator OEDocking::OEProteinConstraintType::Contact OEDocking::OEProteinConstraintType::Donor OEDocking::OEProteinConstraintType::Lipophilic OEDocking::OEProteinConstraintType::Unknown OEDocking::OEReadReceptorFile OEDocking::OEReadReceptorFromByteArray OEDocking::OEReceptorAddCachedScore OEDocking::OEReceptorAddExtraMol OEDocking::OEReceptorClear OEDocking::OEReceptorClearBoundLigand OEDocking::OEReceptorClearCachedScore OEDocking::OEReceptorClearCustomConstraints OEDocking::OEReceptorClearExtraMols OEDocking::OEReceptorClearProteinConstraint OEDocking::OEReceptorClearProteinConstraints OEDocking::OEReceptorGetBoundLigand OEDocking::OEReceptorGetCustomConstraints OEDocking::OEReceptorGetExtraMols OEDocking::OEReceptorGetInnerContourLevel OEDocking::OEReceptorGetNegativeImageGrid OEDocking::OEReceptorGetOuterContourLevel OEDocking::OEReceptorGetProteinConstraints OEDocking::OEReceptorHasBoundLigand OEDocking::OEReceptorHasCachedScore OEDocking::OEReceptorHasCustomConstraints OEDocking::OEReceptorHasExtraMols OEDocking::OEReceptorHasInnerContourLevel OEDocking::OEReceptorHasNegativeImageGrid OEDocking::OEReceptorHasOuterContourLevel OEDocking::OEReceptorHasProteinConstraints OEDocking::OEReceptorSetBoundLigand OEDocking::OEReceptorSetCachedScore OEDocking::OEReceptorSetCustomConstraints OEDocking::OEReceptorSetInnerContourLevel OEDocking::OEReceptorSetOuterContourLevel OEDocking::OEReceptorSetProteinConstraint OEDocking::OEScore AnnotatePose CacheScoringSetup Constructor GetComponentNames GetHighScoresAreBetter GetName Initialize IsInitialized ScoreAtom ScoreAtomComponent ScoreLigand ScoreLigandComponent SystematicSolidBodyOptimize OEDocking::OEScoreType OEDocking::OEScoreType::Chemgauss OEDocking::OEScoreType::Chemgauss3 OEDocking::OEScoreType::Chemgauss4 OEDocking::OEScoreType::Chemscore OEDocking::OEScoreType::Default OEDocking::OEScoreType::INVALID OEDocking::OEScoreType::PLP OEDocking::OEScoreType::Shapegauss OEDocking::OEScoreTypeConfigure OEDocking::OEScoreTypeGetName OEDocking::OEScoreTypeGetValue OEDocking::OESearchResolution OEDocking::OESearchResolution::Default OEDocking::OESearchResolution::High OEDocking::OESearchResolution::INVALID OEDocking::OESearchResolution::Low OEDocking::OESearchResolution::Standard OEDocking::OESearchResolutionConfigure OEDocking::OESearchResolutionGetName OEDocking::OESearchResolutionGetValue OEDocking::OESetEnergyScore OEDocking::OESetEnergyScoreComponent OEDocking::OESetScore OEDocking::OESetScoreComponent OEDocking::OESetSDScore OEDocking::OESetSDScoreComponent OEDocking::OESetupBox, [1] OEDocking::OESetupBoxCenterAndExtents OEDocking::OEShapeFit Constructor Fit operator= SetupRef OEDocking::OEShapeFitOptions Constructor GetFlexiOverlapOptions GetFullConformationSearch GetMaxLocalStrain GetMaxOptSteps GetRigidOverlayOptions GetTorLib MaxLocalStrain operator= SetFlexiOverlapOptions SetFullConformationSearch SetMaxLocalStrain SetMaxOptSteps SetRigidOverlayOptions SetTorLib OEDocking::OEShapeFitResults Constructor GetPose GetScore operator= OEDocking::OESinglePoseResult Constructors GetDesignUnit GetHasClash GetNumClashes GetNumContacts GetPose GetPositMethod GetProbability GetReceptorIndex GetRelaxAttempted GetRelaxed GetRelaxStatus GetRelaxStatusStr GetTargetMask GetTargetPred operator= OEDocking::OESphereArea OEDocking::OESphereBase Destructor GetRad GetX GetY GetZ operator= SetCenter SetRad OEDocking::OESphereVolume OEDocking::OEWriteReceptorFile OEDocking::OEWriteReceptorToByteArray OEEon::OEChargeFunc operator() Overlap Setup SetupRef OEEon::OEEonHit Constructors Destructor GetConformerIndex GetMol Load operator= ToRecord OEEon::OEEonHitlistBuilder AddScore AddScores Build Constructors Destructor GetAddCount GetHitCount GetHits OEEon::OEEonHitlistOptions Constructors GetBestHits GetCutoff GetMaxHits operator= SetBestHits SetCutoff SetMaxHits OEEon::OEEonOverlapFunc OEEon::OEEonOverlapScore Constructors Destructor GetETOverlap GetETTanimoto GetFitSelfET GetRefSelfET GetTanimoto GetTanimotoCombo operator= OEEon::OEEonOverlay BestOverlay Constructors Destructor Overlay SortedOverlay OEEon::OEEonOverlayResults AddScore Clear Constructors Destructor GetScores operator= OEEon::OEEonOverlayScore Constructors Destructor GetETOverlap GetETTanimoto GetFitSelfET GetRefSelfET GetTanimoto GetTanimotoCombo operator= OEEon::OEEonPBFunc Constructors Destructor operator= Overlap OEEon::OEEonPBOptions Constructors GetDielectric GetGridBuffer GetGridSpacing GetInnerMask GetOuterMask GetSaltConcentration operator= SetDielectric SetGridBuffer SetGridSpacing SetInnerMask SetOuterMask SetSaltConcentration

OEEon::OEEonPBOverlay BestOverlay Constructors Destructor SetupRef OEEon::OEEonPBResults Constructors Destructor GetFitSelfOverlap GetOverlap GetRefSelfOverlap GetTanimoto operator= OEEon::OEEonStatusCode OEEon::OEEonStatusCode::Failed OEEon::OEEonStatusCode::Success OEEon::OEEtGetArch OEEon::OEEtGetLicensee OEEon::OEEtGetPlatform OEEon::OEEtGetRelease OEEon::OEEtGetSite OEEon::OEEtGetVersion OEEon::OEEtIsLicensed OEEon::OEExactChargeFunc OEEon::OEGridChargeFunc OEEon::OEHighestChargeTanimoto CreateCopy operator() OEEon::OEHighestShapeChargeTanimotoCombo CreateCopy operator() OEEon::OEHighestShapeTanimoto CreateCopy operator() OEFastROCS::OEDBTracer Constructors GetCounts GetHistogram GetNumBins GetTotal SetTotal Update OEFastROCS::OEDBTracerBase GetNumBins SetTotal Update OEFastROCS::OEFastROCSCacheStuff OEFastROCS::OEFastROCSGetArch OEFastROCS::OEFastROCSGetLicensee OEFastROCS::OEFastROCSGetNumDevices OEFastROCS::OEFastROCSGetPlatform OEFastROCS::OEFastROCSGetRelease OEFastROCS::OEFastROCSGetSite OEFastROCS::OEFastROCSGetVersion OEFastROCS::OEFastROCSGPUStatus OEFastROCS::OEFastROCSHistogram Constructors GetHistogram GetNumBins Update OEFastROCS::OEFastROCSIsGPUReady OEFastROCS::OEFastROCSIsLicensed OEFastROCS::OEFastROCSMode OEFastROCS::OEFastROCSMode::Default OEFastROCS::OEFastROCSMode::FastROCS OEFastROCS::OEFastROCSMode::ROCS OEFastROCS::OEFastROCSOrientation OEFastROCS::OEFastROCSOrientation::AsIs OEFastROCS::OEFastROCSOrientation::Default OEFastROCS::OEFastROCSOrientation::Inertial OEFastROCS::OEFastROCSOrientation::InertialAtColorAtoms OEFastROCS::OEFastROCSOrientation::InertialAtHeavyAtoms OEFastROCS::OEFastROCSOrientation::Random OEFastROCS::OEFastROCSOrientation::Subrocs OEFastROCS::OEFastROCSOrientation::UserInertialStarts OEFastROCS::OEFastROCSReturnCode OEFastROCS::OEFastROCSReturnCode::InitializationError OEFastROCS::OEFastROCSReturnCode::InsufficientDriver OEFastROCS::OEFastROCSReturnCode::NoDevice OEFastROCS::OEFastROCSReturnCode::NoDeviceDetected OEFastROCS::OEFastROCSReturnCode::NotPermitted OEFastROCS::OEFastROCSReturnCode::Success OEFastROCS::OEFastROCSReturnCode::Unknown OEFastROCS::OEIsDatabasePrepared OEFastROCS::OEPrepareFastROCSMol OEFastROCS::OESetCoordsToInertialFrame OEFastROCS::OEShapeDatabase AddMol Constructors GetColorForceFieldType GetColorGridSpacing GetDatabaseType GetMaxNumDevices GetMaxOptIterations GetNumDevices GetNumOpenThreads GetScores GetShapeGridSpacing GetSortedScores NumConfs Open PrintMemoryUsage SetColorGridSpacing SetMaxOptIterations SetNumDevices SetNumOpenThreads SetShapeGridSpacing OEFastROCS::OEShapeDatabaseOptions ClearCutoff ClearTracer ClearUserStarts Constructors GetColorForceFieldType GetColorOptimization GetColorScoreScale GetCutoff GetCutoffGT GetCutoffLT GetFastROCSMode GetInitialOrientation GetLimit GetMaxConfs GetMaxOverlays GetMaxRandomTranslation GetNumColorAtomStarts GetNumHeavyAtomStarts GetNumInertialStarts GetNumRandomStarts GetNumStarts GetNumUserStarts GetRandomSeed GetScoreType GetShapeScoreScale GetSimFunc GetTracer GetTverskyAlpha GetTverskyBeta GetUserStarts HasCutoff HasCutoffGT HasCutoffLT operator= SetColorForceField SetColorForceFieldType SetColorOptimization SetColorScoreScale SetCutoff SetCutoffGT SetCutoffLT SetFastROCSMode SetInitialOrientation SetLimit SetMaxConfs SetMaxOverlays SetMaxRandomTranslation SetNumInertialStarts SetNumRandomStarts SetRandomSeed SetScoreType SetShapeScoreScale SetSimFunc SetTracer SetTverskyCoeffs SetUserStarts OEFastROCS::OEShapeDatabasePrep OEFastROCS::OEShapeDatabaseScore Constructors ExtractTransform GetColorScore GetColorTanimoto GetColorTversky GetConfIdx GetMolIdx GetQuat GetRotMatrix GetScore GetShapeScore GetShapeTanimoto GetShapeTversky GetSimFunc GetTanimotoCombo GetTranslation GetTverskyCombo Transform OEFastROCS::OEShapeDatabaseType OEFastROCS::OEShapeDatabaseType::Color OEFastROCS::OEShapeDatabaseType::Combo OEFastROCS::OEShapeDatabaseType::Default OEFastROCS::OEShapeDatabaseType::Shape OEFastROCS::OEShapeDatabaseType::Sitehopper OEFastROCS::OEShapeSimFuncType OEFastROCS::OEShapeSimFuncType::Default OEFastROCS::OEShapeSimFuncType::Tanimoto OEFastROCS::OEShapeSimFuncType::Tversky OEFF::OEClearForceFieldDummyAtom OEFF::OEClearForceFieldDummyAtoms OEFF::OEComplexEnergies Constructors GetComplexSolvationEnergy GetDesolvationEnergy GetHostComponents GetHostEnergy GetHostSolvationEnergy GetInterComponents GetInterEnergy GetLigandComponents GetLigandEnergy GetLigandSolvationEnergy GetTotalEnergy operator= OEFF::OEComplexFF AdaptHostCoords Constructors GetVar Set SetHostFlex SetNonBondCutoff SetupHost OEFF::OEComplexFFParameter Constructors operator= OEFF::OEFF14SBParsley Constructors operator= OEFF::OEFF14SBParsleyComplex Constructors OEFF::OEFF14SBParsleyParams Constructors operator= OEFF::OEFF14SBSage Constructors operator= OEFF::OEFF14SBSageComplex Constructors OEFF::OEFF14SBSageParams Constructors operator= OEFF::OEFF14SBSmirnoff Constructors operator= PrepMol OEFF::OEFF14SBSmirnoffComplex Constructors OEFF::OEFF14SBSmirnoffParams Constructors Load operator= OEFF::OEFFGetArch OEFF::OEFFGetLicensee OEFF::OEFFGetPlatform OEFF::OEFFGetRelease OEFF::OEFFGetSite OEFF::OEFFGetVersion OEFF::OEFFIsLicensed OEFF::OEForceFieldParameter Constructors operator= OEFF::OEGetMMFFSheffieldFFName OEFF::OEGetMMFFSheffieldFFType OEFF::OEIsForceFieldDummyAtom OEFF::OEIsValidMMFFSheffieldFF OEFF::OELigandFFType OEFF::OELigandFFType::MMFF94 OEFF::OELigandFFType::MMFF94S OEFF::OELigandFFType::PARSLEY OEFF::OELigandFFType::SAGE OEFF::OEMMFFAmberComplex Constructors OEFF::OEMMFFComplex Constructors OEFF::OEMMFFIEFF Constructors OEFF::OEMMFFIEFFOptions Constructors GetIEFFTerms GetMMFFTerms GetUseMMFF94s operator= SetIEFFTerms SetMMFFTerms SetUseMMFF94s OEFF::OEMMFFSheffield Constructors OEFF::OEMMFFSheffieldFFType OEFF::OEMMFFSheffieldFFType::Invalid OEFF::OEMMFFSheffieldFFType::MMFF OEFF::OEMMFFSheffieldFFType::MMFF94S OEFF::OEMMFFSheffieldFFType::MMFF94S_NOESTAT OEFF::OEMMFFSheffieldFFType::MMFF94S_SHEFF OEFF::OEMMFFSheffieldFFType::MMFF94S_TRUNC OEFF::OEMMFFSheffieldFFType::MMFF94Smod OEFF::OEMMFFSheffieldFFType::MMFF94Smod_NOESTAT OEFF::OEMMFFSheffieldFFType::MMFF94Smod_SHEFF OEFF::OEMMFFSheffieldFFType::MMFF94Smod_TRUNC OEFF::OEMMFFSheffieldFFType::MMFF_NOESTAT OEFF::OEMMFFSheffieldFFType::MMFF_SHEFF OEFF::OEMMFFSheffieldFFType::MMFF_TRUNC OEFF::OEMMFFSheffieldOptions Constructors GetDielectric GetExponent GetForceFieldType operator= SetDielectric SetExponent SetForceFieldType OEFF::OESetForceFieldDummyAtom OEFF::OESmirnoffComplex Constructors OEGetMolComplexComponents OEGetMolComplexFragments OEGetResidueAtoms OEGrapheme::OE2DActiveSiteDisplay Constructors GetDisplayedLigand GetDisplayedResidues GetHeight GetOptions GetWidth IsValid OEGrapheme::OE2DActiveSiteDisplayOptions Constructors GetRenderInteractiveLegend GetResidueSVGMarkupFunctor GetSVGMagnifyResidueInHover operator= SetBackgroundColor SetDimensions SetHeight SetRenderInteractiveLegend SetResidueSVGMarkupFunctor SetScale SetSuperAtomStyle SetSVGMagnifyResidueInHover SetWidth OEGrapheme::OE2DActiveSiteLegendDisplayOptions Constructors NumCols NumRows operator= OEGrapheme::OE2DPropMap Constructors GetLegendFont GetLegendFontScale GetLegendLocation GetMaxValue GetMinValue GetNegativeColor GetPositiveColor GetRadiusRatio GetResolution operator= Render SetLegendFont SetLegendFontScale SetLegendLocation SetMaxValue SetMinValue SetNegativeColor SetPositiveColor SetRadiusRatio SetResolution OEGrapheme::OE2DPropMapSetup OEGrapheme::OE2DPropMapSetup::All OEGrapheme::OE2DPropMapSetup::Legend OEGrapheme::OE2DPropMapSetup::MaxValue OEGrapheme::OE2DPropMapSetup::MinValue OEGrapheme::OE2DPropMapSetup::NegativeColor OEGrapheme::OE2DPropMapSetup::PositiveColor OEGrapheme::OE2DPropMapSetup::RadiusRatio OEGrapheme::OE2DPropMapSetup::Resolution OEGrapheme::OEActiveSiteRenderStyle OEGrapheme::OEActiveSiteRenderStyle::BFactorMap OEGrapheme::OEActiveSiteRenderStyle::ContactMap OEGrapheme::OEActiveSiteRenderStyle::Default OEGrapheme::OEActiveSiteRenderStyle::InteractionMap OEGrapheme::OEActiveSiteRenderStyle::UnpairedMap OEGrapheme::OEAddComplexSurfaceArcs OEGrapheme::OEAddGlyph OEGrapheme::OEAddLigandHighlighting OEGrapheme::OEAddResidueHighlighting OEGrapheme::OEAlignedDepictionFrom3DOptions Constructors GetClearCoords GetMaxBondRotations GetSuppressHydrogens operator= SetClearCoords SetMaxBondRotations SetSuppressHydrogens OEGrapheme::OEAlphaRainbowArcFxn Constructors CreateCopy operator() OEGrapheme::OEAtomGlyphBase Constructors CreateCopy RenderGlyph OEGrapheme::OEAtomGlyphCircle Constructors CreateCopy RenderGlyph OEGrapheme::OEBondGlyphArrow Constructors CreateCopy RenderGlyph OEGrapheme::OEBondGlyphBase Constructors CreateCopy RenderGlyph OEGrapheme::OEBondGlyphCircle Constructors CreateCopy RenderGlyph OEGrapheme::OEBondGlyphCross Constructors CreateCopy RenderGlyph OEGrapheme::OEBondGlyphCurvedArrow Constructors CreateCopy RenderGlyph OEGrapheme::OEBondGlyphScissors Constructors CreateCopy RenderGlyph OEGrapheme::OEBondGlyphStitch Constructors CreateCopy RenderGlyph OEGrapheme::OEBondGlyphZigZag Constructors CreateCopy RenderGlyph OEGrapheme::OEBrickRoadArcFxn Constructors CreateCopy operator() OEGrapheme::OECastleArcFxn Constructors CreateCopy operator() OEGrapheme::OECircleStyle OEGrapheme::OECircleStyle::AlphaRainbow OEGrapheme::OECircleStyle::BrickRoad OEGrapheme::OECircleStyle::Castle OEGrapheme::OECircleStyle::Cog OEGrapheme::OECircleStyle::Default OEGrapheme::OECircleStyle::Eyelash OEGrapheme::OECircleStyle::Flower OEGrapheme::OECircleStyle::GreekKey OEGrapheme::OECircleStyle::Necklace OEGrapheme::OECircleStyle::OliveBranch OEGrapheme::OECircleStyle::Pearls OEGrapheme::OECircleStyle::RaceTrack OEGrapheme::OECircleStyle::RailroadTrack OEGrapheme::OECircleStyle::Saw OEGrapheme::OECircleStyle::Simpson OEGrapheme::OECircleStyle::Stitch OEGrapheme::OECircleStyle::Sun OEGrapheme::OECircleStyle::Wreath OEGrapheme::OEClearSurfaceArcFxn OEGrapheme::OECogArcFxn Constructors CreateCopy operator() OEGrapheme::OEColorAtomStyle OEGrapheme::OEColorAtomStyle::Circle OEGrapheme::OEColorAtomStyle::Default OEGrapheme::OEColorAtomStyle::Hidden OEGrapheme::OEColorForceFieldDisplay Constructors GetColor GetColorTypes GetName NumColorTypes operator= SetColor SetName OEGrapheme::OEColorForceFieldLegendDisplayOptions Constructors NumCols NumRows operator= OEGrapheme::OEColorGradientDisplayOptions AddLabel AddMarkedValue AddMarkedValues ClearBoxRange ClearLabels ClearMarkedValues Constructors GetBoxRangeMax GetBoxRangeMin GetBoxRangePen GetColorStopLabelFont GetColorStopLabelFontScale GetColorStopPrecision GetColorStopVisibility GetLabels GetMarkedValuePen GetMarkedValuePrecision GetMarkedValues operator= SetBoxRange SetBoxRangePen SetColorStopLabelFont SetColorStopLabelFontScale SetColorStopPrecision SetColorStopVisibility SetMarkedValuePen SetMarkedValuePrecision SetMarkedValues OEGrapheme::OEColorGradientLabel Constructors GetLabel GetValue operator= OEGrapheme::OEColorOverlapDisplayOptions ClearQuerySurfaceArcFxn Constructors GetClearBackground GetQuerySurfaceArcFxn operator= SetClearBackground SetQuerySurfaceArcFxn OEGrapheme::OEComplexSurfaceArcFxnBase Constructors CreateComplexCopy CreateCopy GetDepth operator() operator= SetDepth OEGrapheme::OEConfigure2DPropMap OEGrapheme::OEDefaultArcFxn Constructors CreateCopy operator() OEGrapheme::OEDefaultBuriedArcFxn Constructors CreateCopy operator() OEGrapheme::OEDefaultCavityArcFxn Constructors CreateCopy operator() OEGrapheme::OEDefaultSolventArcFxn Constructors CreateCopy operator() OEGrapheme::OEDefaultVoidArcFxn Constructors CreateCopy operator() OEGrapheme::OEDepictionFrom3DOptions Constructors GetCoordsToInertialFrame GetMaxBondRotations GetRotateTo2DReference GetSuppressHydrogens operator= SetCoordsToInertialFrame SetMaxBondRotations SetRotateTo2DReference SetSuppressHydrogens OEGrapheme::OEDraw2DSurface OEGrapheme::OEDrawActiveSiteLegend OEGrapheme::OEDrawAlphaRainbowCircle OEGrapheme::OEDrawAlphaRainbowSurfaceArc OEGrapheme::OEDrawBFactorMapLegend OEGrapheme::OEDrawBrickRoadCircle OEGrapheme::OEDrawBrickRoadSurfaceArc OEGrapheme::OEDrawCastleCircle OEGrapheme::OEDrawCastleSurfaceArc OEGrapheme::OEDrawCircle OEGrapheme::OEDrawCogCircle OEGrapheme::OEDrawCogSurfaceArc OEGrapheme::OEDrawColorForceFieldLegend OEGrapheme::OEDrawColorGradient OEGrapheme::OEDrawDefaultCircle OEGrapheme::OEDrawDefaultSurfaceArc OEGrapheme::OEDrawEyelashCircle OEGrapheme::OEDrawEyelashSurfaceArc OEGrapheme::OEDrawFlowerCircle OEGrapheme::OEDrawFlowerSurfaceArc OEGrapheme::OEDrawGreekKeyCircle OEGrapheme::OEDrawIridiumData OEGrapheme::OEDrawNecklaceCircle OEGrapheme::OEDrawNecklaceSurfaceArc OEGrapheme::OEDrawOliveBranchCircle OEGrapheme::OEDrawOliveBranchSurfaceArc OEGrapheme::OEDrawPearlsCircle OEGrapheme::OEDrawPearlsSurfaceArc OEGrapheme::OEDrawPeptide OEGrapheme::OEDrawRaceTrackCircle OEGrapheme::OEDrawRaceTrackSurfaceArc OEGrapheme::OEDrawRailroadTrackCircle OEGrapheme::OEDrawRailroadTrackSurfaceArc OEGrapheme::OEDrawResidues OEGrapheme::OEDrawROCSScores OEGrapheme::OEDrawSawCircle OEGrapheme::OEDrawSawSurfaceArc OEGrapheme::OEDrawSimpsonCircle OEGrapheme::OEDrawSimpsonSurfaceArc OEGrapheme::OEDrawStitchCircle OEGrapheme::OEDrawStitchSurfaceArc OEGrapheme::OEDrawSunCircle OEGrapheme::OEDrawSunSurfaceArc OEGrapheme::OEDrawSurfaceArc OEGrapheme::OEDrawUnpairedInteractionMapLegend OEGrapheme::OEDrawWreathCircle OEGrapheme::OEDrawWreathSurfaceArc OEGrapheme::OEEyelashArcFxn Constructors CreateCopy operator() OEGrapheme::OEFlowerArcFxn Constructors CreateCopy operator() OEGrapheme::OEGet2DSurfaceArcs OEGrapheme::OEGetMoleculeSurfaceScale OEGrapheme::OEGetNearbyAtom OEGrapheme::OEGetNearbyBond OEGrapheme::OEGetNearbyResidue OEGrapheme::OEGetNearestAtom OEGrapheme::OEGetNearestBond OEGrapheme::OEGetNearestResidue OEGrapheme::OEGetSurfaceArcFxn OEGrapheme::OEGraphemeGetArch OEGrapheme::OEGraphemeGetLicensee OEGrapheme::OEGraphemeGetPlatform OEGrapheme::OEGraphemeGetRelease OEGrapheme::OEGraphemeGetSite OEGrapheme::OEGraphemeGetVersion OEGrapheme::OEGraphemeIsLicensed OEGrapheme::OEHasSurfaceArcFxn OEGrapheme::OELegendLocation OEGrapheme::OELegendLocation::Bottom OEGrapheme::OELegendLocation::Default OEGrapheme::OELegendLocation::Hidden OEGrapheme::OELegendLocation::Left OEGrapheme::OELegendLocation::Right OEGrapheme::OELegendLocation::Top OEGrapheme::OENearestResidue Constructors GetDisplayPosition GetDist GetResidue IsValid OEGrapheme::OENecklaceArcFxn Constructors CreateCopy operator() OEGrapheme::OENullArcFxn CreateCopy operator() OEGrapheme::OEOliveBranchArcFxn Constructors CreateCopy operator() OEGrapheme::OEPatternDirection OEGrapheme::OEPatternDirection::Default OEGrapheme::OEPatternDirection::Inside OEGrapheme::OEPatternDirection::Outside OEGrapheme::OEPearlsArcFxn Constructors CreateCopy operator() OEGrapheme::OEPeptideDisplayOptions Constructors GetAminoAcidScale GetInteractive GetLabelStyle operator= SetAminoAcidScale SetInteractive SetLabelStyle OEGrapheme::OEPeptideLabelStyle OEGrapheme::OEPeptideLabelStyle::Default OEGrapheme::OEPeptideLabelStyle::SingleLetter OEGrapheme::OEPeptideLabelStyle::ThreeLetters OEGrapheme::OEPlotMarker Constructors GetPen GetScale GetStyle operator!= operator= operator== OEGrapheme::OEPlotMarkerStyle OEGrapheme::OEPlotMarkerStyle::Circle OEGrapheme::OEPlotMarkerStyle::Default OEGrapheme::OEPlotMarkerStyle::Square OEGrapheme::OEPrepareActiveSiteDepiction OEGrapheme::OEPrepareAlignedDepictionFrom3D OEGrapheme::OEPrepareDepictionFrom3D OEGrapheme::OERaceTrackArcFxn Constructors CreateCopy operator() OEGrapheme::OERailroadTrackArcFxn Constructors CreateCopy operator() OEGrapheme::OERamachandranPlot AddMolecule AddRamachandran Constructors NumDataPoints operator= OEGrapheme::OERenderActiveSite OEGrapheme::OERenderActiveSiteMaps OEGrapheme::OERenderBFactorMap OEGrapheme::OERenderColorOverlap OEGrapheme::OERenderContactMap OEGrapheme::OERenderRamachandranPlot OEGrapheme::OERenderShapeOverlap OEGrapheme::OERenderShapeQuery OEGrapheme::OERenderUnpairedInteractionMap OEGrapheme::OEResidueSVGMarkupBase CreateCopy GetClassName GetGroupId OEGrapheme::OEResidueSVGNoMarkup Constructors CreateCopy GetClassName GetGroupId OEGrapheme::OEResidueSVGStandardMarkup Constructors CreateCopy GetClassName GetGroupId OEGrapheme::OESawArcFxn Constructors CreateCopy operator() OEGrapheme::OESetSurfaceArcFxn OEGrapheme::OESetup2DPropMap OEGrapheme::OEShapeOverlapDisplay Constructors GetTitle IsValid operator= OEGrapheme::OEShapeOverlapDisplayOptions ClearQuerySurfaceArcFxn Constructors GetClearBackground GetOverlapColor GetOverlapDisplayStyle GetQuerySurfaceArcFxn operator= SetClearBackground SetOverlapColor SetOverlapDisplayStyle SetQuerySurfaceArcFxn OEGrapheme::OEShapeOverlapDisplayStyle OEGrapheme::OEShapeOverlapDisplayStyle::Default OEGrapheme::OEShapeOverlapDisplayStyle::PropertyCloud OEGrapheme::OEShapeOverlapDisplayStyle::PropertyMap OEGrapheme::OEShapeQueryDisplay Constructors GetTitle IsValid operator= OEGrapheme::OEShapeQueryDisplayOptions ClearSurfaceArcFxn Constructors GetClearBackground GetColorAtomStyle GetDepictOrientation GetSurfaceArcFxn operator= SetClearBackground SetColorAtomStyle SetDepictOrientation SetSurfaceArcFxn OEGrapheme::OESimpsonArcFxn Constructors CreateCopy operator() OEGrapheme::OEStitchArcFxn Constructors CreateCopy operator() OEGrapheme::OESunArcFxn Constructors CreateCopy operator() OEGrapheme::OESurfaceArc Constructors GetAtomDisplay GetBgnAngle GetCenter GetEndAngle GetRadius operator= SetAtomDisplay SetBgnAngle SetCenter SetEndAngle SetRadius OEGrapheme::OESurfaceArcFxnBase CreateCopy operator() OEGrapheme::OESurfaceArcScale OEGrapheme::OESurfaceArcScale::Default OEGrapheme::OESurfaceArcScale::Maximum OEGrapheme::OESurfaceArcScale::Minimum OEGrapheme::OESurfaceArcStyle OEGrapheme::OESurfaceArcStyle::AlphaRainbow OEGrapheme::OESurfaceArcStyle::BrickRoad OEGrapheme::OESurfaceArcStyle::Castle OEGrapheme::OESurfaceArcStyle::Cog OEGrapheme::OESurfaceArcStyle::Default OEGrapheme::OESurfaceArcStyle::Eyelash OEGrapheme::OESurfaceArcStyle::Flower OEGrapheme::OESurfaceArcStyle::Necklace OEGrapheme::OESurfaceArcStyle::OliveBranch OEGrapheme::OESurfaceArcStyle::Pearls OEGrapheme::OESurfaceArcStyle::RaceTrack OEGrapheme::OESurfaceArcStyle::RailroadTrack OEGrapheme::OESurfaceArcStyle::Saw OEGrapheme::OESurfaceArcStyle::Simpson OEGrapheme::OESurfaceArcStyle::Stitch OEGrapheme::OESurfaceArcStyle::Sun OEGrapheme::OESurfaceArcStyle::Wreath OEGrapheme::OEWreathArcFxn Constructors CreateCopy operator() OEGraphSim::OEAreCompatibleDatabases OEGraphSim::OEConfigureFingerPrint OEGraphSim::OEConfigureFPDatabaseMemoryType OEGraphSim::OEConfigureFPDatabaseOptions OEGraphSim::OECosine OEGraphSim::OECreateFastFPDatabaseFile OEGraphSim::OECreateFastFPDatabaseOptions Constructors GetFPType GetNumProcessors SetNumProcessors SetTracer OEGraphSim::OEDice OEGraphSim::OEEuclid OEGraphSim::OEFastFPDatabase Constructors GetAllScores GetFingerPrint GetFPTypeBase GetHistogram GetMemoryType GetMemoryTypeString GetMoleculeIndex GetRawScores GetScores GetSortedScores GetSparseMatrix GetVariogram IsValid NumFingerPrints SortedSearch OEGraphSim::OEFastFPDatabaseMemoryType OEGraphSim::OEFastFPDatabaseMemoryType::CUDA OEGraphSim::OEFastFPDatabaseMemoryType::Default OEGraphSim::OEFastFPDatabaseMemoryType::InMemory OEGraphSim::OEFastFPDatabaseMemoryType::MemoryMapped OEGraphSim::OEFastFPDatabaseParams Constructors GetFPTypeBase GetMolDatabaseFilename IsInLittleEndian IsValid NumFingerPrints OEGraphSim::OEFingerPrint Constructors GetFPTypeBase operator bool operator!= operator= operator== SetFPTypeBase OEGraphSim::OEFPAtomType OEGraphSim::OEFPAtomType::Aromaticity OEGraphSim::OEFPAtomType::AtomicNumber OEGraphSim::OEFPAtomType::Chiral OEGraphSim::OEFPAtomType::DefaultAtom OEGraphSim::OEFPAtomType::DefaultCircularAtom OEGraphSim::OEFPAtomType::DefaultCircularVSAtom OEGraphSim::OEFPAtomType::DefaultPathAtom OEGraphSim::OEFPAtomType::DefaultPathVSAtom OEGraphSim::OEFPAtomType::DefaultTreeAtom OEGraphSim::OEFPAtomType::DefaultTreeVSAtom OEGraphSim::OEFPAtomType::EqAromatic OEGraphSim::OEFPAtomType::EqHalogen OEGraphSim::OEFPAtomType::EqHBondAcceptor OEGraphSim::OEFPAtomType::EqHBondDonor OEGraphSim::OEFPAtomType::FormalCharge OEGraphSim::OEFPAtomType::HCount OEGraphSim::OEFPAtomType::HvyDegree OEGraphSim::OEFPAtomType::Hybridization OEGraphSim::OEFPAtomType::InRing OEGraphSim::OEFPAtomType::None OEGraphSim::OEFPBondType OEGraphSim::OEFPBondType::BondOrder OEGraphSim::OEFPBondType::Chiral OEGraphSim::OEFPBondType::DefaultBond OEGraphSim::OEFPBondType::DefaultCircularBond OEGraphSim::OEFPBondType::DefaultCircularVSBond OEGraphSim::OEFPBondType::DefaultPathBond OEGraphSim::OEFPBondType::DefaultPathVSBond OEGraphSim::OEFPBondType::DefaultTreeBond OEGraphSim::OEFPBondType::DefaultTreeVSBond OEGraphSim::OEFPBondType::InRing OEGraphSim::OEFPBondType::None OEGraphSim::OEFPDatabase AddFP ClearCutoff Constructors GetCutoff GetDescendingOrder GetFingerPrints GetFPTypeBase GetScores GetSortedScores HasCutoff NumFingerPrints SetCutoff SetDescendingOrder SetSimFunc OEGraphSim::OEFPDatabaseOptions ClearCutoff Constructors GetCutoff GetDescendingOrder GetLimit GetNumProcessors GetSimFunc GetTverskyAlpha GetTverskyBeta HasCutoff operator= SetCutoff SetDescendingOrder SetLimit SetNumProcessors SetSimFunc SetTverskyCoeffs OEGraphSim::OEFPDatabaseOptionsSetup OEGraphSim::OEFPDatabaseOptionsSetup::All OEGraphSim::OEFPDatabaseOptionsSetup::Cutoff OEGraphSim::OEFPDatabaseOptionsSetup::DescendingOrder OEGraphSim::OEFPDatabaseOptionsSetup::Limit OEGraphSim::OEFPDatabaseOptionsSetup::SimFunc OEGraphSim::OEFPHistogram AddSample Constructors GetBinBoundaries GetBinCenters GetBinIdx GetBinWidth GetCounts GetDensity GetMax GetMin Mean NumBins NumSamples Std OEGraphSim::OEFPPattern Constructors GetBit GetSmarts GetUnhashed operator= OEGraphSim::OEFPType OEGraphSim::OEFPType::Circular OEGraphSim::OEFPType::Lingo OEGraphSim::OEFPType::MACCS166 OEGraphSim::OEFPType::Path OEGraphSim::OEFPType::Tree OEGraphSim::OEFPTypeBase Constructors GetFPType GetFPTypeString GetFPVersion GetFPVersionString OEGraphSim::OEFPTypeParams Constructors GetAtomTypes GetBondTypes GetFPType GetMaxDistance GetMinDistance GetNumBits GetVersion IsValid OEGraphSim::OEFPVariogram AddSample Constructors GetVariogram OEGraphSim::OEGetBitCounts OEGraphSim::OEGetCircularFPType OEGraphSim::OEGetFingerPrintVersion OEGraphSim::OEGetFingerPrintVersionString OEGraphSim::OEGetFPAtomType OEGraphSim::OEGetFPBondType OEGraphSim::OEGetFPCoverage OEGraphSim::OEGetFPDatabaseMemoryType OEGraphSim::OEGetFPOverlap OEGraphSim::OEGetFPPatterns OEGraphSim::OEGetFPType OEGraphSim::OEGetPathFPType OEGraphSim::OEGetPopCountMethod OEGraphSim::OEGetSimilarityMeasureName OEGraphSim::OEGetTreeFPType OEGraphSim::OEGraphSimGetArch OEGraphSim::OEGraphSimGetLicensee OEGraphSim::OEGraphSimGetPlatform OEGraphSim::OEGraphSimGetRelease OEGraphSim::OEGraphSimGetSite OEGraphSim::OEGraphSimGetVersion OEGraphSim::OEGraphsimIsGPUReady OEGraphSim::OEGraphSimIsLicensed OEGraphSim::OEIsFastFPDatabaseReady OEGraphSim::OEIsFPType OEGraphSim::OEIsSameFPType OEGraphSim::OEIsValidFPTypeString OEGraphSim::OEMakeCircularFP OEGraphSim::OEMakeFP OEGraphSim::OEMakeLingoFP OEGraphSim::OEMakeMACCS166FP OEGraphSim::OEMakePathFP OEGraphSim::OEMakeTreeFP OEGraphSim::OEManhattan OEGraphSim::OEPopCountMethod OEGraphSim::OEPopCountMethod::BitCount OEGraphSim::OEPopCountMethod::NoSupport OEGraphSim::OEPopCountMethod::PopCount OEGraphSim::OESetupFingerPrint OEGraphSim::OESetupFPDatabaseOptions OEGraphSim::OESimFuncBase Constructors CreateCopy GetSimTypeString operator() OEGraphSim::OESimMeasure OEGraphSim::OESimMeasure::Cosine OEGraphSim::OESimMeasure::Dice OEGraphSim::OESimMeasure::Euclid OEGraphSim::OESimMeasure::Manhattan OEGraphSim::OESimMeasure::Tanimoto OEGraphSim::OESimMeasure::Tversky OEGraphSim::OESimScore Constructors GetIdx GetScore OEGraphSim::OESimScorePair Constructors GetIdxA GetIdxB GetScore OEGraphSim::OESimSearchResult Constructor GetSearchStatus GetSortedScores IsValid NumSearched NumTargets OEGraphSim::OESimSearchStatus OEGraphSim::OESimSearchStatus::Finished OEGraphSim::OESimSearchStatus::InProgress OEGraphSim::OESimSearchStatus::Uninitialized OEGraphSim::OESimSearchStatusToName OEGraphSim::OETanimoto OEGraphSim::OETanimotoSim Constructors CreateCopy GetSimTypeString operator() OEGraphSim::OETversky OEGraphSim::OETverskySim Constructors CreateCopy GetAlpha GetBeta GetSimTypeString operator() OEHasAtomIdx OEHasBondIdx OEHasConfIdx OEHierChain OEHierFragment OEHierResidue OEHierView OEIsStandardProteinResidue OEIUPAC::OECapitalizeName OEIUPAC::OECharSet OEIUPAC::OECharSet::ASCII OEIUPAC::OECharSet::DEFAULT OEIUPAC::OECharSet::EUCJP OEIUPAC::OECharSet::HTML OEIUPAC::OECharSet::SJIS OEIUPAC::OECharSet::UTF8 OEIUPAC::OECreateIUPACName OEIUPAC::OEFromBritish OEIUPAC::OEFromChinese OEIUPAC::OEFromDanish OEIUPAC::OEFromDutch OEIUPAC::OEFromFrench OEIUPAC::OEFromGerman OEIUPAC::OEFromGreek OEIUPAC::OEFromHTML OEIUPAC::OEFromHungarian OEIUPAC::OEFromIrish OEIUPAC::OEFromItalian OEIUPAC::OEFromJapanese OEIUPAC::OEFromKOI8R OEIUPAC::OEFromLanguage OEIUPAC::OEFromLatin1 OEIUPAC::OEFromPolish OEIUPAC::OEFromRomanian OEIUPAC::OEFromRussian OEIUPAC::OEFromSlovak OEIUPAC::OEFromSpanish OEIUPAC::OEFromSwedish OEIUPAC::OEFromUTF8 OEIUPAC::OEFromWelsh OEIUPAC::OEGetCIPStereo OEIUPAC::OEGetIUPACCharSet OEIUPAC::OEGetIUPACLanguage OEIUPAC::OEGetIUPACNamStyle OEIUPAC::OEIUPAC OEIUPAC::OEIUPAC::OENamStyleACDName OEIUPAC::OEIUPAC::OENamStyleAutoNom OEIUPAC::OEIUPAC::OENamStyleCAS OEIUPAC::OEIUPAC::OENamStyleCASIndex OEIUPAC::OEIUPAC::OENamStyleIUPAC OEIUPAC::OEIUPAC::OENamStyleIUPAC79 OEIUPAC::OEIUPAC::OENamStyleIUPAC93 OEIUPAC::OEIUPAC::OENamStyleOpenEye OEIUPAC::OEIUPAC::OENamStyleSystematic OEIUPAC::OEIUPAC::OENamStyleTraditional OEIUPAC::OEIUPACGetArch OEIUPAC::OEIUPACGetLicensee OEIUPAC::OEIUPACGetPlatform OEIUPAC::OEIUPACGetRelease OEIUPAC::OEIUPACGetSite OEIUPAC::OEIUPACGetVersion OEIUPAC::OEIUPACIsLicensed OEIUPAC::OELanguage OEIUPAC::OELanguage::AMERICAN OEIUPAC::OELanguage::BRITISH OEIUPAC::OELanguage::CHINESE OEIUPAC::OELanguage::DANISH OEIUPAC::OELanguage::DUTCH OEIUPAC::OELanguage::ENGLISH OEIUPAC::OELanguage::FRENCH OEIUPAC::OELanguage::GERMAN OEIUPAC::OELanguage::GREEK OEIUPAC::OELanguage::HUNGARIAN OEIUPAC::OELanguage::INTERNATIONAL OEIUPAC::OELanguage::IRISH OEIUPAC::OELanguage::ITALIAN OEIUPAC::OELanguage::JAPANESE OEIUPAC::OELanguage::POLISH OEIUPAC::OELanguage::PORTUGUESE OEIUPAC::OELanguage::ROMANIAN OEIUPAC::OELanguage::RUSSIAN OEIUPAC::OELanguage::SLOVAK OEIUPAC::OELanguage::SPANISH OEIUPAC::OELanguage::SWEDISH OEIUPAC::OELanguage::WELSH OEIUPAC::OELowerCaseName OEIUPAC::OENameLocant OEIUPAC::OEParseIUPACName OEIUPAC::OEReorderIndexName OEIUPAC::OESetCIPStereo OEIUPAC::OEToASCII OEIUPAC::OEToBritish OEIUPAC::OEToChinese OEIUPAC::OEToDanish OEIUPAC::OEToDutch OEIUPAC::OEToEUCJP OEIUPAC::OEToFrench OEIUPAC::OEToGerman OEIUPAC::OEToGreek OEIUPAC::OEToHTML OEIUPAC::OEToHungarian OEIUPAC::OEToIrish OEIUPAC::OEToItalian OEIUPAC::OEToJapanese OEIUPAC::OEToLanguage OEIUPAC::OEToLatin1 OEIUPAC::OEToPolish OEIUPAC::OEToRomanian OEIUPAC::OEToRussian OEIUPAC::OEToSJIS OEIUPAC::OEToSlovak OEIUPAC::OEToSpanish OEIUPAC::OEToSwedish OEIUPAC::OEToUTF8 OEIUPAC::OEToWelsh OEKekulize OELibraryGen, [1] OEMatchAtom OEMatchGraphMol OEMatchMolBase OEMath::OEBox Constructors Extend GetArea GetVolume GetXDim GetXMax GetXMid GetXMin GetYDim GetYMax GetYMid GetYMin GetZDim GetZMax GetZMid GetZMin IsInside operator= Setup OEMath::OEBoxArea OEMath::OEBoxExtend OEMath::OEBoxTranslate OEMath::OEBoxVolume OEMath::OEBoxXDim OEMath::OEBoxXMid OEMath::OEBoxYDim OEMath::OEBoxYMid OEMath::OEBoxZDim OEMath::OEBoxZMid OEMath::OECenter OEMath::OEConst OEMath::OEConst::c OEMath::OEConst::cal2J OEMath::OEConst::e OEMath::OEConst::eps0 OEMath::OEConst::h OEMath::OEConst::hbar OEMath::OEConst::k OEMath::OEConst::me OEMath::OEConst::mp OEMath::OEConst::mu OEMath::OEConst::NA OEMath::OEConst::R OEMath::OEGeom2DAdd OEMath::OEGeom2DAngle OEMath::OEGeom2DCopy OEMath::OEGeom2DDistance OEMath::OEGeom2DDistance2 OEMath::OEGeom2DDotProd OEMath::OEGeom2DMagnitude OEMath::OEGeom2DMidpoint OEMath::OEGeom2DNormalize OEMath::OEGeom2DRotate OEMath::OEGeom2DScale OEMath::OEGeom2DSetLength OEMath::OEGeom2DSubtract OEMath::OEGeom2DTranslate OEMath::OEGeom3DAbsTorsion OEMath::OEGeom3DAdd OEMath::OEGeom3DAllZero OEMath::OEGeom3DAngle OEMath::OEGeom3DAngleCoord OEMath::OEGeom3DCopy OEMath::OEGeom3DCrossProd OEMath::OEGeom3DDistance OEMath::OEGeom3DDistance2 OEMath::OEGeom3DDotProd OEMath::OEGeom3DEulerRotate OEMath::OEGeom3DEulerToQuaternion OEMath::OEGeom3DEulerToRotMatrix OEMath::OEGeom3DGetCenterAndExtents OEMath::OEGeom3DGetCenterOfMass OEMath::OEGeom3DMagnitude OEMath::OEGeom3DMakeQuaternion OEMath::OEGeom3DMatrixIdentity OEMath::OEGeom3DMatrixInvert OEMath::OEGeom3DMatrixMultiply OEMath::OEGeom3DMatrixTranspose OEMath::OEGeom3DNormalize OEMath::OEGeom3DNormalizeQuaternion OEMath::OEGeom3DPlanarCoord OEMath::OEGeom3DQuaternionIdentity OEMath::OEGeom3DQuaternionInvert OEMath::OEGeom3DQuaternionRotate OEMath::OEGeom3DQuaternionToRotMatrix OEMath::OEGeom3DReflect OEMath::OEGeom3DReflectCoord OEMath::OEGeom3DRotate OEMath::OEGeom3DRotVectorToTransform OEMath::OEGeom3DScale OEMath::OEGeom3DSetLength OEMath::OEGeom3DSubtract OEMath::OEGeom3DTetraCoord OEMath::OEGeom3DTorsion OEMath::OEGeom3DTranslate OEMath::OEGeom3DUnitQuaternionRotate OEMath::OEGeom3DVolume OEMath::OEGeomDotProd OEMath::OEGeomNormalizeQuaternion OEMath::OEGeomQuaternionMultiply, [1] OEMath::OEInBox OEMath::OEInSphere OEMath::OEKernelPLS Constructor Fit GetB0 GetBValues GetNumFeaturesUsed operator= Predict OEMath::OEMath OEMath::OEMath::Deg2Rad OEMath::OEMath::Pi OEMath::OEMath::Pi2 OEMath::OEMath::Rad2Deg OEMath::OEMatrix AddRow Clear Constructors GetData GetNumColumns GetNumRows operator= Resize SetRowData Transpose OEMath::OESetupBox OEMath::OESetupBoxCenterAndExtents OEMath::OESphere Constructor GetArea GetRad GetVolume GetX GetY GetZ IsInside operator= SetCenter SetRad OEMath::OESphereArea OEMath::OESphereVolume OEMath::OESquareMatrix Constructors operator= Resize OEMedChem::OEApplyChEMBL18SolubilityTransforms OEMedChem::OEApplyChEMBL24SolubilityTransforms OEMedChem::OEBemisMurckoOptions Constructors CreateCopy GetRegionType GetSubstituentSearch GetUnsaturatedHeteroBonds SetRegionType SetSubstituentSearch SetUnsaturatedHeteroBonds Validate OEMedChem::OECalculateComboBelief OEMedChem::OECalculateETComboBelief OEMedChem::OEConfigureMatchedPairIndexOptions OEMedChem::OEConfigureMCSFragDatabaseOptions OEMedChem::OECreateIDString OEMedChem::OECreateIDStrings OEMedChem::OECreateMMPIndexFile OEMedChem::OECreateMMPIndexOptions Constructors GetMaxRecord GetMMPOptions GetNumThreads GetVerbose SetMaxRecord SetNumThreads SetTracer SetVerbose OEMedChem::OECreateMMPIndexStatus AddIndexedMol AddUnindexedMol Constructors GetNumMatchedPairs GetNumMols GetTotalMols GetUnindexedMols operator+ operator= SetNumMatchedPairs SetNumMols SetUnindexedMols SetValid OEMedChem::OEDetermineConnectiveComplexity OEMedChem::OEDetermineElementalComplexity OEMedChem::OEDetermineMolecularComplexity OEMedChem::OEDetermineRingComplexity OEMedChem::OEDetermineStereoComplexity OEMedChem::OEDetermineSymmetryComplexity OEMedChem::OEGetBemisMurcko OEMedChem::OEGetFuncGroupFragments OEMedChem::OEGetMatchedMolecularPairs OEMedChem::OEGetMatchedPairAnalyzerFileType OEMedChem::OEGetRegionType OEMedChem::OEGetRegionTypeName OEMedChem::OEGetRingChainFragments OEMedChem::OEGetRingLinkerSideChainFragments OEMedChem::OEGetRingValue OEMedChem::OEIsMatchedPairAnalyzerFileType OEMedChem::OEIsMCSFragDatabaseFileType OEMedChem::OEIsReadableMatchedPairAnalyzer OEMedChem::OEIsWriteableMatchedPairAnalyzer OEMedChem::OEMatchedPair AddSDData ClearSDData Constructors CreateCopy FromIndex FromSmiles GetDataTags GetFromSDData GetSDData GetToSDData HasSDData NumDataTags operator= ToIndex ToSmiles OEMedChem::OEMatchedPairAnalyzer AddMol Constructors GetMaxMolIdx GetMolecule GetOptions GetProcessorID GetProcessorType IsIndexed ModifyOptions NumIndexNodes NumMatchedPairs NumMols OEMedChem::OEMatchedPairAnalyzerFileType OEMedChem::OEMatchedPairAnalyzerFileType::MCSFrags OEMedChem::OEMatchedPairAnalyzerFileType::MMPIndex OEMedChem::OEMatchedPairAnalyzerFileType::UNDEFINED OEMedChem::OEMatchedPairAnalyzerOptions ClearIndexableFragmentRange Constructors GetFragmentationLimit GetIndexableFragmentRangeMax GetIndexableFragmentRangeMin GetMaxAtomFilter GetOptions GetProcessorType HasIndexableFragmentHeavyAtomRange ModifyOptions operator= SetFragmentationLimit SetIndexableFragmentRange SetMaxAtomFilter SetOptions SetProcessorType OEMedChem::OEMatchedPairApplyTransforms OEMedChem::OEMatchedPairContext OEMedChem::OEMatchedPairContext::AllBonds OEMedChem::OEMatchedPairContext::Bond0 OEMedChem::OEMatchedPairContext::Bond1 OEMedChem::OEMatchedPairContext::Bond2 OEMedChem::OEMatchedPairContext::Bond3 OEMedChem::OEMatchedPairContext::Default OEMedChem::OEMatchedPairContext::Undefined OEMedChem::OEMatchedPairContextName OEMedChem::OEMatchedPairContextType OEMedChem::OEMatchedPairGetTransforms OEMedChem::OEMatchedPairIndexSetup OEMedChem::OEMatchedPairIndexSetup::All OEMedChem::OEMatchedPairIndexSetup::BondFragLimit OEMedChem::OEMatchedPairIndexSetup::FragmentationCuts OEMedChem::OEMatchedPairIndexSetup::FragMinMaxRange OEMedChem::OEMatchedPairIndexSetup::HeavyAtomLimit OEMedChem::OEMatchedPairIndexSetup::IndexHydrogenSingleCuts OEMedChem::OEMatchedPairIndexSetup::IndexHydrogenSites OEMedChem::OEMatchedPairIndexSetup::ProcessorType OEMedChem::OEMatchedPairIndexSetup::UniquesOnly OEMedChem::OEMatchedPairIndexStatus OEMedChem::OEMatchedPairIndexStatus::BinaryIOError OEMedChem::OEMatchedPairIndexStatus::CopyMolError OEMedChem::OEMatchedPairIndexStatus::Deactivated OEMedChem::OEMatchedPairIndexStatus::DuplicateRecordID OEMedChem::OEMatchedPairIndexStatus::DuplicateStructure OEMedChem::OEMatchedPairIndexStatus::FragmentationLimitFilter OEMedChem::OEMatchedPairIndexStatus::FragmentRangeFilter OEMedChem::OEMatchedPairIndexStatus::HeavyAtomFilter OEMedChem::OEMatchedPairIndexStatus::IncompatibleOptions OEMedChem::OEMatchedPairIndexStatus::NoError OEMedChem::OEMatchedPairIndexStatus::NoFragmentationBonds OEMedChem::OEMatchedPairIndexStatus::NoStructure OEMedChem::OEMatchedPairIndexStatus::ProcessorError OEMedChem::OEMatchedPairIndexStatus::ProcessorFilter OEMedChem::OEMatchedPairIndexStatus::Unspecified OEMedChem::OEMatchedPairIndexStatusName OEMedChem::OEMatchedPairIndexStatusType OEMedChem::OEMatchedPairOptions OEMedChem::OEMatchedPairOptions::AllCuts OEMedChem::OEMatchedPairOptions::ComboCuts OEMedChem::OEMatchedPairOptions::Default OEMedChem::OEMatchedPairOptions::DefaultFragIndex OEMedChem::OEMatchedPairOptions::DoubleCuts OEMedChem::OEMatchedPairOptions::ExportCompression OEMedChem::OEMatchedPairOptions::ExportHKeys OEMedChem::OEMatchedPairOptions::IndexHSingleCuts OEMedChem::OEMatchedPairOptions::IndexHSites OEMedChem::OEMatchedPairOptions::SingleCuts OEMedChem::OEMatchedPairOptions::TripleCuts OEMedChem::OEMatchedPairOptions::UniquesOnly OEMedChem::OEMatchedPairOptions::ValidAlterOpts OEMedChem::OEMatchedPairOptions::ValidFragIndexOpts OEMedChem::OEMatchedPairOptions::ValidIndexOpts OEMedChem::OEMatchedPairOptions::ValidOptions OEMedChem::OEMatchedPairOptionsName OEMedChem::OEMatchedPairOptionsType OEMedChem::OEMatchedPairProcessor OEMedChem::OEMatchedPairProcessor::BemisMurcko OEMedChem::OEMatchedPairProcessor::Custom OEMedChem::OEMatchedPairProcessor::Default OEMedChem::OEMatchedPairProcessor::HussainRea OEMedChem::OEMatchedPairProcessor::Undefined OEMedChem::OEMatchedPairProcessorName OEMedChem::OEMatchedPairProcessorType OEMedChem::OEMatchedPairTransform AddMatchedPair Constructors CreateCopy GetMatchedPairContext GetMatchedPairs GetMolecule GetMoleculeTitle GetTransform HasMatchedPair Invert NumMatchedPairs operator= SetMoleculeTitle SetTransform OEMedChem::OEMatchedPairTransformExtractMode OEMedChem::OEMatchedPairTransformExtractMode::AddAttachmentPts OEMedChem::OEMatchedPairTransformExtractMode::AddMCSCorrespondence OEMedChem::OEMatchedPairTransformExtractMode::Backward OEMedChem::OEMatchedPairTransformExtractMode::Default OEMedChem::OEMatchedPairTransformExtractMode::Forward OEMedChem::OEMatchedPairTransformExtractMode::NoIsotopes OEMedChem::OEMatchedPairTransformExtractMode::NoMatchedPairData OEMedChem::OEMatchedPairTransformExtractMode::NoMatchedPairs OEMedChem::OEMatchedPairTransformExtractMode::NoSMARTS OEMedChem::OEMatchedPairTransformExtractMode::Sorted OEMedChem::OEMatchedPairTransformExtractMode::SubstLimitSkip OEMedChem::OEMatchedPairTransformExtractMode::SuppressNodeSort OEMedChem::OEMatchedPairTransformExtractMode::Unspecified OEMedChem::OEMatchedPairTransformExtractOptions Constructors GetAttachmentPoints GetContext GetDirection GetIsotopes GetMatchedPairData GetMatchedPairs GetMaxMMPLimit GetMaxSubstituentLimit GetMaxSubstituentLimitSkip GetMCSCorrespondence GetMinMMPLimit GetMinSubstituentLimit GetOptions GetSMARTS operator= SetAttachmentPoints SetContext SetDirection SetIsotopes SetMatchedPairData SetMatchedPairs SetMaxSubstituentLimitSkip SetMCSCorrespondence SetMMPLimit SetOptions SetSMARTS SetSubstituentLimit OEMedChem::OEMCSFragDatabase AddConstMol AddMol ClearIndexedMols Constructors CoreToMoleculeCount CoreToMolecules GetMaxCoreMolecule GetMaxCoreMoleculeCount GetMaxMolIdx GetOptions GetScores GetSortedScores IsIndexed MoleculeToCores NumFragments NumMols ProcessMol OEMedChem::OEMCSFragDatabaseCoreQuery OEMedChem::OEMCSFragDatabaseOptions ClearIndexableFragmentRange Constructors GetFragmentationLimit GetIndexableFragmentRangeMax GetIndexableFragmentRangeMin GetMaxAtomFilter GetMaxFragLimit GetMinFragLimit GetOptions GetRingFragLimit HasIndexableFragmentHeavyAtomRange operator= operator== SetFragLimits SetFragmentationLimit SetIndexableFragmentRange SetMaxAtomFilter SetOptions SetRingFragLimit OEMedChem::OEMCSFragDatabaseSetup OEMedChem::OEMCSFragDatabaseSetup::All OEMedChem::OEMCSFragDatabaseSetup::AllFrags OEMedChem::OEMCSFragDatabaseSetup::BondFragLimit OEMedChem::OEMCSFragDatabaseSetup::FragCutsRange OEMedChem::OEMCSFragDatabaseSetup::FragmentationCuts OEMedChem::OEMCSFragDatabaseSetup::FragMinMaxRange OEMedChem::OEMCSFragDatabaseSetup::HeavyAtomLimit OEMedChem::OEMCSFragDatabaseSetup::IndexHydrogenSites OEMedChem::OEMCSFragDatabaseSetup::RingCuts OEMedChem::OEMCSMolSimScore Constructors GetIdx GetMCSCore GetScore operator= Set OEMedChem::OEMCSScoreType OEMedChem::OEMCSScoreType::AtomCount OEMedChem::OEMCSScoreType::BondCount OEMedChem::OEMCSScoreType::Default OEMedChem::OEMCSScoreType::Undefined OEMedChem::OEMCSSimFuncBase Constructors CreateCopy GetMCSSimTypeString operator() OEMedChem::OEMCSTanimotoSim Constructors CreateCopy GetMCSSimTypeString operator() OEMedChem::OEMCSTverskySim Constructors CreateCopy GetAlpha GetBeta GetMCSSimTypeString operator() OEMedChem::OEMedChemGetArch OEMedChem::OEMedChemGetLicensee OEMedChem::OEMedChemGetPlatform OEMedChem::OEMedChemGetRelease OEMedChem::OEMedChemGetSite OEMedChem::OEMedChemGetVersion OEMedChem::OEMedChemIsLicensed OEMedChem::OEMoleculeToCores OEMedChem::OENormalMolecularComplexity OEMedChem::OENormalStereoComplexity OEMedChem::OEReadMatchedPairAnalyzer OEMedChem::OEReadMCSFragDatabase OEMedChem::OEReadMMPIndexMolecules OEMedChem::OERegionType OEMedChem::OERegionType::All OEMedChem::OERegionType::Framework OEMedChem::OERegionType::Linker OEMedChem::OERegionType::Ring OEMedChem::OERegionType::Sidechain OEMedChem::OESetupMatchedPairIndexOptions OEMedChem::OESetupMCSFragDatabaseOptions OEMedChem::OETotalMolecularComplexity OEMedChem::OEWriteMatchedPairAnalyzer OEMedChem::OEWriteMCSFragDatabase OEMedChem::OEWriteMMPIndexMolecules oemedcheminfo.java Example Code OEModels::OEROCSQueryModelBuilder AddLigand Build ClearLigands Constructor GetROCSQueryModelOptions operator= SetLigands OEModels::OEROCSQueryModelOptions Constructor GetColorForceField GetMaxMoleculesPerModel GetMergeColorAtoms GetNumModels operator= SetColorForceField SetMaxMoleculesPerModel SetMergeColorAtoms SetNumModels OEMolAM1::OEAM1 CalcAM1 Constructors GetOptions GetResults operator= OEMolAM1::OEAM1Options Constructors GetMaxScfIter GetNumericGradDelta GetSCFTolerance GetSemiMethod operator= SetMaxScfIter SetNumericGradDelta SetSCFTolerance SetSemiMethod OEMolAM1::OEAM1Results Constructors GetAtomicBondOrder GetBondOrder GetBondOrders GetCharges GetEnergy GetNumSCFCycles IsConverged operator= OEMolAM1::OEMethodType OEMolAM1::OEMethodType::AM1 OEMolAM1::OEMethodType::PM3 OEMolAM1::OEOptimizedAM1 CalcAM1 Constructors operator= OEMolBase OEMolDatabase oemolistream OEMolMMFF::OEIsValidMMFFMolecule OEMolMMFF::OEMMFF Constructors operator= OEMolMMFF::OEMMFF94sParams Constructors OEMolMMFF::OEMMFFCalcVdw OEMolMMFF::OEMMFFOutOfPlane Constructors operator= Set OEMolMMFF::OEMMFFParams Constructors OEMolMMFF::OEMMFFStretchBend Constructors operator= Set oemolostream OEMolPotential::OEBendParams Constructors GetAtomIndex1 GetAtomIndex2 GetAtomIndex3 IsAngle IsValid operator= OEMolPotential::OEBendPotential Assignment operator Constructors Set OEMolPotential::OECoulombPotential Assignment operator Constructors OEMolPotential::OEFFParam OEMolPotential::OEFFParam::a0 OEMolPotential::OEFFParam::BendConst OEMolPotential::OEFFParam::ContactDist OEMolPotential::OEFFParam::eps OEMolPotential::OEFFParam::Epsilon OEMolPotential::OEFFParam::EqAngle OEMolPotential::OEFFParam::EqDist OEMolPotential::OEFFParam::EqDistance OEMolPotential::OEFFParam::k OEMolPotential::OEFFParam::ka OEMolPotential::OEFFParam::kb1 OEMolPotential::OEFFParam::kb2 OEMolPotential::OEFFParam::ko OEMolPotential::OEFFParam::listDv OEMolPotential::OEFFParam::listKv OEMolPotential::OEFFParam::listPhv OEMolPotential::OEFFParam::listPv OEMolPotential::OEFFParam::ntt OEMolPotential::OEFFParam::OOP OEMolPotential::OEFFParam::OutOfPlaneConst OEMolPotential::OEFFParam::p1 OEMolPotential::OEFFParam::ph1 OEMolPotential::OEFFParam::r0 OEMolPotential::OEFFParam::r1 OEMolPotential::OEFFParam::r2 OEMolPotential::OEFFParam::rij, [1] OEMolPotential::OEFFParam::StretchBendConst1 OEMolPotential::OEFFParam::StretchBendConst2 OEMolPotential::OEFFParam::StretchConst OEMolPotential::OEFFParam::V1 OEMolPotential::OEFFParam::v1 OEMolPotential::OEFFParam::V2 OEMolPotential::OEFFParam::v2 OEMolPotential::OEFFParam::V3 OEMolPotential::OEFFParam::v3 OEMolPotential::OEFFParams Assignment operator Constructors CreateCopy GetAtomTypeIndex GetAtomTypeName GetBendParams GetContactDistance GetCoulombParams GetEquilibriumAngle GetEquilibriumBondLength GetOutOfPlaneParams GetStretchBendParams GetStretchParams GetTitle GetTorsionParams GetVdwParams GetVdwRadius HasBendParams HasStretchParams HasTorsionParams HasVdwParams PrepMol OEMolPotential::OEFFPotential Assignment operator Constructors Set OEMolPotential::OEForceField GetTitle HasCoulomb HasInternalCharges PrepMol Set SetNonBondCutoff SetTitle OEMolPotential::OEFuncType OEMolPotential::OEFuncType::All OEMolPotential::OEFuncType::AllRepel OEMolPotential::OEFuncType::Bend OEMolPotential::OEFuncType::Bond OEMolPotential::OEFuncType::Coulomb OEMolPotential::OEFuncType::HarmonicPot OEMolPotential::OEFuncType::ImproperTorsion OEMolPotential::OEFuncType::InterAdapt OEMolPotential::OEFuncType::InterMolCoulomb OEMolPotential::OEFuncType::InterMolVdW OEMolPotential::OEFuncType::OutOfPlane OEMolPotential::OEFuncType::QuatAdapt OEMolPotential::OEFuncType::Sheffield OEMolPotential::OEFuncType::Stretch OEMolPotential::OEFuncType::StretchBend OEMolPotential::OEFuncType::SubsetAdapt OEMolPotential::OEFuncType::SubsetAdaptor OEMolPotential::OEFuncType::TorAdapt OEMolPotential::OEFuncType::Torsion OEMolPotential::OEFuncType::Undefined OEMolPotential::OEFuncType::VdW OEMolPotential::OEFuncType::VdWRepel OEMolPotential::OEGenericFF AddMolFunc Constructors GetComponents RemoveMolFunc OEMolPotential::OEGenericFF2 AddMolFunc Constructors GetComponents RemoveMolFunc OEMolPotential::OEInteraction Constructors GetAtoms GetName GetValues NumAtoms NumValues operator= OEMolPotential::OEInteractParams Assignment operator Clear Constructors Get GetList Set SetList OEMolPotential::OEInterAdaptor AdaptGrad Constructors Set OEMolPotential::OEInterCoulombPotential Assignment operator Constructors OEMolPotential::OEInterMolFunc1 AdaptHostCoords GetVar SetHostFlex SetupHost OEMolPotential::OEInterMolFunc2 OEMolPotential::OEInterNonBondPotBase Assignment operator Constructors Set SetNonBondCutoff OEMolPotential::OEInterNonBondPotential Assignment operator Constructors OEMolPotential::OEInterVdwPotential Assignment operator Constructors OEMolPotential::OEMolAdaptor SetMolFunc OEMolPotential::OEMolAdaptor2 SetMolFunc2 OEMolPotential::OEMolFunc Clear ClearPredicates GetInteractions Set Setup OEMolPotential::OEMolFunc0 OEMolPotential::OEMolFunc1 OEMolPotential::OEMolFunc2 OEMolPotential::OENonBondIntcsOptions Assignment operator Constructors CreateCopy GetCutoff GetUseCoulomb GetUseVdW SetCutoff SetUseCoulomb SetUseVdW OEMolPotential::OENonBondPotBase Assignment operator Constructors GetNonBondOptions Set OEMolPotential::OENonBondPotential Assignment operator Constructors OEMolPotential::OENumericMolFunc2 Constructors Set OEMolPotential::OEOutOfPlaneParams Constructors GetAtomIndex1 GetAtomIndex2 GetAtomIndex3 GetAtomIndex4 IsValid operator= OEMolPotential::OEOutOfPlanePotential Assignment operator Constructors OEMolPotential::OEQuatAdaptor AdaptGrad Constructors IsRedundant OEMolPotential::OEScaledMolFunc Constructors Set OEMolPotential::OEStretchParams Constructors GetAtomIndex1 GetAtomIndex2 IsBond IsValid operator= OEMolPotential::OEStretchPotential Assignment operator Constructors Set OEMolPotential::OESubsetAdaptor AdaptGrad AdaptHessian Constructors Set OEMolPotential::OETorAdaptor AdaptGrad Constructors Set OEMolPotential::OETorQuatAdaptor AdaptGrad Constructors Set OEMolPotential::OETorsionParams Constructors GetAtomIndex1 GetAtomIndex2 GetAtomIndex3 GetAtomIndex4 IsTorsion IsValid operator= OEMolPotential::OETorsionPotential Assignment operator Constructors Set OEMolPotential::OEVarType OEMolPotential::OEVarType::Cart OEMolPotential::OEVarType::SolidBody OEMolPotential::OEVarType::Torsions OEMolPotential::OEVarType::TranRotTor OEMolPotential::OEVdwParams Constructors GetAtom1 GetAtom2 GetAtomIndex1 GetAtomIndex2 IsPair IsValid operator= OEMolPotential::OEVdwPotential Assignment operator Constructors OEMolProp::OECheckXLogXType OEMolProp::OECheckXLogXTypes OEMolProp::OEConfigureFilterParams OEMolProp::OEConfigureFilterType OEMolProp::OEFilter AddNormalizationRule ClearNormalizationRules Constructors GetCanonOrder GetFilterType GetFlagTableFailures GetMessage GetMMFFTypeCheck GetpKaNormalize GetSDTag GetTable GetTypeCheck operator bool operator() operator= ParseNewRules PrintConfig SetCanonOrder SetErrorLevel SetFlagTableFailures SetMMFFTypeCheck SetpKaNormalize SetSDTag SetTable SetTypeCheck OEMolProp::OEFilterParamName OEMolProp::OEFilterParamName::Type OEMolProp::OEFilterParamSetup OEMolProp::OEFilterParamSetup::All OEMolProp::OEFilterParamSetup::Type OEMolProp::OEFilterType OEMolProp::OEFilterType::BlockBuster OEMolProp::OEFilterType::BlockBusterPAINS OEMolProp::OEFilterType::Default OEMolProp::OEFilterType::Drug OEMolProp::OEFilterType::Fragment OEMolProp::OEFilterType::Lead OEMolProp::OEFilterType::Max OEMolProp::OEFilterType::PAINS OEMolProp::OEGet2dPSA OEMolProp::OEGetAnionicCarbonCount OEMolProp::OEGetAromaticRingCount OEMolProp::OEGetFilterType OEMolProp::OEGetFractionCsp3 OEMolProp::OEGetHalideFraction OEMolProp::OEGetHBondAcceptorCount OEMolProp::OEGetHBondDonorCount OEMolProp::OEGetLipinskiAcceptorCount OEMolProp::OEGetLipinskiDonorCount OEMolProp::OEGetLongestUnbranchedCarbonsChain OEMolProp::OEGetLongestUnbranchedHeavyAtomsChain OEMolProp::OEGetNumUnspecifiedAtomStereos OEMolProp::OEGetNumUnspecifiedBondStereos OEMolProp::OEGetRotatableBondCount OEMolProp::OEGetXLogP OEMolProp::OEGetXLogPResult OEMolProp::OEGetXLogPVersion OEMolProp::OEMolPropGetArch OEMolProp::OEMolPropGetLicensee OEMolProp::OEMolPropGetPlatform OEMolProp::OEMolPropGetRelease OEMolProp::OEMolPropGetSite OEMolProp::OEMolPropGetVersion OEMolProp::OEMolPropIsLicensed OEMolProp::OEWritePropertyDataToCSV OEMolProp::OEXLogPResult Constructors GetValue IsValid() OEMolSmirnoff::OEParsley Constructors operator= OEMolSmirnoff::OEParsleyParams Constructors operator= OEMolSmirnoff::OESage Constructors operator= OEMolSmirnoff::OESageParams Constructors operator= OEMolSmirnoff::OESmirnoff Constructors operator= OEMolSmirnoff::OESmirnoffParams Constructors Load operator= OEMolSmirnoff::OESmirnoffType OEMolSmirnoff::OESmirnoffType::PARSLEY_OPENFF OEMolSmirnoff::OESmirnoffType::SAGE_OPENFF OEMolSmirnoff::OESmirnoffType::SMIRNOFF99FROSST oemolstreambase OEOpt::OEAdaptor AdaptVar GetVar OEOpt::OEBFGSOpt Constructors GetHessianDimension GetInverseHessian GetKeepHessian operator= SetKeepHessian UseSavedHessian OEOpt::OECGLineMinimize Constructors OEOpt::OECheckpoint0 operator() OEOpt::OECheckpoint1 operator() OEOpt::OEConjGradOpt Constructors operator= OEOpt::OEDFPOpt Constructors operator= OEOpt::OEFComponent Constructors OEOpt::OEFletcherReevesOpt Constructors operator= OEOpt::OEFunc0 GetFComponents NumVar operator() OEOpt::OEFunc1 operator() OEOpt::OEFunc2 operator() OEOpt::OEHestenesStiefelOpt Constructors operator= OEOpt::OELineMinimize CreateCopy operator() SetMaxStep OEOpt::OEMaxStepLineMinimize Constructors operator= OEOpt::OENewtonOpt Constructors operator= OEOpt::OENRLineSearch Constructors OEOpt::OEOptimizer0 GetIterLimit operator() SetIterLimit OEOpt::OEOptimizer1 GetIterLimit GetTolerance operator() SetIterLimit SetLineMinimize SetTolerance OEOpt::OEOptimizer2 GetIterLimit GetTolerance operator() SetIterLimit SetTolerance OEOpt::OEQNLineMinimize Constructors OEOpt::OERibierePolakOpt Constructors operator= OEOpt::OESteepestDescentOpt Constructors SetInitialStep OEPartPredAtom OEPB::OEArea Constructors GetArea GetMethod GetUseHydrogens operator= SetMethod SetUseHydrogens OEPB::OEAreaMethod OEPB::OEAreaMethod::Default OEPB::OEAreaMethod::Discrete OEPB::OEAreaMethod::Gaussian OEPB::OEAreaMethod::Undefined OEPB::OEBind Bind Constructors GetZap operator= SetProtein SetZap SimpleBind OEPB::OEBindResults Constructors GetAnalyticCoulombicBindingEnergy GetBoundLigandCoulombEnergy GetBoundProteinCoulombEnergy GetComplexCoulombEnergy GetCoulombEnergy GetDesolvationEnergy GetLigandDesolvationEnergy GetProteinDesolvationEnergy GetUnboundLigandCoulombEnergy GetUnboundProteinCoulombEnergy operator= Print OEPB::OECalculateCoulombicBinding OEPB::OECoulombicAtomPotentials OEPB::OECoulombicSelfEnergy OEPB::OEET Constructors GetDielectric GetGridBuffer GetGridSpacing GetInnerDielectric GetInnerMask GetJoin GetOuterMask GetSaltConcentration operator= SetDielectric SetGridBuffer SetGridSpacing SetInnerDielectric SetInnerMask SetJoin SetOuterMask SetRefMol SetSaltConcentration Tanimoto OEPB::OEMakeETGrid OEPB::OESimpleBindResults Constructors GetBindingEnergy GetBoundLigandArea GetBoundLigandAreaEnergy GetBoundLigandZapEnergy GetBoundProteinArea GetBoundProteinAreaEnergy GetBoundProteinZapEnergy GetBuriedArea GetBuriedAreaEnergy GetComplexArea GetComplexAreaEnergy GetComplexZapEnergy GetConf GetUnboundLigandArea GetUnboundLigandAreaEnergy GetUnboundLigandZapEnergy GetUnboundProteinArea GetUnboundProteinAreaEnergy GetUnboundProteinZapEnergy GetZapEnergy operator= Print OEPB::OEZap CalcAtomPotentials CalcForces CalcPotentialGrid CalcSolvationEnergy ClearFocusTarget Constructors GetBoundarySpacing GetDielectricModel GetError GetFocusTarget GetGridSpacing GetInnerDielectric GetIterations GetMolecule GetOuterDielectric GetProbeRadius GetSaltConcentration GetVerbose IsFocusTargetSet operator= SetBoundarySpacing SetDielectricModel SetError SetFocusTarget SetGridSpacing SetInnerDielectric SetIterations SetMolecule SetOuterDielectric SetProbeRadius SetSaltConcentration SetVerbose OEPB::OEZapBind OEPB::OEZapDielectricModel OEPB::OEZapDielectricModel::Default OEPB::OEZapDielectricModel::Gaussian OEPB::OEZapDielectricModel::Molecular OEPB::OEZapGetArch OEPB::OEZapGetLicensee OEPB::OEZapGetPlatform OEPB::OEZapGetRelease OEPB::OEZapGetSite OEPB::OEZapGetVersion OEPDBClassify OEPlatform::OEAddLicenseData OEPlatform::OEAddLicenseFromHttp OEPlatform::OEAddLicenseKey OEPlatform::OEBigEndian OEPlatform::OECloseIStream OEPlatform::OECloseOStream OEPlatform::OECompress OEPlatform::OECompressionAvailable OEPlatform::OECondition Acquire Broadcast Constructors Release Signal Wait OEPlatform::OECreateDirectory OEPlatform::OECurrentTime OEPlatform::OEDirectoryScan Close Constructors Next operator bool OEPlatform::oeendl OEPlatform::oeends OEPlatform::OEFile AbsPath Constructors DirContents DirPath Exists FileName IsDirectory IsExecutable IsFile IsLink IsReadable IsWritable operator= Refresh Set Size OEPlatform::OEFileCorrectSeparators OEPlatform::OEFileCreate OEPlatform::OEFileDelete OEPlatform::OEFileDetermineName OEPlatform::OEFileDeterminePath OEPlatform::OEFileDeterminePathAndName OEPlatform::OEFileExists OEPlatform::OEFileIsDirectory OEPlatform::OEFileIsFile OEPlatform::OEFileIsLink OEPlatform::OEFileIsReadable OEPlatform::OEFileIsWritable OEPlatform::OEFileRandomName OEPlatform::OEFileSize OEPlatform::OEFileTempDescriptor OEPlatform::OEFileTempDirectory OEPlatform::OEFileTempPath OEPlatform::oeflush OEPlatform::OEGetAbsolutePath OEPlatform::OEGetAllocaThreshold OEPlatform::OEGetCurrentWorkingDirectory OEPlatform::OEGetDomainName OEPlatform::OEGetHostIdent OEPlatform::OEGetHostName OEPlatform::OEGetIPAddress OEPlatform::OEGetMachineName OEPlatform::OEGetNumProcessors OEPlatform::OEGetPlatformInfo OEPlatform::OEGetProcessMemUsage OEPlatform::OEGetProcessorInfo OEPlatform::OEGetTimeOfDay OEPlatform::OEGetUserAppDataDir OEPlatform::OEGetUserDocumentsDir OEPlatform::OEGetUserHomeDir OEPlatform::OEGetUserName OEPlatform::OEHalfFloat Constructors GetValue operator double operator float operator long double OEPlatform::oeifstream Constructors fd openfd pread OEPlatform::oeigzstream Constructors OEPlatform::oeiofstream Constructors pread OEPlatform::OEIsNaN OEPlatform::OEIsNormalNum OEPlatform::oeisstream clear Constructors getbuffer operator= reset set OEPlatform::oeistdstream clear Constructors set stream OEPlatform::oeistream close Constructors get getbyte getline gettoken open operator>> peekbyte read skip skipbyte skipline OEPlatform::oeiwrapperstream clear Constructors set stream OEPlatform::OELocalTime OEPlatform::OELock OEPlatform::OELockCondition Constructors OEPlatform::OELockSpinlock OEPlatform::oemultiostream addstream clear Constructors OEPlatform::OEMutex Acquire Constructors Release OEPlatform::oeofstream append Constructors fd openfd OEPlatform::oeogzstream Constructors OEPlatform::OEOnce GetValue operator T * operator* operator-> OEPlatform::OEOpenIStream OEPlatform::OEOpenOStream OEPlatform::oeosstream clear Constructors set str OEPlatform::oeostdstream clear Constructors set stream OEPlatform::oeostream close Constructors flush open operator<< putbyte write OEPlatform::oeowrapperstream clear Constructors set stream OEPlatform::OEPlatform OEPlatform::OEPlatform::oeerr OEPlatform::OEPlatform::oein OEPlatform::OEPlatform::oenul OEPlatform::OEPlatform::oeout OEPlatform::OEProcessFileName OEPlatform::OEProcessSystemCommand OEPlatform::OERegisterIStream OEPlatform::OERegisterOStream OEPlatform::OERenameFile OEPlatform::OESetAllocaThreshold OEPlatform::OESetLicenseFile OEPlatform::OESleep OEPlatform::OESpinlock Acquire Constructors Release OEPlatform::oestream Constructors eof length operator bool rewind seek size tell OEPlatform::OEThread Constructors GetArg GetReturn GetStackSize Join Run SetArg SetReturn SetStackSize Start OEPlatform::OEThreadLocal Constructors operator T & operator T * operator* operator-> OEPlatform::OEToolkitsGetRelease OEPlatform::OETryMutex Acquire Constructors Release Try OEPlatform::OEUncompress OEPlatform::OEUnlink OEPlatform::OEUnlinkDirectory OEProton::OEAdjTypeAtNeutralpH OEProton::OEAdjTypeAtNeutralpH::Deprotonation OEProton::OEAdjTypeAtNeutralpH::NoChange OEProton::OEAdjTypeAtNeutralpH::NoChangeAndDeprotonation OEProton::OEAdjTypeAtNeutralpH::NoChangeAndProtonation OEProton::OEAdjTypeAtNeutralpH::Protonation OEProton::OEAdjTypeAtNeutralpH::Unknown OEProton::OEAM1BCCCharges Constructors GetOptimize GetPermissiveBCCs GetSizeLimit GetSymmetrize SetOptimize SetPermissiveBCCs SetSizeLimit SetSymmetrize OEProton::OEAM1BCCELF10Charges Constructors OEProton::OEAM1Charges Constructors GetOptimize GetSizeLimit GetSymmetrize SetOptimize SetSizeLimit SetSymmetrize OEProton::OEAmberFF94Charges Constructors OEProton::OEAssignCharges OEProton::OEAssignPartialCharges OEProton::OEChargeEngineBase CheckCharges CreateCopy GetExpectValidMol GetName GetRepairRequestedHint GetRequirements IsValid operator!= operator== SetExpectValidMol SetRepairRequestedHint TransferCharge OEProton::OEChargeEngineNoOp Constructors OEProton::OEChargeParameter Constructors operator= OEProton::OECharges OEProton::OECharges::AM1 OEProton::OECharges::AM1BCC OEProton::OECharges::AM1BCCNoSym OEProton::OECharges::AM1BCCNoSymSPt OEProton::OECharges::AM1BCCSPt OEProton::OECharges::AM1BCCSym OEProton::OECharges::AM1BCCSymSPt OEProton::OECharges::AM1SPt OEProton::OECharges::AmberFF94 OEProton::OECharges::AmberFF99 OEProton::OECharges::AmberFF99bsc0 OEProton::OECharges::AmberFF99SB OEProton::OECharges::Default OEProton::OECharges::Formal OEProton::OECharges::Gasteiger OEProton::OECharges::Initial OEProton::OECharges::Max OEProton::OECharges::MMFF94 OEProton::OECharges::None OEProton::OECharges::NoOp OEProton::OECharges::OPLS OEProton::OEChargingRequirement OEProton::OEChargingRequirement::AltersResidueName OEProton::OEChargingRequirement::BondedResidues OEProton::OEChargingRequirement::Compact OEProton::OEChargingRequirement::Coords3D OEProton::OEChargingRequirement::ExplicitHydrogens OEProton::OEChargingRequirement::MolComplexPrep OEProton::OEChargingRequirement::MultiConfOnly OEProton::OEChargingRequirement::Nothing OEProton::OEChargingRequirement::Parameters OEProton::OEChargingRequirement::PDBOrder OEProton::OEChargingRequirement::Precharged OEProton::OEChargingRequirement::ResPerceived OEProton::OEChargingRequirement::ReturnSelectedConfs OEProton::OEChargingRequirement::SetsAromaticity OEProton::OEChargingRequirement::SetsType OEProton::OEChargingRequirement::SizeWithinLimits OEProton::OEChargingRequirement::StandardResidues OEProton::OEClearCharges Constructors OEProton::OECombineChargeEngines Constructors OEProton::OEDesignUnitCharges ApplyCharges Constructors CreateCopy IsValid operator= SetCoFactorChargeEngine SetFallbackChargeEngine SetFinalizationChargeEngine SetLigandChargeEngine SetMetalChargeEngine SetNucleicChargeEngine SetOtherChargeEngine SetProteinChargeEngine SetProteinNonStandardChargeEngine SetSolventChargeEngine TransferCharge UseSZMAPWaterModel OEProton::OEELF Constructors operator= Select OEProton::OEELFCharges Constructors GetLimit GetPercentage GetReturnSelectedConfs SetLimit SetPercentage SetReturnSelectedConfs OEProton::OEELFOptions Constructors GetElfLimit GetPercent operator= SetElfLimit SetPercent OEProton::OEEnumerateFormalCharges OEProton::OEEnumerateTautomers OEProton::OEFormalChargeOptions Constructors GetMaxCount GetVerbose GetWarts operator= SetMaxCount SetVerbose SetWarts OEProton::OEFormalToPartialCharges Constructors OEProton::OEGasteigerCharges Constructors OEProton::OEGetAtomAdjTypeAtNeutralpHName OEProton::OEGetAtomAdjTypeAtNeutralpHType OEProton::OEGetAtompKaRangeName OEProton::OEGetAtompKaRangeType OEProton::OEGetChargeTypeName OEProton::OEGetMultistatepKaModelpHName OEProton::OEGetMultistatepKaModelpHType OEProton::OEGetReasonableProtomer OEProton::OEGetReasonableProtomers OEProton::OEGetReasonableTautomers OEProton::OEGetUniqueProtomer OEProton::OEHybridizationLevel OEProton::OEHybridizationLevel::Default OEProton::OEHybridizationLevel::DoubleBondNbr OEProton::OEHybridizationLevel::EnolEnamine OEProton::OEHybridizationLevel::Original OEProton::OEHypervalentNormalization OEProton::OEInitialCharges Constructors OEProton::OEMMFF94Charges Constructors OEProton::OEMultistatepKaModel CalculateNumOfMicrostates Constructors GenerateMicrostates GetAtomAdjTypeAtNeutralpH GetAtompKaRange GetMicrostates GetModelMolecule HasAdjTypeAtNeutralpH HaspKaRange Init operator= SetAllAtomspKaData OEProton::OEMultistatepKaModelOptions Constructors GetMaxNumMicrostates GetpH GetProcessCarbons SetMaxNumMicrostates SetpH SetProcessCarbons OEProton::OEMultistatepKaModelpH OEProton::OEMultistatepKaModelpH::Neutral OEProton::OEMultistatepKaModelpH::Unknown OEProton::OEpKaRange OEProton::OEpKaRange::Acidic OEProton::OEpKaRange::Basic OEProton::OEpKaRange::Neutral OEProton::OEpKaRange::Unidentified OEProton::OEpKaRange::Unknown OEProton::OEQuacPacGetArch OEProton::OEQuacPacGetLicensee OEProton::OEQuacPacGetPlatform OEProton::OEQuacPacGetRelease OEProton::OEQuacPacGetSite OEProton::OEQuacPacGetVersion OEProton::OEQuacPacIsLicensed OEProton::OERacemicType OEProton::OERacemicType::Default OEProton::OERacemicType::EverSampled OEProton::OERacemicType::LocalSampled OEProton::OERacemicType::None OEProton::OERemoveFormalCharge OEProton::OESetNeutralpHModel OEProton::OESpreadMetalCharges Constructors CreateCopy GetChargeAliquot GetMaxNbrDist GetRadiusMargin SetChargeAliquot SetMaxNbrDist SetRadiusMargin OEProton::OETautomerMolFunction Constructors CreateCopy GetCount GetMolecule operator() Reset OEProton::OETautomerOptions Constructors GetApplyWarts GetCarbonHybridization GetClearCoordinates GetHybridizationLevel GetKekule GetLevel GetMaxSearchTime GetMaxTautomericAtoms GetMaxTautomersGenerated GetMaxTautomersToReturn GetMaxZoneSize GetRacemicType GetRankTautomers GetSaveStereo operator= SetApplyWarts SetCarbonHybridization SetClearCoordinates SetHybridizationLevel SetKekule SetLevel SetMaxSearchTime SetMaxTautomericAtoms SetMaxTautomersGenerated SetMaxTautomersToReturn SetMaxZoneSize SetRacemicType SetRankTautomers SetSaveStereo OEProton::OETautomersLargestZoneSize OEProton::OETyperMolFunction Constructors CreateCopy operator() Reset OEReadMDLQueryFile OEReadMDLReactionQueryFile OEResidue OEResidues OESequenceAlignment OEShape::OEAddColorAtom OEShape::OEAddColorAtoms OEShape::OEAddCoordsToColorAtom OEShape::OEAnalyticColorFunc Constructors GetAnalyticOptions operator= OEShape::OEAnalyticOptions Constructors GetExpType GetProxyGridCutoff GetUseProxyGrid operator= SetExpType SetProxyGridCutoff SetUseProxyGrid OEShape::OEAnalyticShapeFunc Constructors GetAnalyticOptions operator= OEShape::OEAsIsStarts Constructors operator= OEShape::OEAtAtomStarts Constructors operator= OEShape::OEBestOverlay ClearColorForceField ClearUserStarts Constructors GetCarbonRadius GetInitialOrientation GetMaxRandomTranslation GetMethod GetMinimizeType GetNumRandomStarts GetNumUserStarts GetRadiiApproximation GetRandomSeed GetRefGrid GetRefMol GetRefSelfColor GetRefSymmetry GetSymmetryThreshold GetUseHydrogens GetUserStarts operator= Overlay SetCarbonRadius SetColorForceField SetColorOptimize SetInitialOrientation SetMaxRandomTranslation SetMethod SetMinimizeType SetNumRandomStarts SetRadiiApproximation SetRandomSeed SetRefGrid SetRefMol SetSymmetryThreshold SetUseHydrogens SetUserStarts OEShape::OEBestOverlayResults AddScore Clear Constructors GetScores operator= OEShape::OEBestOverlayScore Constructors GetFitConfIdx GetRefConfIdx GetRotMatrix GetTranslation operator= Transform OEShape::OEBOMinType OEShape::OEBOMinType::Autoscale OEShape::OEBOMinType::Default OEShape::OEBOMinType::Overlap OEShape::OEBOMinType::Tanimoto OEShape::OEBOOrientation OEShape::OEBOOrientation::AsIs OEShape::OEBOOrientation::Default OEShape::OEBOOrientation::Inertial OEShape::OEBOOrientation::InertialAtColorAtoms OEShape::OEBOOrientation::InertialAtHeavyAtoms OEShape::OEBOOrientation::Random OEShape::OEBOOrientation::Subrocs OEShape::OEBOOrientation::UserInertialStarts OEShape::OECalcShapeMultipoles OEShape::OECalcVolume OEShape::OECartesianStarts ClearStartPoints Constructors GetNumStartPoints GetStartPoints operator= SetStartPoints OEShape::OEClearCachedSelfColor OEShape::OEClearCachedSelfShape OEShape::OEColorFFParameter Constructors operator= OEShape::OEColorFFType OEShape::OEColorFFType::Custom OEShape::OEColorFFType::ExplicitMillsDean OEShape::OEColorFFType::ExplicitMillsDeanNoRings OEShape::OEColorFFType::ImplicitMillsDean OEShape::OEColorFFType::ImplicitMillsDeanNoRings OEShape::OEColorFFType::Max OEShape::OEColorFFType::OEDefault OEShape::OEColorFFType::Undefined OEShape::OEColorForceField AddColorer AddInteraction AddType Clear ClearInteractions Constructors GetTitle GetType GetTypeName GetTypes Init operator= Ready SetTitle Write OEShape::OEColorFunc GetColorOptions OEShape::OEColorOptions Constructors GetColorForceField GetMultiplier GetScoreType operator= SetColorForceField SetMultiplier SetScoreType OEShape::OEColorOverlap ColorScore Constructors GetAllColor GetSelfColor operator= SetAllColor SetColorForceField SetFitMol SetRefMol OEShape::OEColorResults Constructors GetFitTversky GetRefTversky GetTanimoto GetTversky OEShape::OEColorTanimotoCutoff Constructors OEShape::OEColorType OEShape::OEColorType::Analytic OEShape::OEColorType::Exact OEShape::OEColorType::Grid OEShape::OEColorType::None OEShape::OECompressColorAtoms OEShape::OECountColorAtoms OEShape::OEDeleteCompressedColorAtoms OEShape::OEDerivativeType OEShape::OEDerivativeType::Interpolated OEShape::OEDerivativeType::NearestValue OEShape::OEExactColorFunc Constructors operator= OEShape::OEExactShapeFunc Constructors operator= OEShape::OEExponentialType OEShape::OEExponentialType::Standard OEShape::OEExponentialType::Tabulated OEShape::OEFitColorTverskyCutoff Constructors OEShape::OEFitTverskyComboCutoff Constructors OEShape::OEFitTverskyCutoff Constructors OEShape::OEFlexiOverlapFunc Overlap SetupRef UpdateColorCoords OEShape::OEFlexiOverlapOptions Constructor GetColorFuncType GetColorOptions GetForceField GetHarmonic GetOverlapFunc GetShapeFuncType GetShapeOptions operator= SetColorFuncType SetColorOptions SetForceField SetHarmonic SetOverlapFunc SetShapeFuncType SetShapeOptions Validate OEShape::OEFlexiOverlapResults Constructor GetInternalEnergy operator= OEShape::OEFlexiOverlay BestOverlay Constructor operator= Overlay SetupRef SortedOverlay OEShape::OEFlexiOverlayOptions Constructor GetFlexiOverlapOptions GetMaxOptSteps GetRigidOverlay GetRigidOverlayOptions operator= SetFlexiOverlapOptions SetMaxOptSteps SetRigidOverlay SetRigidOverlayOptions OEShape::OEGetCachedSelfColor OEShape::OEGetCachedSelfShape OEShape::OEGetCenterAndExtents OEShape::OEGetColorAtoms OEShape::OEGetColorParents OEShape::OEGetColorType OEShape::OEGetMomentsOfInertiaTransform OEShape::OEGridColorFunc Constructors GetGridOptions operator= OEShape::OEGridShapeFunc Constructors GetGridOptions operator= OEShape::OEHasCachedSelfColor OEShape::OEHasCachedSelfShape OEShape::OEHasColorAtoms OEShape::OEHasCompressedColorAtoms OEShape::OEHasPerceivedColorAtoms OEShape::OEHermite Constructors CreateGrid GetCoefficients GetOptions GetSelfOverlap operator= Setup OEShape::OEHermiteOptions Constructors GetLambdaX GetLambdaY GetLambdaZ GetNPolyMax GetUseOptimalLambdas operator= SetLambdaX SetLambdaY SetLambdaZ SetNPolyMax SetUseOptimalLambdas OEShape::OEHermiteShapeFunc Constructors GetFitHermiteOptions GetRefHermiteOptions operator= OEShape::OEHighestColorTanimoto CreateCopy operator() OEShape::OEHighestComboScore CreateCopy operator() OEShape::OEHighestFitColorTversky CreateCopy operator() OEShape::OEHighestFitTversky CreateCopy operator() OEShape::OEHighestFitTverskyCombo CreateCopy operator() OEShape::OEHighestOverlap CreateCopy operator() OEShape::OEHighestRefColorTversky CreateCopy operator() OEShape::OEHighestRefTversky CreateCopy operator() OEShape::OEHighestRefTverskyCombo CreateCopy operator() OEShape::OEHighestScaledColor CreateCopy operator() OEShape::OEHighestTanimoto CreateCopy operator() OEShape::OEHighestTanimotoCombo CreateCopy operator() OEShape::OEHighestTverskyCombo Constructors CreateCopy operator() OEShape::OEInertialStarts Constructors GetSymmetryThreshold operator= SetSymmetryThreshold OEShape::OEIsColorAtom OEShape::OEIsColorAtomPred Constructors CreateCopy operator() OEShape::OEIsFastROCSShapeQuery OEShape::OEMol2Query OEShape::OEMomentSymmetry OEShape::OEMomentSymmetry::NoSymmetry OEShape::OEMomentSymmetry::Oblate OEShape::OEMomentSymmetry::Prolate OEShape::OEMomentSymmetry::Spherical OEShape::OEMomentSymmetry::Unknown OEShape::OEMultiRefOverlay BestOverlay Constructors GetOverlayOptions operator= Overlay SetupRef OEShape::OEOrientByMomentsOfInertia OEShape::OEOverlap Constructors GetCarbonRadius GetGridSpacing GetMethod GetRadiiApproximation GetUseHydrogens operator= Overlap SetCarbonRadius SetFitMol SetGridSpacing SetMethod SetRadiiApproximation SetRefGrid SetRefMol SetUseHydrogens OEShape::OEOverlapCutoff Constructors OEShape::OEOverlapFunc Constructors GetColorFunc GetShapeFunc operator= OEShape::OEOverlapFuncBase Overlap SetupFlex SetupRef OEShape::OEOverlapMethod OEShape::OEOverlapMethod::Analytic OEShape::OEOverlapMethod::Analytic2 OEShape::OEOverlapMethod::Exact OEShape::OEOverlapMethod::Grid OEShape::OEOverlapMethod::Max OEShape::OEOverlapPrep Constructors GetAssignBondiRadii GetAssignColor GetColorForceField GetUseHydrogens operator= Prep SetAssignBondiRadii SetAssignColor SetColorForceField SetUseHydrogens OEShape::OEOverlapPrepOptions Constructor GetAssignBondiRadii GetAssignColor GetColorForceField GetDuplicateDistance GetRemoveDuplicate GetUseHydrogens operator= SetAssignBondiRadii SetAssignColor SetColorForceField SetDuplicateDistance SetRemoveDuplicate SetUseHydrogens OEShape::OEOverlapRadii OEShape::OEOverlapRadii::All OEShape::OEOverlapRadii::Carbon OEShape::OEOverlapRadii::Default OEShape::OEOverlapRadii::Max OEShape::OEOverlapRepresentation OEShape::OEOverlapRepresentation::All OEShape::OEOverlapRepresentation::Atomic OEShape::OEOverlapRepresentation::Atoms OEShape::OEOverlapRepresentation::Bonding OEShape::OEOverlapRepresentation::Bonds OEShape::OEOverlapRepresentation::Default OEShape::OEOverlapRepresentation::Full OEShape::OEOverlapRepresentation::Gaussian OEShape::OEOverlapRepresentation::Max OEShape::OEOverlapResults Constructors GetColorScore GetColorTanimoto GetColorTversky GetFitColorTversky GetFitSelfColor GetFitSelfOverlap GetFitTversky GetFitTverskyCombo GetOverlap GetRefColorTversky GetRefSelfColor GetRefSelfOverlap GetRefTversky GetRefTverskyCombo GetTanimoto GetTanimotoCombo GetTversky operator= OEShape::OEOverlay BestOverlay Constructors GetOverlayOptions operator= Overlay SetupRef SortedOverlay OEShape::OEOverlayOptions Constructors GetColorFuncType GetColorOptions GetMaxOptSteps GetOverlapFunc GetShapeFuncType GetShapeOptions GetStarts operator= SetColorFuncType SetColorOptions SetMaxOptSteps SetOverlapFunc SetShapeFuncType SetShapeOptions SetStarts OEShape::OEOverlayScoreCutoff CreateCopy operator() OEShape::OEQuatStarts ClearStarts Constructors operator= SetStarts OEShape::OERandomStarts Constructors GetMaxRandomTranslation GetNumRandomStarts GetRandomSeed operator= SetMaxRandomTranslation SetNumRandomStarts SetRandomSeed OEShape::OEReadShapeQuery OEShape::OERefColorTverskyCutoff Constructors OEShape::OERefTverskyComboCutoff Constructors OEShape::OERefTverskyCutoff Constructors OEShape::OERemoveColorAtoms OEShape::OEROCS AddMolecule ClearMolecules Constructors GetROCSOptions operator= Overlay SetDatabase OEShape::OEROCSOptions AddCutoff ClearCutoffs Constructors GetConfsPerHit GetMaxHits GetNumBestHits GetOverlayOptions GetPerformPrep GetRankPredicate GetUseMaxHits HasCutoff MeetsCutoff operator= SetConfsPerHit SetMaxHits SetNumBestHits SetOverlayOptions SetPerformPrep SetRankPredicate SetUseMaxHits OEShape::OEROCSOverlay OEShape::OEROCSResult AddScore Constructors GetOverlayConf GetOverlayConfs operator= OEShape::OEScoreType OEShape::OEScoreType::Overlap OEShape::OEScoreType::Tanimoto OEShape::OESelfColor OEShape::OESelfShape OEShape::OESetCachedSelfColor OEShape::OESetCachedSelfShape OEShape::OESetColorParents OEShape::OESetColorType OEShape::OESetCoordsFromColorParents OEShape::OEShapeFunc GetShapeOptions OEShape::OEShapeGetArch OEShape::OEShapeGetLicensee OEShape::OEShapeGetPlatform OEShape::OEShapeGetRelease OEShape::OEShapeGetSite OEShape::OEShapeGetVersion OEShape::OEShapeGridOptions Constructors GetDerivativeType GetGridSpacing operator= SetDerivativeType SetGridSpacing OEShape::OEShapeIsLicensed OEShape::OEShapeOptions Constructors GetCarbonRadius GetRadiiApproximation GetScoreType operator= SetCarbonRadius SetRadiiApproximation SetScoreType OEShape::OEShapeQuery AddColorGaussian AddColorGaussians AddShapeGaussian Clear ClearColorGaussians ClearMolecule ClearShapeGaussians ClearShapeGrid Constructors DeleteColorGaussian DeleteShapeGaussian operator= SetAtomStrength SetMolecule SetShapeGrid OEShape::OEShapeQueryBase GetAtomStrength GetColorForceField GetColorGaussians GetCompositeMolecule GetMolecule GetShapeGaussians GetShapeGrid GetTitle HasColor HasMolecule HasShape HasShapeGrid IsEmpty SetTitle OEShape::OEShapeQueryPublic Constructors GetColorForceField GetTitle operator bool operator= OEShape::OEShapeType OEShape::OEShapeType::Analytic OEShape::OEShapeType::Exact OEShape::OEShapeType::Grid OEShape::OEShapeType::Hermite OEShape::OEShapeType::None OEShape::OESortOverlayScores OEShape::OEStarts CreateCopy GetNumOfStarts GetStarts Setup SetupRef OEShape::OESubrocsStarts Constructors operator= OEShape::OETanimotoComboCutoff Constructors OEShape::OETanimotoCutoff Constructors OEShape::OEUncompressColorAtoms OEShape::OEWriteShapeQuery OESheff::OESheffield Constructors GetDielectricDerivative operator= Set SetCharges SetRadii OESheff::OESheffieldOptions Constructors GetA GetB GetC GetSoluteDielectricConstant GetSolventDielectricConstant operator= SetA SetB SetC SetSoluteDielectricConstant SetSolventDielectricConstant OESheff::OESheffieldParamType OESheff::OESheffieldParamType::Protein OESheff::OESheffieldParamType::SmallMol OESiteHopper::OEAddPatchSurface OESiteHopper::OEGetPatchSurface OESiteHopper::OEHasPatchSurface OESiteHopper::OEMakePatchFromDesignUnit OESiteHopper::OESetPatchSurface OESiteHopper::OESetProteinSDData OESiteHopper::OESiteHopperDatabase Add AddDirectory Close Constructors GetDesignUnit GetIDByTitle GetMaxMolIdx GetMolecule GetOptions GetSequenceInfo GetTitle Open operator bool OESiteHopper::OESiteHopperDatabaseMode OESiteHopper::OESiteHopperDatabaseMode::APPEND OESiteHopper::OESiteHopperDatabaseMode::CREATE OESiteHopper::OESiteHopperDatabaseMode::MAX OESiteHopper::OESiteHopperDatabaseMode::READONLY OESiteHopper::OESiteHopperDatabaseMode::SEARCH OESiteHopper::OESiteHopperDatabaseMode::UNDEFINED OESiteHopper::OESiteHopperDatabaseOptions Constructors CreateCopy GetPatchOptions operator= SetPatchOptions OESiteHopper::OESiteHopperGetArch OESiteHopper::OESiteHopperGetLicensee OESiteHopper::OESiteHopperGetPlatform OESiteHopper::OESiteHopperGetRelease OESiteHopper::OESiteHopperGetSite OESiteHopper::OESiteHopperGetVersion OESiteHopper::OESiteHopperIsGPUReady OESiteHopper::OESiteHopperIsLicensed OESiteHopper::OESiteHopperPatchOptions Constructors CreateCopy GetColorForceField GetResidueCutoff GetScaleFactor GetSiteSize GetSurfaceCutoff GetUserStartsScaleFactor operator= SetResidueCutoff SetScaleFactor SetSiteSize SetSurfaceCutoff SetUserStartsScaleFactor OESiteHopper::OESiteHopperResults Constructors GetColorScale GetColorTanimoto GetPatchScore GetRank GetSequenceSimilarity GetShapeTanimoto operator= SetColorScale SetColorTanimoto SetRank SetSequenceSimilarity SetShapeTanimoto OESiteHopper::OESiteHopperScore Constructors GetDesignUnit GetID GetTitle GetTransform operator= SetDesignUnit SetID SetTitle SetTransform OESiteHopper::OESiteHopperSearch Constructors operator bool Search OESiteHopper::OESiteHopperSearchBase Constructors operator bool Search OESiteHopper::OESiteHopperSearchOptions Constructors CreateCopy GetMaxHits GetNCPU GetNormalizeAndRescore GetScoreCutoff GetSequenceCutoff GetUseGPU operator= SetMaxHits SetNCPU SetNormalizeAndRescore SetScoreCutoff SetSequenceCutoff OESpicoli::OEAddSurfaces OESpicoli::OECalculateFaceNormals OESpicoli::OECalculateNormals OESpicoli::OECalculateSurfaceCurvature OESpicoli::OECalculateSurfacePotentials OESpicoli::OECalculateTriangleAreas OESpicoli::OEColorSurfaceByPotential OESpicoli::OEEdgeReductionType OESpicoli::OEEdgeReductionType::MinimumDistance OESpicoli::OEGetCenterAndExtents OESpicoli::OEGetSurface OESpicoli::OEGetSurfaceFileType OESpicoli::OEGetSurfaceFormatExtension OESpicoli::OEGetSurfaceFormatString OESpicoli::OEInitSurfaceHandlers OESpicoli::OEInvertSurface OESpicoli::OEIsReadableSurface OESpicoli::OEIsWriteableSurface OESpicoli::OEMakeAccessibleSurface OESpicoli::OEMakeBitGridFromSurface OESpicoli::OEMakeBoxSurface OESpicoli::OEMakeCavitySurfaces OESpicoli::OEMakeCliqueSurface OESpicoli::OEMakeComplexCavities OESpicoli::OEMakeConnectedSurfaceCliques OESpicoli::OEMakeEllipsoidSurface OESpicoli::OEMakeGridFromSurface OESpicoli::OEMakeMolecularSurface OESpicoli::OEMakeProteinRibbonSurface OESpicoli::OEMakeSphericalSurface OESpicoli::OEMakeSurfaceFromGrid OESpicoli::OEMakeVoidVolume OESpicoli::OEPolygonizeMethod OESpicoli::OEPolygonizeMethod::Compact OESpicoli::OEPolygonizeMethod::Default OESpicoli::OEPolygonizeMethod::Grasp OESpicoli::OEReadSurface OESpicoli::OEReduceSurface OESpicoli::OERibbonType OESpicoli::OERibbonType::CAlpha OESpicoli::OERibbonType::Pretty OESpicoli::OERotateSurface OESpicoli::OESetSurface OESpicoli::OESetSurfaceColor OESpicoli::OESetSurfacePotentials OESpicoli::OESmoothSurfaceEdges OESpicoli::OESpicoliGetArch OESpicoli::OESpicoliGetLicensee OESpicoli::OESpicoliGetPlatform OESpicoli::OESpicoliGetRelease OESpicoli::OESpicoliGetSite OESpicoli::OESpicoliGetVersion OESpicoli::OESpicoliIsLicensed OESpicoli::OESplitSurfaceByAtoms OESpicoli::OESurface Clear ClearVertexClique Constructors CreateCopy GetAtoms GetAtomsElement GetColor GetColorElement GetCurvature GetCurvatureElement GetDataType GetDistance GetDistanceElement GetFaceNormal GetFaceNormals GetFaceNormalsElement GetNormal GetNormals GetNormalsElement GetNumTriangles GetNumVertices GetPotential GetPotentialElement GetPotentialName GetProbeRadius GetResolution GetTitle GetTriangle GetTriangles GetTrianglesElement GetVertex GetVertexClique GetVertexCliqueElement GetVertices GetVerticesElement IsAtomsSet IsColorSet IsCurvatureSet IsDataType IsDistanceSet IsFaceNormalsSet IsNormalsSet IsPotentialSet IsVertexCliqueSet operator bool operator+= operator= SetAtoms SetAtomsElement SetColor SetColorElement SetCurvature SetCurvatureElement SetDistance SetDistanceElement SetFaceNormal SetFaceNormals SetFaceNormalsElement SetNormal SetNormals SetNormalsElement SetNumTriangles SetNumVertices SetPotential SetPotentialElement SetPotentialName SetTitle SetTriangle SetTriangles SetTrianglesElement SetVertex SetVertexClique SetVertexCliqueElement SetVertices SetVerticesElement OESpicoli::OESurfaceArea OESpicoli::OESurfaceCliqueArea OESpicoli::OESurfaceCliqueCentroid OESpicoli::OESurfaceCliqueVolume OESpicoli::OESurfaceCropToClique OESpicoli::OESurfaceFileType OESpicoli::OESurfaceFileType::Grasp OESpicoli::OESurfaceFileType::OESurface OESpicoli::OESurfaceFileType::UNDEFINED OESpicoli::OESurfaceIsOpen OESpicoli::OESurfaceToMoleculeDistance OESpicoli::OESurfaceVolume OESpicoli::OETransformSurface OESpicoli::OETranslateSurface OESpicoli::OEVoxelizeMethod OESpicoli::OEVoxelizeMethod::Blank OESpicoli::OEVoxelizeMethod::Blur OESpicoli::OEVoxelizeMethod::Default OESpicoli::OEVoxelizeMethod::Distance OESpicoli::OEVoxelizeMethod::Gaussian OESpicoli::OEWriteSurface OESplitMolComplex OESpruce::OEAlternateLocationOption OESpruce::OEAlternateLocationOption::Combinatorial OESpruce::OEAlternateLocationOption::Default OESpruce::OEAlternateLocationOption::Enumerate OESpruce::OEAlternateLocationOption::Max OESpruce::OEAlternateLocationOption::Primary OESpruce::OEAlternateLocationOption::Unknown OESpruce::OEBioUnitExtractionOptions Constructors GetMaxAtoms GetMaxParts GetMinScore GetPreferAuthorRecord GetSuperpose operator= SetMaxAtoms SetMaxParts SetMinScore SetPreferAuthorRecord SetSuperpose OESpruce::OEBuildLoops OESpruce::OEBuildSidechains OESpruce::OEBuildSingleLoop OESpruce::OECapBuilderOptions Constructors GetAllowTruncate GetDeleteClashingSolvent GetForceCapping operator= SetAllowTruncate SetDeleteClashingSolvent SetForceCapping OESpruce::OECapCTermini OESpruce::OECapNTermini OESpruce::OECapTermini OESpruce::OEDesignUnitBuildOptions Constructors GetBuildLoops GetBuildSidechains GetCapBuilderOptions GetCapCTermini GetCapNTermini GetLoopBuilderOptions GetSidechainBuilderOptions operator= SetBuildLoops SetBuildSidechains SetCapBuilderOptions SetCapCTermini SetCapNTermini SetLoopBuilderOptions SetSidechainBuilderOptions OESpruce::OEDesignUnitEnumerateSitesOptions Constructors GetAddInteractionHints GetAddStyle GetCollapseNonSiteAlts GetDuplicateRemoval GetEnumerateCofactorSites GetRestrictToRefSite GetSiteSize operator= SetAddInteractionHints SetAddStyle SetCollapseNonSiteAlts SetDuplicateRemoval SetEnumerateCofactorSites SetRestrictToRefSite SetSiteSize OESpruce::OEDesignUnitIssueCodes OESpruce::OEDesignUnitIssueCodes::All OESpruce::OEDesignUnitIssueCodes::BrokenChains OESpruce::OEDesignUnitIssueCodes::HeavyAtomsOverlap OESpruce::OEDesignUnitIssueCodes::ImplicitH OESpruce::OEDesignUnitIssueCodes::MissingLoop OESpruce::OEDesignUnitIssueCodes::PartialSideChain OESpruce::OEDesignUnitIssueCodes::Success OESpruce::OEDesignUnitIssueCodes::TerminiNotCapped OESpruce::OEDesignUnitMutationOptions AddMutation ClearMutations Constructors GetMutations operator= SetMutations OESpruce::OEDesignUnitPrepOptions Constructors GetAssignPartialChargesAndRadii GetBuildOptions GetChargeEngine GetEnumerateSitesOptions GetProtonate GetProtonateOptions GetStrictProtonationMode operator= SetAssignPartialChargesAndRadii SetBuildOptions SetChargeEngine SetEnumerateSitesOptions SetProtonate SetProtonateOptions SetStrictProtonationMode OESpruce::OEDesignUnitSplitOptions AddCofactorCode AddExcipientCode AddLipidCode ClearCofactorCodes ClearExcipientCodes ClearLipidCodes Constructors GetAlternateLocationHandling GetCofactorCodes GetExcipientCodes GetLipidCodes GetMakePackingResidues GetMaxLigAtoms GetMaxLigResidues GetMaxSystemAtoms GetMinLigAtoms GetTargetComponentID operator= SetAlternateLocationHandling SetCofactorCodes SetExcipientCodes SetLipidCodes SetMakePackingResidues SetMaxLigAtoms SetMaxLigResidues SetMaxSystemAtoms SetMinLigAtoms SetTargetComponentID OESpruce::OEEnumerateSites OESpruce::OEExperimentType OESpruce::OEExperimentType::ElectronCrystallography OESpruce::OEExperimentType::ElectronMicroscopy OESpruce::OEExperimentType::FiberDiffraction OESpruce::OEExperimentType::NeutronDiffraction OESpruce::OEExperimentType::PowderDiffraction OESpruce::OEExperimentType::SolidStateNMR OESpruce::OEExperimentType::SolutionNMR OESpruce::OEExperimentType::SolutionScattering OESpruce::OEExperimentType::TheoreticalModel OESpruce::OEExperimentType::Unknown OESpruce::OEExperimentType::XRayDiffraction OESpruce::OEExtractBioUnits OESpruce::OEFindPockets OESpruce::OEFixBackbone OESpruce::OEGetAlternateLocationOptionID OESpruce::OEGetAlternateLocationOptionName OESpruce::OEGetExperimentTypeID OESpruce::OEGetExperimentTypeName OESpruce::OEGetHeterogenTypeID OESpruce::OEGetHeterogenTypeName OESpruce::OEGetPartialResidues OESpruce::OEGetSuperposeMethodFromName OESpruce::OEGetSuperposeMethodName OESpruce::OEHeterogenMetadata AddTautomer AddTautomers ClearTautomers Constructors GetID GetSmiles GetTautomers GetTitle GetType operator= SetID SetSmiles SetTitle SetType OESpruce::OEHeterogenType OESpruce::OEHeterogenType::Cofactors OESpruce::OEHeterogenType::CounterIons OESpruce::OEHeterogenType::Excipients OESpruce::OEHeterogenType::Ligand OESpruce::OEHeterogenType::Lipids OESpruce::OEHeterogenType::Metals OESpruce::OEHeterogenType::Polymers OESpruce::OEHeterogenType::Solvent OESpruce::OEHeterogenType::Sugars OESpruce::OEHeterogenType::Unknown OESpruce::OEIsModeledAtom Constructors CreateCopy operator() OESpruce::OELoopBuilderOptions Constructors GetAllowBuildDisulfideBridges GetBackboneClashRejectThreshold GetBuildTails GetConnectBufferDistance GetCropLength GetLoopClashRejectThreshold GetLoopDBFilename GetOptimizationInclSurfaceAreaTerm GetOptimizationMaxLoops GetOptimizationShell GetOptimizationStage1IterMultiplier GetOptimizationStage2IterMultiplier GetOptimizationTolerance GetOptimizationUseSolventModel GetSeqAlignExtendPenalty GetSeqAlignGapPenalty GetSeqAlignMethod GetStrictProlineMatch GetTransformThreshold GetUsePackingResidues operator= SetAllowBuildDisulfideBridges SetBackboneClashRejectThreshold SetBuildTails SetConnectBufferDistance SetCropLength SetLoopClashRejectThreshold SetLoopDBFilename SetOptimizationInclSurfaceAreaTerm SetOptimizationMaxLoops SetOptimizationShell SetOptimizationStage1IterMultiplier SetOptimizationStage2IterMultiplier SetOptimizationTolerance SetOptimizationUseSolventModel SetSeqAlignExtendPenalty SetSeqAlignGapPenalty SetSeqAlignMethod SetStrictProlineMatch SetTransformThreshold SetUsePackingResidues OESpruce::OEMakeBioDesignUnits OESpruce::OEMakeDesignUnit OESpruce::OEMakeDesignUnitFromPocket OESpruce::OEMakeDesignUnitOptions Constructors GetBioUnitExtractionOptions GetPrepOptions GetSplitOptions GetSuperpose GetSuperpositionMethod operator= SetBioUnitExtractionOptions SetPrepOptions SetSplitOptions SetSuperpose SetSuperpositionMethod OESpruce::OEMakeDesignUnits OESpruce::OEMutateResidue OESpruce::OEMutateResidues OESpruce::OEPocket Constructors GetAtoms GetLocalDensity GetPocketPredicate GetPocketSurface GetResidues GetSurfaceArea operator= OESpruce::OEPocketOptions Constructors GetBurialFactor GetMaxSurfaceArea GetMinSurfaceArea operator= SetBurialFactor SetMaxSurfaceArea SetMinSurfaceArea OESpruce::OEProtonateDesignUnit OESpruce::OEProtonateDesignUnitOptions Constructors GetGenerateTautomers GetHetGroupNbrDist GetOptimizeExpProtons GetPlaceHydrogensOptions operator= SetGenerateTautomers SetHetGroupNbrDist SetOptimizeExpProtons SetPlaceHydrogensOptions OESpruce::OESecondaryStructureSuperposition Constructors GetFitChains GetRefChains GetRotMatrix GetTanimoto GetTranslation operator bool operator= Transform OESpruce::OESequenceMetadata Constructors GetChainID GetEndResidueInsertCode GetEndResidueNumber GetSequence GetStartResidueInsertCode GetStartResidueNumber operator= SetChainID SetEndResidueInsertCode SetEndResidueNumber SetSequence SetStartResidueInsertCode SetStartResidueNumber OESpruce::OESetPackingResidueProperties OESpruce::OESidechainBuilderOptions Constructors GetDeleteClashingSolvent GetMinimizeSidechains GetMinimizeSidechainsShell GetRotamerLibrary GetStrictMode operator= SetDeleteClashingSolvent SetMinimizeSidechains SetMinimizeSidechainsShell SetRotamerCoverage SetRotamerLibrary SetStrictMode OESpruce::OESpruceFilter Constructors GetAtoms GetMessages operator= StandardizeAndFilter OESpruce::OESpruceFilterIssueCodes OESpruce::OESpruceFilterIssueCodes::All OESpruce::OESpruceFilterIssueCodes::InvalidCRYST1 OESpruce::OESpruceFilterIssueCodes::InvalidElectronDensityOverlap OESpruce::OESpruceFilterIssueCodes::InvalidMetalBond OESpruce::OESpruceFilterIssueCodes::InvalidNames OESpruce::OESpruceFilterIssueCodes::InvalidResidueStates OESpruce::OESpruceFilterIssueCodes::InvalidSeqAlign OESpruce::OESpruceFilterIssueCodes::Success OESpruce::OESpruceFilterOptions Constructors GetDeleteFloatingRes GetFixBackboneAtoms GetFixBondOrder GetFixBondsToMetals GetFixLigandState GetFixNames operator= SetDeleteFloatingRes SetFixBackboneAtoms SetFixBondOrder SetFixBondsToMetals SetFixLigandState SetFixNames OESpruce::OESpruceGetArch OESpruce::OESpruceGetLicensee OESpruce::OESpruceGetPlatform OESpruce::OESpruceGetRelease OESpruce::OESpruceGetSite OESpruce::OESpruceGetVersion OESpruce::OESpruceIsLicensed OESpruce::OEStructuralSuperposition ConstraintsMet Constructors GetFitChains GetRefChains GetRegion GetRMSD GetRotMatrix GetScore GetTranslation operator bool operator= Transform OESpruce::OEStructureMetadata AddHeterogenMetadata AddKeyword AddKeywords AddSequenceMetadata ClearHeterogenMetadata ClearKeywords ClearSequenceMetadata Constructors GetAuthor GetExperimentDate GetExperimentType GetHeterogenMetadata GetIridiumData GetKeywords GetRevision GetRevisionDate GetSequenceMetadata GetStructureID operator= SetAuthor SetExperimentDate SetExperimentType SetIridiumData SetRevision SetRevisionDate SetStructureID OESpruce::OESuperpose Clear Constructors HasConstraintMol HasRef operator= SetMethod SetOptions SetupRef Superpose OESpruce::OESuperposeMethod OESpruce::OESuperposeMethod::DDM OESpruce::OESuperposeMethod::Default OESpruce::OESuperposeMethod::DifferenceDistanceMatrix OESpruce::OESuperposeMethod::Global OESpruce::OESuperposeMethod::GlobalCarbonAlpha OESpruce::OESuperposeMethod::SecondaryStructureElements OESpruce::OESuperposeMethod::Site OESpruce::OESuperposeMethod::SiteHopper OESpruce::OESuperposeMethod::SiteSequence OESpruce::OESuperposeMethod::SSE OESpruce::OESuperposeMethod::Undefined OESpruce::OESuperposeMethod::Weighted OESpruce::OESuperposeMethod::WeightedDifferenceDistanceMatrix OESpruce::OESuperposeOptions Constructors GetMethod GetUseConstraints GetValidRMSD GetValidSeqScore GetValidTanimoto operator= SetMethod SetUseConstraints SetValidRMSD SetValidSeqScore SetValidTanimoto OESpruce::OESuperposeResults Constructors GetFitChains GetRefChains GetRMSD GetRotMatrix GetSeqScore GetTanimoto GetTransform GetTranslation HasRMSD HasSeqScore HasTanimoto IsValid operator bool operator= Transform OESpruce::OESuperpositionOptions AddSiteResidue ClearLigandConstraints ClearSiteResidues Constructors GetDist GetLigandConstraints GetSiteResidues GetSuperpositionType HasLigandConstraints operator= SetDist SetLigandConstraints SetSiteResidues SetSuperpositionType OESpruce::OESuperpositionType OESpruce::OESuperpositionType::DDM OESpruce::OESuperpositionType::Default OESpruce::OESuperpositionType::Global OESpruce::OESuperpositionType::Site OESpruce::OESuperpositionType::SSE OESpruce::OESuperpositionType::Undefined OESpruce::OESuperpositionType::Weighted OESpruce::OEValidateDesignUnit Constructors GetAtoms GetMessages operator= Validate OESwapAIEResidueAtoms OESystem::IsFalse OESystem::IsTrue OESystem::OEAddContour OESystem::OEAddGrid OESystem::OEAnd Constructors CreateCopy operator() operator= OESystem::OEAnnotateArrow OESystem::OEAnnotateBox OESystem::OEAnnotateCylinder OESystem::OEAnnotateEllipsoid OESystem::OEAnnotateLine OESystem::OEAnnotateSphere OESystem::OEAnnotateSpline OESystem::OEAnnotateSplineSurface OESystem::OEAnnotateSymbol OESystem::OEAnnotateText OESystem::OEAnnotateTorus OESystem::OEAnnotation AddChild Constructors CreateCopy GetChildren GetColor GetDataType GetRenderHint GetTitle GetType IsDataType operator= SetColor SetRenderHint SetTitle SetType OESystem::OEAnnotationPrimitive OESystem::OEAnnotationPrimitive::Arrow OESystem::OEAnnotationPrimitive::Box OESystem::OEAnnotationPrimitive::Container OESystem::OEAnnotationPrimitive::Cylinder OESystem::OEAnnotationPrimitive::Ellipsoid OESystem::OEAnnotationPrimitive::Line OESystem::OEAnnotationPrimitive::Sphere OESystem::OEAnnotationPrimitive::Spline OESystem::OEAnnotationPrimitive::SplineSurface OESystem::OEAnnotationPrimitive::Surface OESystem::OEAnnotationPrimitive::Symbol OESystem::OEAnnotationPrimitive::Text OESystem::OEAnnotationPrimitive::Torus OESystem::OEAnnotationRenderHint OESystem::OEAnnotationRenderHint::Mesh OESystem::OEAnnotationRenderHint::Points OESystem::OEAnnotationRenderHint::Solid OESystem::OEAttachData OESystem::OEBase AddBaseData AddData Clear Constructors CreateCopy DeleteData GetBoolData GetData GetDataIter GetDataType GetDoubleData GetFloatData GetIntData GetStringData HasData IsDataType operator+= operator= SetBaseData SetBoolData SetData SetDoubleData SetFloatData SetIntData SetStringData OESystem::OEBaseData Constructors CreateCopy GetDataType GetSize GetTag OESystem::OEBaseDataT Constructors CreateCopy GetData GetDataType GetSize operator= SetData OESystem::OEBaseDataTPtr OESystem::OEBDataLengthBytes OESystem::OEBFloatEndian OESystem::OEBFPosTEndian OESystem::OEBinaryAnd Constructors CreateCopy operator() operator= OESystem::OEBinaryFalse CreateCopy operator() OESystem::OEBinaryFunction CreateCopy operator() OESystem::OEBinaryIOHandler Clear Constructors CreateCopy GetBaseWriteFxns GetDataType GetDefaultReadFxn GetDefaultWriteFxn GetReadFxns GetWriteFxns IsDataType operator= ReplaceReadFxn ReplaceWriteFxn SetBaseWriteFxn SetReadFxn SetWriteFxn OESystem::OEBinaryIOHandlerBase Clear GetBaseWriteFxns GetDefaultReadFxn GetDefaultWriteFxn GetReadFxns GetWriteFxns ReplaceReadFxn ReplaceWriteFxn SetBaseWriteFxn SetReadFxn SetWriteFxn OESystem::OEBinaryNot Constructors CreateCopy operator() operator= OESystem::OEBinaryOr Constructors CreateCopy operator() operator= OESystem::OEBinaryPredicate CreateCopy CreatePredicateCopy operator() OESystem::OEBinaryTrue CreateCopy operator() OESystem::OEBInitializer Constructors OESystem::OEBIntEndian OESystem::OEBitIsPowerOf2 OESystem::OEBitVector ClearBits Constructors CountBits CountRangeBits FirstBit FromHexString GetData GetSize IsBitOn IsEmpty LastBit NegateBits NextBit operator&= operator-= operator< operator= operator[] operator^= operator|= PrevBit SetBitOff SetBitOn SetData SetRangeOff SetRangeOn SetSize ToggleBit ToHexString OESystem::OEBitVectorAnd OESystem::OEBitVectorEqual OESystem::OEBitVectorNot OESystem::OEBitVectorNumBytes OESystem::OEBitVectorNumWords OESystem::OEBitVectorOr OESystem::OEBitVectorSub OESystem::OEBitVectorXor OESystem::OEBoolParameter Constructors operator= OESystem::OEBoundedBuffer Constructors Empty Full Get Peek Put Size OESystem::OEBPeekTag OESystem::OEBReadData OESystem::OEBReadDataLength OESystem::OEBReadOEBase OESystem::OEBReadPOD OESystem::OEBReadTag OESystem::OEBShortEndian OESystem::OEBWriteData OESystem::OEBWriteDataLength OESystem::OEBWriteOEBase OESystem::OEBWritePOD OESystem::OEBWriteTag OESystem::OECastData OESystem::OECheckHelp OESystem::OEClearGridBoundary OESystem::OEColor Constructors CreateCopy GetA GetB GetG GetPackedColor GetR GetRGBA GetText operator!= operator== Set SetA SetB SetG SetPackedColor SetR SetRGBA SetText OESystem::OEColorCreate OESystem::OEColorGet OESystem::OEColorGradientBase AddStop Constructors DeleteStop GetColorAt GetMaxColor GetMaxValue GetMinColor GetMinValue GetStops IsEmpty NumStops operator= TransformValue OESystem::OEColorPacked OESystem::OEColorSet OESystem::OEColorStop Constructors GetColor GetValue operator= OESystem::OEConcatIter Constructors Copy operator bool operator* operator++ operator+= operator-- operator-= operator-> Push ToFirst ToLast OESystem::OEConfigure OESystem::OEConfigureItf OESystem::OEConfigureOpts OESystem::OEConsoleProgressTracer Aborted Constructors Pop Push Refresh SetProgress SetTask OESystem::OEConstParameter AddLegalEntry Constructors operator= OESystem::OEContainer Constructors CreateCopy GetDataType IsDataType operator= OESystem::OECopyArray OESystem::OECopyBaseData OESystem::OECopyBits OESystem::OECount OESystem::OECycleTimer Constructors Elapsed Lap Start OESystem::OEDivideGrid OESystem::OEDots Constructors GetBigStep GetCounts GetSmallStep SetBigStep SetSmallStep Total Update OESystem::OEDoubleParameter Constructors operator= OESystem::OEErrorHandler Clear Constructors Count Debug Error Fatal GetHandlerImpl GetLevel GetStrict Info Msg operator= SetHandlerImpl SetLevel SetOutputStream SetStrict Usage Verbose Warning OESystem::OEErrorHandlerImplBase Clear Constructors Count CreateCopy GetLevel GetStrict IncrementCount Msg SetLevel SetStrict OESystem::OEErrorLevel OESystem::OEErrorLevel::Debug OESystem::OEErrorLevel::Default OESystem::OEErrorLevel::Error OESystem::OEErrorLevel::Fatal OESystem::OEErrorLevel::Info OESystem::OEErrorLevel::MAX OESystem::OEErrorLevel::MIN OESystem::OEErrorLevel::Quiet OESystem::OEErrorLevel::Undefined OESystem::OEErrorLevel::Usage OESystem::OEErrorLevel::Verbose OESystem::OEErrorLevel::Warning OESystem::OEErrorLevelToString OESystem::OEExponentColorGradient Constructors GetExponent operator= SetExponent TransformValue OESystem::OEExponentialColorGradient Constructors operator= TransformValue OESystem::OEFileExtension OESystem::OEFileExtensions OESystem::OEFixedGrid CreateCopy GetDataType GetValues IsDataType operator() operator[] SetValues OESystem::OEFixedMultiGrid CreateCopy GetDataType GetNumGrids GetValues IsDataType operator[] SetNumGrids OESystem::OEFloatParameter Constructors operator= OESystem::OEGaussian Constructors CreateCopy GetCenter GetColor GetDataType GetPrefactor GetWidth GetX GetY GetZ IsDataType operator= SetCenter SetColor SetPrefactor SetWidth SetX SetY SetZ OESystem::OEGaussianBase GetCenter GetColor GetDataType GetPrefactor GetWidth GetX GetY GetZ IsDataType SetCenter SetColor SetPrefactor SetWidth SetX SetY SetZ OESystem::OEGaussianContainer AddGaussian Clear Constructors CreateCopy DeleteGaussian DeleteGaussians GetColors GetCoords GetDataType GetGaussians GetPrefactors GetWidths IsDataType NumGaussians operator= OESystem::OEGaussianContainerBase AddGaussian Clear DeleteGaussian DeleteGaussians GetColors GetCoords GetDataType GetGaussians GetPrefactors GetWidths IsDataType NumGaussians OESystem::OEGetBitCounts OESystem::OEGetByteArrayFromScalarGrid OESystem::OEGetByteArrayFromSkewGrid OESystem::OEGetBytesFromGrid OESystem::OEGetCenterAndExtents OESystem::OEGetColors OESystem::OEGetContourColor OESystem::OEGetContourLevel OESystem::OEGetContrastColors OESystem::OEGetDataType OESystem::OEGetDeepColors OESystem::OEGetFileEndian OESystem::OEGetGridFileType OESystem::OEGetGridFormatExtension OESystem::OEGetGridFormatString OESystem::OEGetHostEndian OESystem::OEGetKappa OESystem::OEGetLightColors OESystem::OEGetMemPoolMode OESystem::OEGetOEBReturnString OESystem::OEGetPrefactor OESystem::OEGetRadius OESystem::OEGetScalarGridFromByteArray OESystem::OEGetScalarGridFromBytes OESystem::OEGetSkewGridFromByteArray OESystem::OEGetSkewGridFromBytes OESystem::OEGetTag OESystem::OEGetThreadSafe OESystem::OEGetVividColors OESystem::OEGetWidth OESystem::OEGrid Clear Constructors CreateCopy GetDataType IsDataType operator= SetAll SetDim SetMid SetSpacing SetXDim SetXMid SetYDim SetYMid SetZDim SetZMid OESystem::OEGridAbstractBase Clear GetDataType GetDim GetMid GetSize GetSpacing GetTitle GetXDim GetXMid GetYDim GetYMid GetZDim GetZMid IsDataType IsSpacingSet SetTitle OESystem::OEGridAvgVal OESystem::OEGridBase Clear CreateCopy ElementToGridIdx ElementToSpatialCoord GetDataType GetDim GetMid GetSize GetSpacing GetTitle GetX GetXDim GetXIdx GetXInc GetXMax GetXMid GetXMin GetY GetYDim GetYIdx GetYInc GetYMax GetYMid GetYMin GetZ GetZDim GetZIdx GetZInc GetZMax GetZMid GetZMin GridIdxToElement GridIdxToSpatialCoord IsDataType IsInGrid IsSpacingSet IsTitleSet IsXMidSet IsYMidSet IsZMidSet SetTitle SpatialCoordToElement SpatialCoordToGridIdx OESystem::OEGridCopyContents OESystem::OEGridCopyGeometry OESystem::OEGridFileType OESystem::OEGridFileType::Ascii OESystem::OEGridFileType::CCP4 OESystem::OEGridFileType::Grasp OESystem::OEGridFileType::GRD OESystem::OEGridFileType::UNDEFINED OESystem::OEGridFileType::XPLOR OESystem::OEGridGetArch OESystem::OEGridGetLicensee OESystem::OEGridGetPlatform OESystem::OEGridGetRelease OESystem::OEGridGetSite OESystem::OEGridGetVersion OESystem::OEGridHasNonZeroValue OESystem::OEGridIsLicensed OESystem::OEGridMaskType OESystem::OEGridMaskType::Default OESystem::OEGridMaskType::Gaussian OESystem::OEGridMaskType::GaussianMinus OESystem::OEGridMaskType::GaussianSmooth OESystem::OEGridMaskType::GaussianSmoothMinus OESystem::OEGridMaskType::GridMinus OESystem::OEGridMaskType::GridPlus OESystem::OEGridMaskType::ValueMinus OESystem::OEGridMaskType::ValuePlus OESystem::OEGridMaxVal OESystem::OEGridMinVal OESystem::OEGridSameGeometry OESystem::OEGridSetAllElements OESystem::OEGridSizeMultiply OESystem::OEGridType OESystem::OEGridType::DifferenceMap OESystem::OEGridType::ElectrostaticGrid OESystem::OEGridType::EonGrid OESystem::OEGridType::ETGrid OESystem::OEGridType::FredGrid OESystem::OEGridType::GenericGrid OESystem::OEGridType::MaxGridType OESystem::OEGridType::RegularMap OESystem::OEHasRole Constructors CreateCopy operator() OESystem::OEHasTag OESystem::OEHeader AddHistory Constructors GetCommandLine GetComment GetDate GetHistory GetInterface GetOERelease GetOEVersion GetPlatform GetProgram GetVersion SetCommandLine SetComment SetDate SetInterface SetOERelease SetOEVersion SetPlatform SetProgram SetVersion OESystem::OEInitAnnotationHandlers OESystem::OEInitGridHandlers OESystem::OEInitializeHandler OESystem::OEInterface AddDetail AddInterface AddParameter Clear Constructors DeleteInterface DeleteParameter Factory Get GetBrief GetDetail GetInterface GetInterfaces GetList GetName GetOrderPriority GetParameter GetParameters GetTypedParameter Has operator= Parent SetBrief SetName SetOrderPriority OESystem::OEInterpolateBetweenGrids OESystem::OEIntParameter Constructors operator= OESystem::OEIsEmpty OESystem::OEIsFalse CreateCopy operator() OESystem::OEIsGrid OESystem::OEIsReadableGrid OESystem::OEIsSafeCast OESystem::OEIsSameTypeTester OESystem::OEIsTrue CreateCopy operator() OESystem::OEIsWriteableGrid OESystem::OEIter Constructors Copy operator A & operator A * operator bool operator! operator!= operator* operator++ operator+= operator-- operator-= operator-> operator= operator== Push Sort ToFirst ToLast OESystem::OEIterBase Constructors Copy operator A * operator bool operator* operator++ operator+= operator-- operator-= operator-> Push ToFirst ToLast OESystem::OELinearColorGradient Constructors operator= TransformValue OESystem::OELinearInterpolate OESystem::OELogarithmicColorGradient Constructors operator= TransformValue OESystem::OEMakeGaussians OESystem::OEMakeGridFromCenterAndExtents OESystem::OEMakeHex OESystem::OEMakeMolecularGaussianGrid OESystem::OEMakeRegularGrid OESystem::OEMakeRegularSubGrid OESystem::OEMakeString OESystem::OEMaskGrid OESystem::OEMaskGridByCoordsAndRadii OESystem::OEMaskGridByMolecule OESystem::OEMaskGridValues OESystem::OEMemPoolMode OESystem::OEMemPoolMode::BoundedCache OESystem::OEMemPoolMode::Default OESystem::OEMemPoolMode::Mutexed OESystem::OEMemPoolMode::SingleThreaded OESystem::OEMemPoolMode::Spinlocked OESystem::OEMemPoolMode::System OESystem::OEMemPoolMode::ThreadLocal OESystem::OEMemPoolMode::UnboundedCache OESystem::OEMoveArray OESystem::OEMTZMapType OESystem::OEMTZMapType::Fc OESystem::OEMTZMapType::Fdelwt OESystem::OEMTZMapType::FiveFoThreeFc OESystem::OEMTZMapType::Fo OESystem::OEMTZMapType::FoFc OESystem::OEMTZMapType::FoFcSigmaA OESystem::OEMTZMapType::FoFom OESystem::OEMTZMapType::FoSquared OESystem::OEMTZMapType::Fwt OESystem::OEMTZMapType::None OESystem::OEMTZMapType::ThreeFoTwoFc OESystem::OEMTZMapType::TwoFoFc OESystem::OEMTZMapType::TwoFoFcSigmaA OESystem::OEMTZMapType::User OESystem::OEMTZMapType::UserDiff OESystem::OEMTZMapTypeFromString OESystem::OEMTZMapTypeToString OESystem::OEMultiGrid Clear Constructors CreateCopy GetDataType IsDataType operator= SetDim SetMid SetSpacing SetValues SetXDim SetXMid SetYDim SetYMid SetZDim SetZMid OESystem::OEMultiParameter AddLegalEntry Constructors GetDefault GetSetting GetValue operator= SetDefault SetValue OESystem::OEMultiplicationWillOverflow OESystem::OEMultiplyGrid OESystem::OENot Constructors CreateCopy operator() operator= OESystem::OENumberToString OESystem::OENumContours OESystem::OEOptions AddDetail AddOption AddParameter AddParameterPrefix AddParameterSuffix Clear DeleteOptions DeleteParameter FindDupParameters GetBrief GetDetail GetName GetOption GetOptions GetOrderPriority GetParameter GetParameters HasDupParameters HasOption HasParameter SetBrief SetName SetOrderPriority SetParameterVisibility UpdateValues OESystem::OEOptsConfigureStatus OESystem::OEOptsConfigureStatus::Failed OESystem::OEOptsConfigureStatus::Help OESystem::OEOptsConfigureStatus::Success OESystem::OEOr Constructors CreateCopy operator() operator= OESystem::OEOwnedPtr Constructors Get operator const T * operator T * operator* operator-> operator= Release OESystem::OEParameter AddAlias AddDetail AddIllegalRange AddIllegalValue AddLegalRange AddLegalValue AddStringDefault AddStringValue ClearDefaults ClearValues CreateCopy GetAliases GetBrief GetDetail GetHasDefault GetHasValue GetIllegalRanges GetIllegalValues GetIsList GetKeyless GetLegalRanges GetLegalValues GetName GetOrderPriority GetPrettyLegalValues GetRequired GetStringDefault GetStringDefaults GetStringValue GetStringValues GetVisibility IsLegalString IsSet IsSetToString Load LoadDefault LoadValue SetBrief SetIsList SetKeyless SetName SetOrderPriority SetRequired SetStringDefault SetStringValue SetVisibility OESystem::OEParamVisibility OESystem::OEParamVisibility::Hidden OESystem::OEParamVisibility::MAX OESystem::OEParamVisibility::Normal OESystem::OEParamVisibility::Simple OESystem::OEParseCommandLine OESystem::OEParseCommandLineLW OESystem::OEParseHex OESystem::OEParseParameterFile OESystem::OEPODParameter GetDefaultsVector GetSettingsVector GetValuesVector OESystem::OEPointerParameter OESystem::OEPredIter Constructors Copy operator bool operator* operator++ operator+= operator-- operator-= operator-> operator= Predicate ToFirst ToLast OESystem::oeprogressstream Constructors SetTracer OESystem::OEProtectedBuffer Constructors Get Null Peek Put OESystem::OERandom Constructors GetSeed NextFloat NextInt Seed TimeSeed OESystem::OEReadGrid OESystem::OEReadMTZ OESystem::OEReadOldStyleGrid OESystem::OERegisterMolParameters OESystem::OERegisterOEBInitializer OESystem::OERole Constructors GetName operator< operator= operator== OESystem::OERoles Constructors CreateCopy operator= OESystem::OERoleSet AddRole ClearRoles DeleteRole GetRoles HasRole NumRoles OESystem::OERotate OESystem::OEScalarGrid Clear Constructors CreateCopy GetDataType GetType IsDataType operator= SetType OESystem::OESetMemPoolMode OESystem::OESetThreadSafe OESystem::OESetupGrid OESystem::OESharedPtr Constructors Get operator const T * operator T * operator* operator-> OESystem::OESigmaNormalizeGrid OESystem::OESkewGrid AsRegularGrid Clear Constructors CreateCopy ElementToGridIdx ElementToSpatialCoord GetDataType GetDim GetMid GetReentrant GetSize GetSpaceGroup GetSpacing GetTitle GetType GetUnitCell GetValues GetXDim GetXMid GetYDim GetYMid GetZDim GetZMid HasSpaceGroup HasUnitCell IsDataType IsRegular IsSpacingSet IsTitleSet operator bool operator= SetDim SetMid SetReentrant SetSpaceGroup SetSpacing SetTitle SetType SetUnitCell SetValues OESystem::OESNPrintf OESystem::OEStaticGetTag OESystem::OEStopwatch Constructors Elapsed Lap Start OESystem::OEStringCollapseQuotes OESystem::OEStringCSVJoin OESystem::OEStringCSVQuote OESystem::OEStringCSVTokenize OESystem::OEStringEquals OESystem::OEStringJoin OESystem::OEStringLower OESystem::OEStringMatch OESystem::OEStringParameter Constructors operator= OESystem::OEStringSimplifyWhiteSpace OESystem::OEStringStripQuotes OESystem::OEStringStripWhiteSpace OESystem::OEStringTabsToSpaces OESystem::OEStringTokenize OESystem::OEStringTokenizeQuoted OESystem::OEStringToNumber OESystem::OEStringTranslate OESystem::OEStringUpper OESystem::OESubtractGrid OESystem::OESystem OESystem::OESystem::OEBlack OESystem::OESystem::OEBlue OESystem::OESystem::OEBlueTint OESystem::OESystem::OEBrass OESystem::OESystem::OEBrown OESystem::OESystem::OECopper OESystem::OESystem::OECyan OESystem::OESystem::OEDarkBlue OESystem::OESystem::OEDarkBrown OESystem::OESystem::OEDarkCyan OESystem::OESystem::OEDarkGreen OESystem::OESystem::OEDarkGrey OESystem::OESystem::OEDarkMagenta OESystem::OESystem::OEDarkOrange OESystem::OESystem::OEDarkPurple OESystem::OESystem::OEDarkRed OESystem::OESystem::OEDarkRose OESystem::OESystem::OEDarkSalmon OESystem::OESystem::OEDarkYellow OESystem::OESystem::OEGold OESystem::OESystem::OEGreen OESystem::OESystem::OEGreenBlue OESystem::OESystem::OEGreenTint OESystem::OESystem::OEGrey OESystem::OESystem::OEHotPink OESystem::OESystem::OELightBlue OESystem::OESystem::OELightBrown OESystem::OESystem::OELightGreen OESystem::OESystem::OELightGrey OESystem::OESystem::OELightOrange OESystem::OESystem::OELightPurple OESystem::OESystem::OELightSalmon OESystem::OESystem::OELimeGreen OESystem::OESystem::OEMagenta OESystem::OESystem::OEMandarin OESystem::OESystem::OEMediumBlue OESystem::OESystem::OEMediumBrown OESystem::OESystem::OEMediumGreen OESystem::OESystem::OEMediumOrange OESystem::OESystem::OEMediumPurple OESystem::OESystem::OEMediumSalmon OESystem::OESystem::OEMediumYellow OESystem::OESystem::OEOliveBrown OESystem::OESystem::OEOliveGreen OESystem::OESystem::OEOliveGrey OESystem::OESystem::OEOrange OESystem::OESystem::OEPewter OESystem::OESystem::OEPink OESystem::OESystem::OEPinkTint OESystem::OESystem::OEPurple OESystem::OESystem::OERed OESystem::OESystem::OERedOrange OESystem::OESystem::OERoyalBlue OESystem::OESystem::OESeaGreen OESystem::OESystem::OESilver OESystem::OESystem::OESkyBlue OESystem::OESystem::OETransparentColor OESystem::OESystem::OEViolet OESystem::OESystem::OEWhite OESystem::OESystem::OEYellow OESystem::OESystem::OEYellowTint OESystem::OETanimoto OESystem::OEThreadedDots Constructors Total Update OESystem::OEThrow OESystem::OETracerBase Aborted Pop Push Refresh SetProgress SetTask OESystem::OETranslate OESystem::OETrimToSigFigs OESystem::OETypedParameter AddDefault AddValue GetDefault GetDefaults GetSetting GetSettings GetValue GetValues SetDefault SetValue OESystem::OEUIntParameter Constructors operator= OESystem::OEUnaryFalse OESystem::OEUnaryFunction CreateCopy operator() OESystem::OEUnaryPredicate CreateCopy CreatePredicateCopy operator() OESystem::OEUnaryTrue OESystem::OEUnboundedBuffer Constructors Empty Full Get Peek Put Size OESystem::OEUnknownOEBDataTagName OESystem::OEUnownedPtr Constructors Get operator const T * operator T * operator* operator-> operator= Release OESystem::OEUpdateOpts OESystem::OEWallTimer Constructors Elapsed Lap Start OESystem::OEWriteGrid OESystem::OEWriteHtml OESystem::OEWriteInterfaceConfigurationFile OESystem::OEWriteOldStyleGrid OESystem::OEWriteSettings OESz::OEAtomicRadii OESz::OEAtomicRadii::Bondi OESz::OEAtomicRadii::ZAP7 OESz::OEAtomicRadii::ZAP9 OESz::OEBoundEntropyOptions Constructors GetForceField GetLigandCharge operator= SetForceField SetLigandCharge OESz::OEBoundLigandEntropy OESz::OEComplexFFType OESz::OEComplexFFType::FF14SB_PARSLEY OESz::OEComplexFFType::FF14SB_SAGE OESz::OEComplexFFType::MMFF94 OESz::OEComplexFFType::MMFF94S OESz::OEComplexFFType::MMFF_AMBER OESz::OEComplexFFType::MMFFS_AMBER OESz::OEEntropyMethod OESz::OEEntropyMethod::Analytic OESz::OEEntropyMethod::ExternalHessian OESz::OEEntropyMethod::QNewton OESz::OEEntropyResults Constructors GetConfigurationalEntropy GetSolvationEntropy GetTotalEntropy in J/(mol K). GetTranslationalEntropy GetVibrationalRotationalEntropy operator= SetResults OESz::OEEnvType OESz::OEEnvType::Gas OESz::OEEnvType::Protein OESz::OEEnvType::Solution OESz::OEEnvType::SolutionSA OESz::OEEnvType::SolutionSPT OESz::OEEstimateConfFreeEnergies OESz::OEEstimateSolvFreeEnergy OESz::OEFixedProteinLigandOptimizer Constructor Energy operator= Optimize SetProtein OESz::OEFlexProteinLigandOptimizer Constructor Energy operator= Optimize OESz::OEForceFieldType OESz::OEForceFieldType::FF14SB_SMIRNOFF OESz::OEForceFieldType::MMFF94 OESz::OEForceFieldType::MMFF94S OESz::OEForceFieldType::MMFF_AMBER OESz::OEForceFieldType::MMFF_IEFF OESz::OEForceFieldType::MMFFS_AMBER OESz::OEForceFieldType::MMFFS_IEFF OESz::OEForceFieldType::PARSLEY_OPENFF OESz::OEForceFieldType::PARSLEY_OPENFF100 OESz::OEForceFieldType::PARSLEY_OPENFF111 OESz::OEForceFieldType::PARSLEY_OPENFF121 OESz::OEForceFieldType::PARSLEY_OPENFF131 OESz::OEForceFieldType::SAGE_OPENFF OESz::OEForceFieldType::SAGE_OPENFF200 OESz::OEForceFieldType::SAGE_OPENFF210 OESz::OEForceFieldType::SMIRNOFF99FROSST OESz::OEFreeFormConf Constructors EstimateFreeEnergies FindSimilarConfs operator= OESz::OEFreeFormConfAdvanced Constructors EstimateEnergies EstimateRestrictionEnergy IdentifyConformer operator= Optimize OptimizeRestraint PreOptimizeEnsemble PrepareEnsemble RemoveDuplicates OESz::OEFreeFormConfOptions Constructors GetCorrSolventOptions GetIonicState GetOmegaOptions GetOptimizeOptions GetPreOptimizeOptions GetSolventOptions GetSzybkiGeneralOptions GetUseInputEnsemble GetUseSolventCorr operator= SetCorrSolventOptions SetIonicState SetOmegaOptions SetOptimizeOptions SetPreOptimizeOptions SetSolventOptions SetSzybkiGeneralOptions SetUseInputEnsemble SetUseSolventCorr OESz::OEFreeFormConfResults Constructors GetConfResult GetLowestdGConfIdx GetLowestRelEneConfIdx GetNumUniqueConfs GetResultsForConformations GetTemperature GetTotalEntropy operator= PrintCsv PrintTxt OESz::OEFreeFormIonicState OESz::OEFreeFormIonicState::Default OESz::OEFreeFormIonicState::Input OESz::OEFreeFormIonicState::PH74 OESz::OEFreeFormIonicState::Uncharged OESz::OEFreeFormReturnCode OESz::OEFreeFormReturnCode::AtomTypeFailure OESz::OEFreeFormReturnCode::ChargeAssignFailure OESz::OEFreeFormReturnCode::ChargeMismatch OESz::OEFreeFormReturnCode::ConfGenFailure OESz::OEFreeFormReturnCode::GraphMismatch OESz::OEFreeFormReturnCode::ImplicitHydrogens OESz::OEFreeFormReturnCode::InputGeometry OESz::OEFreeFormReturnCode::MissingFFConfEne OESz::OEFreeFormReturnCode::MissingPartnerConf OESz::OEFreeFormReturnCode::No3DCoordinates OESz::OEFreeFormReturnCode::NotSupportedCharges OESz::OEFreeFormReturnCode::PartnerConfNotFound OESz::OEFreeFormReturnCode::Success OESz::OEFreeFormReturnCode::TooManyRotors OESz::OEFreeFormReturnCode::UnequalNumConfs OESz::OEFreeFormReturnCode::UnrecognizedChargeState OESz::OEFreeFormReturnCode::UnsupportedRadiiType OESz::OEFreeFormSolvOptions Constructors GetAtomicRadiiType GetChargeType GetConfGenRMS GetIonicState GetMaxConfGen GetUseInput3D GetUseInputEnsemble operator= SetAtomicRadiiType SetChargeType SetConfGenRMS SetIonicState SetMaxConfGen SetUseInput3D SetUseInputEnsemble OESz::OEFreeFormSolvResults Constructors GetAtomicPotentials GetElectrostaticSolvationFreeEnergy GetHydrophobicSolvationFreeEnergy GetReturnCode GetSolvationFreeEnergy GetWarnings operator= OESz::OEFreeFormWarning OESz::OEFreeFormWarning::HSamplingSkipped OESz::OEFreeFormWarning::Missing3DCoordinates OESz::OEFreeFormWarning::NotRemovableCharge OESz::OEFreeFormWarning::UnspecifiedStereo OESz::OEFreeFormWarning::ZeroPartialCharges OESz::OEGetEnergyTermName OESz::OEGetFreeFormError OESz::OEGetSzybkiError OESz::OELigandChargeType OESz::OELigandChargeType::AM1BCC OESz::OELigandChargeType::AM1BCCELF10 OESz::OELigandChargeType::CURRENT OESz::OELigandChargeType::MMFF OESz::OELigandEntropy OESz::OELigandEntropyOptions Constructors GetEnvironment GetForceField GetLigandCharge operator= SetEnvironment SetForceField SetLigandCharge OESz::OEOptimizationType OESz::OEOptimizationType::Cartesian OESz::OEOptimizationType::PoseCartesian OESz::OEOptType OESz::OEOptType::BFGS OESz::OEOptType::CG OESz::OEOptType::NEWTON OESz::OEOptType::SD OESz::OEOptType::SD_BFGS OESz::OEOptType::SD_CG OESz::OEPotentialTerms OESz::OEPotentialTerms::Bend OESz::OEPotentialTerms::Bond OESz::OEPotentialTerms::CavitySolvation OESz::OEPotentialTerms::Coulomb OESz::OEPotentialTerms::CoulombProteinLigand OESz::OEPotentialTerms::ExactCoulomb OESz::OEPotentialTerms::GridCoulomb OESz::OEPotentialTerms::HarmonicConstraint OESz::OEPotentialTerms::IEFFInteraction OESz::OEPotentialTerms::ImproperTorsion OESz::OEPotentialTerms::InterLigandIEFF OESz::OEPotentialTerms::LigandBend OESz::OEPotentialTerms::LigandBond OESz::OEPotentialTerms::LigandCoulomb OESz::OEPotentialTerms::LigandDesolvation OESz::OEPotentialTerms::LigandImproperTorsion OESz::OEPotentialTerms::LigandStretchBend OESz::OEPotentialTerms::LigandTorsion OESz::OEPotentialTerms::LigandVdW OESz::OEPotentialTerms::Max OESz::OEPotentialTerms::PBSolvation OESz::OEPotentialTerms::ProteinBend OESz::OEPotentialTerms::ProteinBond OESz::OEPotentialTerms::ProteinCoulomb OESz::OEPotentialTerms::ProteinDesolvation OESz::OEPotentialTerms::ProteinImproperTorsion OESz::OEPotentialTerms::ProteinLigandAmberCoulomb OESz::OEPotentialTerms::ProteinLigandAmberVdW OESz::OEPotentialTerms::ProteinLigandCoulomb OESz::OEPotentialTerms::ProteinLigandInteraction OESz::OEPotentialTerms::ProteinLigandVdW OESz::OEPotentialTerms::ProteinPseudoLigandInteraction OESz::OEPotentialTerms::ProteinStretchBend OESz::OEPotentialTerms::ProteinTorsion OESz::OEPotentialTerms::ProteinVdW OESz::OEPotentialTerms::SheffieldSolvation OESz::OEPotentialTerms::SolventScreening OESz::OEPotentialTerms::StretchBend OESz::OEPotentialTerms::Torsion OESz::OEPotentialTerms::TorsionHarmonicConstraint OESz::OEPotentialTerms::VdW OESz::OEPotentialTerms::VdWProteinLigand OESz::OEProteinElectrostatics OESz::OEProteinElectrostatics::ExactCoulomb OESz::OEProteinElectrostatics::GridCoulomb OESz::OEProteinElectrostatics::GridPB OESz::OEProteinElectrostatics::NoElectrostatics OESz::OEProteinElectrostatics::SolventPBForces OESz::OEProteinFlexOptions Constructor GetFlexRange GetResidueID operator= SetFlexRange SetResidueID OESz::OEProteinLigandOptOptions Constructor GetForceField GetGradTolerance GetLigandCharge GetMaxIter GetNonBondCutoff GetOptimizationType GetSolventModel operator= SetForceField SetGradTolerance SetLigandCharge SetMaxIter SetNonBondCutoff SetOptimizationType SetSolventModel OESz::OEProteinLigandOptResults Constructors GetFinalEnergies GetInitialEnergies GetLigandRMSD GetProteinRMSD GetReturnCode GetTotalRMSD operator= OESz::OEProtFlex OESz::OEProtFlex::NoFlex OESz::OEProtFlex::PolarH OESz::OEProtFlex::PolarHResList OESz::OEProtFlex::ResidueList OESz::OEProtFlex::Residues OESz::OEProtFlex::SideChains OESz::OEProtFlex::SideChainsList OESz::OERestrictionEnergyResult Constructors GetGlobalStrain GetLocalStrain operator= OESz::OERunType OESz::OERunType::CartesiansOpt OESz::OERunType::SinglePoint OESz::OERunType::SolidBodyOpt OESz::OERunType::TorsionsOpt OESz::OESingleConfResult Constructors GetConfIdx GetDeltaG GetLnQrotational GetLnQvibrational GetMMFFEnergy GetProbability GetRelativeEnergy GetRelLnQ GetRotationalEntropy GetSolvEnergy GetTotalEnergy GetVibrationalEntropy operator= OESz::OESolventModel OESz::OESolventModel::Cavity OESz::OESolventModel::NoSolv OESz::OESolventModel::PB OESz::OESolventModel::Sheffield OESz::OESzybki ClearFixAtoms ClearHarmonicConstraints ClearTorsionConstraint Constructors FixAtoms GetEntropy GetEntropy(const OEChem::OEMCMolBase&, unsigned int, unsigned int) GetFixPattern GetFixPredicate GetHarmonicConstraints GetProtein GetSheffieldParameters LoadPotentialGrid operator() SavePotentialGrid SetHarmonicConstraints SetProtein SetSheffieldParameters SetTorsionConstraint UnsetProtein OESz::OESzybkiEnsembleResults Constructors GetChargeType GetConfigurationalEntropy GetEnsembleLigPartialSolvEntropy GetEnsembleLigSolvEntropy GetEnsembleProtDesolvEntropy GetEntropicEnergy GetResultsForConformations GetTemperature GetTotalEntropy HasEntropy NumConfs operator= OESz::OESzybkiGeneralOptions Constructors GetCalculateGradients GetForceField GetForceFieldType GetIEFFCluster GetIntramolecularVdWCutoff GetLigandRMSDHeavy GetRemoveAttractiveVdWForces GetRemoveCoulombTerms GetSoluteDielectric GetTemperature GetVerbose operator= SetCalculateGradients SetForceField SetForceFieldType SetIEFFCluster SetIntramolecularVdWCutoff SetLigandRMSDHeavy SetRemoveAttractiveVdWForces SetRemoveCoulombTerms SetSoluteDielectric SetTemperature SetVerbose OESz::OESzybkiGetArch OESz::OESzybkiGetLicensee OESz::OESzybkiGetPlatform OESz::OESzybkiGetRelease OESz::OESzybkiGetSite OESz::OESzybkiGetVersion OESz::OESzybkiOptions Constructors GetGeneralOptions GetOptOptions GetProteinOptions GetRunType GetSolventOptions operator= SetGeneralOptions SetOptOptions SetProteinOptions SetRunType SetSolventOptions OESz::OESzybkiOptOptions Constructors GetCalculateFrozenTerms GetGradTolerance GetMaxIter GetOptimizerType operator= SetCalculateFrozenTerms SetGradTolerance SetMaxIter SetOptimizerType OESz::OESzybkiProteinOptions AddFlexibleResidue ClearFlexibleResidues Constructors GetExactVdWProteinLigand GetIntermolecularVdWCutoff GetProteinDielectric GetProteinElectrostaticModel GetProteinFlexibilityRange GetProteinFlexibilityType HasFlexibleResidues operator= SetExactVdWProteinLigand SetIntermolecularVdWCutoff SetProteinDielectric SetProteinElectrostaticModel SetProteinFlexibilityRange SetProteinFlexibilityType OESz::OESzybkiResults Clear Constructors GetConfFreeEnergyFromEnsemble GetConfIdx GetCPUTime GetEnergyTerm GetFinalRMSGradient GetFinalTotalPotential GetGradients GetInitialRMSGradient GetInitialTotalPotential GetInterEnergy GetIntramolecularLigandEnergy GetLnQrot GetLnQvib GetMaxDisplacement GetNumCycles GetNumFixAtoms GetNumRotors GetProteinRMSD GetRMSD GetRotEntropy GetTotalEnergy GetTotalEnergyWithHarmConstraint GetVibEntropy IsActiveTerm IsUnique operator= Print OESz::OESzybkiReturnCode OESz::OESzybkiReturnCode::ContainsImplicitH OESz::OESzybkiReturnCode::ExcessiveOverlap OESz::OESzybkiReturnCode::Failed OESz::OESzybkiReturnCode::FFNeedHessiens OESz::OESzybkiReturnCode::IncompleteOpt OESz::OESzybkiReturnCode::InvalidOptions OESz::OESzybkiReturnCode::LigandFailedCharge OESz::OESzybkiReturnCode::LigandFailedFF OESz::OESzybkiReturnCode::LigandMissing3D OESz::OESzybkiReturnCode::LigandMissingCharge OESz::OESzybkiReturnCode::ProteinFailedFF OESz::OESzybkiReturnCode::ProteinMissing3D OESz::OESzybkiReturnCode::ProteinMissingCharge OESz::OESzybkiReturnCode::ProteinNotSet OESz::OESzybkiReturnCode::Success OESz::OESzybkiSolventOptions Constructors GetAtomicRadiiType GetCavitySolventParameter GetSaltConcentration GetSolventDielectric GetSolventModel operator= SetAtomicRadiiType SetCavitySolventParameter SetChargeEngine SetSaltConcentration SetSolventDielectric SetSolventModel SetUseCurrentCharges OESz::OETorsionScan OESz::OETorsionScanner Constructor GetLowestEneResults GetLowestEnergyConfs GetScannedAngles GetSinglePointConfs operator= Scan OESz::OETorsionScanOptions Constructors GetDelta GetForceField GetForceFieldType GetMaxIter GetNumStarts GetOverlapDiv GetPenaltyForceConstant GetSolvationType GetTolerance GetUseInternalCoord GetUserDefinedAngles GetUseSinglePointPB operator= SetDelta SetForceField SetForceFieldType SetMaxIter SetNumStarts SetOverlapDiv SetPenaltyForceConstant SetSolvationType SetTolerance SetUseInternalCoord SetUserDefinedAngles SetUseSinglePointPB OESz::OETorsionScanResult Constructors GetAngle GetEnergy operator= OESzmap::OECalcSzmapResults OESzmap::OECalcSzmapValue OESzmap::OEComponent OESzmap::OEComponent::Interaction OESzmap::OEComponent::NumTypes OESzmap::OEComponent::ProbeBurial OESzmap::OEComponent::PSolv OESzmap::OEComponent::VDW OESzmap::OEComponent::WSolv OESzmap::OEEnsemble OESzmap::OEEnsemble::CalcPoint OESzmap::OEEnsemble::Default OESzmap::OEEnsemble::DeltaG OESzmap::OEEnsemble::DeltaH OESzmap::OEEnsemble::Interaction OESzmap::OEEnsemble::InteractionPlusVDW OESzmap::OEEnsemble::Mask OESzmap::OEEnsemble::NeutralDeltaG OESzmap::OEEnsemble::NeutralDeltaH OESzmap::OEEnsemble::NeutralDiffDeltaG OESzmap::OEEnsemble::NeutralDiffDeltaH OESzmap::OEEnsemble::NeutralDiffTDeltaS OESzmap::OEEnsemble::NeutralTDeltaS OESzmap::OEEnsemble::NumTypes OESzmap::OEEnsemble::OrderParam OESzmap::OEEnsemble::ProbeBurial OESzmap::OEEnsemble::PSolv OESzmap::OEEnsemble::TDeltaS OESzmap::OEEnsemble::VacuumDiffDeltaG OESzmap::OEEnsemble::VacuumDiffDeltaH OESzmap::OEEnsemble::VDW OESzmap::OEEnsemble::WSolv OESzmap::OEGetComponentName OESzmap::OEGetEnsembleName OESzmap::OEIsClashing OESzmap::OESzmapEngine CheckAtomTypes Constructors GetContext GetOptions operator bool operator= SetContext OESzmap::OESzmapEngineOptions Constructors GetMaskCutoff GetProbe GetProbeMol GetProbeName NumOrientations operator= SetMaskCutoff SetProbe OESzmap::OESzmapGetArch OESzmap::OESzmapGetLicensee OESzmap::OESzmapGetPlatform OESzmap::OESzmapGetRelease OESzmap::OESzmapGetSite OESzmap::OESzmapGetVersion OESzmap::OESzmapIsLicensed OESzmap::OESzmapResults Clear Constructors GetComponent GetCoords GetEnsembleValue GetProbabilities GetProbabilityOrder NumOrientations operator bool operator= PlaceNewAtom PlaceProbeMol PlaceProbeSet OEUniMolecularRxn, [1] Open OEChem::OEMolDatabase OEChem::OESubSearchDatabase OEFastROCS::OEShapeDatabase OESiteHopper::OESiteHopperDatabase open OEChem::oemolstreambase OEPlatform::oeistream OEPlatform::oeostream openByteArray OEChem::oemolistream OpenEye-Toolkits.sln openfd OEPlatform::oeifstream OEPlatform::oeofstream openstring OEChem::oemolithread OEChem::oemolostream OEChem::oemolothread operator * OEDepict::OE2DPoint operator A & OESystem::OEIter operator A * OESystem::OEIter OESystem::OEIterBase operator bool OEBio::OEAltGroup OEBio::OEAltLocation OEBio::OEAltLocationState OEBio::OEDesignUnit OEBio::OEInteractionHintContainer OEBio::OEIridiumData OEBio::OESequenceAlignment OEBio::OEStructureQuality OEChem::OECliqueSearch OEChem::OECSVHeader OEChem::OEFuzzy OEChem::OELibraryGen OEChem::OEMatchBase OEChem::OEMatchFunc OEChem::OEMCSSearch OEChem::OEMolBase OEChem::oemolistream OEChem::oemolostream OEChem::oemolthreadbase OEChem::OEResidue OEChem::OESubSearch OEChem::OETrans OEChem::OEUniMolecularRxn OEConfGen::OETorLib OEGraphSim::OEFingerPrint OEMolProp::OEFilter OEPlatform::OEDirectoryScan OEPlatform::oestream OEShape::OEShapeQueryPublic OESiteHopper::OESiteHopperDatabase OESiteHopper::OESiteHopperSearch OESiteHopper::OESiteHopperSearchBase OESpicoli::OESurface OESpruce::OESecondaryStructureSuperposition OESpruce::OEStructuralSuperposition OESpruce::OESuperposeResults OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEPredIter OESystem::OESkewGrid OESzmap::OESzmapEngine OESzmap::OESzmapResults operator const T * OEChem::OEConstCoords OESystem::OEOwnedPtr OESystem::OESharedPtr OESystem::OEUnownedPtr operator double OEPlatform::OEHalfFloat operator double * OEChem::OECoordArray operator float OEPlatform::OEHalfFloat operator long double OEPlatform::OEHalfFloat operator OEMCMolBase & OEChem::OEMol operator OEMolBase & OEChem::OEGraphMol OEChem::OEQMol operator OEPlatform::oeistream & OEChem::oemolistream operator OEPlatform::oeostream & OEChem::oemolostream operator OEQMolBase & OEChem::OEQMol operator T & OEPlatform::OEThreadLocal operator T * OEChem::OEMutableCoords OEPlatform::OEOnce OEPlatform::OEThreadLocal OESystem::OEOwnedPtr OESystem::OESharedPtr OESystem::OEUnownedPtr operator! OEChem::OEFuzzy OESystem::OEIter operator!= OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintTypeBase OEBio::OESplitMolComplexOptions OEChem::OEFuzzy OEDepict::OEFont OEDepict::OEPen OEGrapheme::OEPlotMarker OEGraphSim::OEFingerPrint OEProton::OEChargeEngineBase OESystem::OEColor OESystem::OEIter operator&& OEChem::OEFuzzy operator&= OESystem::OEBitVector operator() OEBio::OEAtomMatchResidue OEBio::OEHasAlternateLocation OEBio::OEHasInteractionHint OEBio::OEHasInteractionHintType OEBio::OEHasPDBAtomIndex OEBio::OEHasResidueInteractionHint OEBio::OEHasSecondaryStructure OEBio::OEIsBackboneAtom OEBio::OEIsCationPiInteractionHint OEBio::OEIsChelatorInteractionHint OEBio::OEIsClashInteractionHint OEBio::OEIsContactInteractionHint OEBio::OEIsCovalentInteractionHint OEBio::OEIsCTerminalAtom OEBio::OEIsDisulfideBond OEBio::OEIsHalogenBondInteractionHint OEBio::OEIsHBondInteractionHint OEBio::OEIsHetAtom OEBio::OEIsInterInteractionHint OEBio::OEIsIntermolecularChelatorInteractionHint OEBio::OEIsIntermolecularHBondInteractionHint OEBio::OEIsIntraInteractionHint OEBio::OEIsIntramolecularChelatorInteractionHint OEBio::OEIsIntramolecularHBondInteractionHint OEBio::OEIsNonIdealHBondInteractionHint OEBio::OEIsNTerminalAtom OEBio::OEIsNucleicAcidBase OEBio::OEIsNucleicAcidPhosphate OEBio::OEIsNucleicAcidSugar OEBio::OEIsSaltBridgeInteractionHint OEBio::OEIsStackingInteractionHint OEBio::OEIsStandardAminoAcid OEBio::OEIsStandardNucleicAcid OEBio::OEIsUnpairedLigandInteractionHint OEBio::OEIsUnpairedProteinInteractionHint OEBio::OEIsWater OEBio::OEMolComplexCategorizer OEBio::OEMolComplexCategorizerBase OEBio::OEMolComplexFilter OEChem::OEAtomIsInAgent OEChem::OEAtomIsInChain OEChem::OEAtomIsInProduct OEChem::OEAtomIsInReactant OEChem::OEAtomIsInResidue OEChem::OEAtomIsInRing OEChem::OEBondIsInChain OEChem::OEBondIsInRing OEChem::OEGetNbrAtom OEChem::OEHasAlphaBetaUnsat OEChem::OEHasAnisou OEChem::OEHasAtomicNum OEChem::OEHasAtomInGroup OEChem::OEHasAtomName OEChem::OEHasAtomStereoSpecified 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::OEIsReactantGroup OEChem::OEIsRGroup OEChem::OEIsRotor OEChem::OEIsRxnComponentGroup OEChem::OEIsSulfur OEChem::OEIsTermHeavyAtom OEChem::OEIsValidAtomValence OEChem::OEIsValidMDLAtomValence OEChem::OELibraryGen OEChem::OEMatchFunc OEChem::OEMCSFunc OEChem::OEMCSMaxAtoms OEChem::OEMCSMaxAtomsCompleteCycles OEChem::OEMCSMaxBonds OEChem::OEMCSMaxBondsCompleteCycles OEChem::OENthAtom OEChem::OEPartPredT OEChem::OESimilarByRMSD OEChem::OEUnaryToBinaryAnd OEChem::OEUnaryToBinaryOr OEChem::OEUniMolecularRxn OEDepict::OEDisplayAtomIdx OEDepict::OEDisplayAtomMapIdx OEDepict::OEDisplayAtomPropBase OEDepict::OEDisplayBondIdx OEDepict::OEDisplayBondPropBase OEDepict::OEDisplayNoAtomProp OEDepict::OEDisplayNoBondProp OEDocking::OEAlignReceptorFunction OEEon::OEChargeFunc OEEon::OEHighestChargeTanimoto OEEon::OEHighestShapeChargeTanimotoCombo OEEon::OEHighestShapeTanimoto OEGrapheme::OEAlphaRainbowArcFxn 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::OESawArcFxn OEGrapheme::OESimpsonArcFxn OEGrapheme::OEStitchArcFxn OEGrapheme::OESunArcFxn OEGrapheme::OESurfaceArcFxnBase OEGrapheme::OEWreathArcFxn OEGraphSim::OESimFuncBase OEGraphSim::OETanimotoSim OEGraphSim::OETverskySim OEMedChem::OEMCSSimFuncBase OEMedChem::OEMCSTanimotoSim OEMedChem::OEMCSTverskySim OEMolProp::OEFilter OEOpt::OECheckpoint0 OEOpt::OECheckpoint1 OEOpt::OEFunc0 OEOpt::OEFunc1 OEOpt::OEFunc2 OEOpt::OELineMinimize OEOpt::OEOptimizer0 OEOpt::OEOptimizer1 OEOpt::OEOptimizer2 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 OESpruce::OEIsModeledAtom OESystem::OEAnd OESystem::OEBinaryAnd OESystem::OEBinaryFalse OESystem::OEBinaryFunction OESystem::OEBinaryNot OESystem::OEBinaryOr OESystem::OEBinaryPredicate OESystem::OEBinaryTrue OESystem::OEFixedGrid OESystem::OEHasRole OESystem::OEIsFalse OESystem::OEIsTrue OESystem::OENot OESystem::OEOr OESystem::OEUnaryFunction OESystem::OEUnaryPredicate OESz::OESzybki operator* OEPlatform::OEOnce OEPlatform::OEThreadLocal OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEOwnedPtr OESystem::OEPredIter OESystem::OESharedPtr OESystem::OEUnownedPtr operator*= OEDepict::OE2DPoint operator+ OEDepict::OE2DPoint OEMedChem::OECreateMMPIndexStatus operator++ OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEPredIter operator+= OEChem::OETrans OEChem::OETranslation OEDepict::OE2DPoint OESpicoli::OESurface OESystem::OEBase OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEPredIter operator- OEDepict::OE2DPoint operator-- OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEPredIter operator-= OEDepict::OE2DPoint OESystem::OEBitVector OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEPredIter operator-> OEPlatform::OEOnce OEPlatform::OEThreadLocal OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEOwnedPtr OESystem::OEPredIter OESystem::OESharedPtr OESystem::OEUnownedPtr operator/ OEDepict::OE2DPoint operator/= OEDepict::OE2DPoint operator< OEChem::OE3DMolStyle OEChem::OEMolStyleColorer OESystem::OEBitVector OESystem::OERole operator<< OEPlatform::oeostream operator= OEBio::OEAltGroup OEBio::OEAltLocation OEBio::OEAltLocationFactory OEBio::OEAltLocationState OEBio::OECationPiInteractionHint OEBio::OEChelatorInteractionHint OEBio::OEClashInteractionHint OEBio::OEContactInteractionHint OEBio::OECovalentInteractionHint OEBio::OEDesignUnit OEBio::OEHalogenBondInteractionHint OEBio::OEHasInteractionHint OEBio::OEHasInteractionHintType OEBio::OEHasResidueInteractionHint OEBio::OEHBondInteractionHint OEBio::OEHierChain OEBio::OEHierFragment OEBio::OEHierResidue OEBio::OEHierView OEBio::OEInteractionHint OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintFragment OEBio::OEInteractionHintTypeBase OEBio::OEIridiumData OEBio::OELigandInteractionHintComponent OEBio::OEMolComplexCategorizer OEBio::OEMolComplexFilter OEBio::OEPlaceHydrogensDetails OEBio::OEPlaceHydrogensMoverNote OEBio::OEPlaceHydrogensOptions OEBio::OEProteinInteractionHintComponent OEBio::OEReceptor OEBio::OEReceptorConstraintFeature OEBio::OEReceptorCustomConstraints OEBio::OEResidueCategoryData OEBio::OESaltBridgeInteractionHint OEBio::OESequenceAlignment OEBio::OESplitMolComplexOptions OEBio::OEStackingInteractionHint OEBio::OEStructureQuality OEBioisostere::OEBroodBuildOptions OEBioisostere::OEBroodDBFilter OEBioisostere::OEBroodDBPacket OEBioisostere::OEBroodGeneralOptions OEBioisostere::OEBroodHit OEBioisostere::OEBroodHitlistOptions OEBioisostere::OEBroodQuery OEBioisostere::OEBroodScore OEBioisostere::OEBroodScoreOptions OEBioisostere::OEDBScreenOptions OEBioisostere::OEExtrinsicPropOptions OEBioisostere::OEFragmentOptions OEBioisostere::OEIntrinsicPropOptions OEBioisostere::OEMolPropertyOptions OEChem::OE2DRingDictionaryCreatorOptions OEChem::OE3DMolStyle OEChem::OEAtomBase OEChem::OEAtomBondSet OEChem::OEBondBase OEChem::OECliqueSearch OEChem::OEConfBase OEChem::OEConfRMSDOptions OEChem::OECoordArray OEChem::OECSVHeader OEChem::OEEuler OEChem::OEExtractRingTemplateOptions OEChem::OEFileStringParameter OEChem::OEGraphMol OEChem::OEHydrogenCounter OEChem::OEInChIOptions OEChem::OEInSamePart OEChem::OEIsMember OEChem::OEIsMemberPtr OEChem::OELibraryGen OEChem::OELingoSim OEChem::OEMatch OEChem::OEMatchPair OEChem::OEMCMolBase OEChem::OEMCSFuncParameter OEChem::OEMCSSearch OEChem::OEMol OEChem::OEMolBase OEChem::OEMolGDPropertyFxn OEChem::OEMolParameter OEChem::OEMolPropertyList OEChem::OEMolReaderParameter OEChem::OEMolSDPropertyFxn OEChem::OEMolStyleColorer OEChem::OEMolTaggedPropertyFxn OEChem::OEMolWriterParameter OEChem::OEOutFileStringParameter OEChem::OEPartPredT OEChem::OEPredicateParameter OEChem::OEQMol OEChem::OEQMolBase OEChem::OEQuaternion OEChem::OERefInputAppOptions OEChem::OEResidue OEChem::OERotMatrix OEChem::OERxnAutomapper OEChem::OERxnAutomapperOptions OEChem::OESimilarByRMSD OEChem::OESimpleAppOptions OEChem::OESubSearch OEChem::OESubSearchScreen OEChem::OETrans OEChem::OETranslation OEChem::OEUnAtomPredParameter OEChem::OEUnBondPredParameter OEChem::OEUniMolecularRxn OEChem::OEUniMolecularRxnOptions OEChem::OEVectorBindings OEConfGen::OEConfFixOptions OEConfGen::OEConformerBuilder OEConfGen::OEConfSlicer OEConfGen::OEFlipperClassicOptions 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::OEThompsonOptions OEConfGen::OETorDriveOptions OEConfGen::OETorDriver OEConfGen::OETorLibParameter OEConstr::OEDihedralQuadPenalty OEConstr::OEHarmonicPotential OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay OEDepict::OE2DMolDisplay OEDepict::OE2DMolDisplayOptions OEDepict::OE2DPath OEDepict::OE2DPathPoint OEDepict::OE2DPoint OEDepict::OEAlignmentOptions OEDepict::OEAlignmentResult OEDepict::OEFont OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByColor OEDepict::OEHighlightByLasso OEDepict::OEHighlightByStick OEDepict::OEHighlightOverlayByBallAndStick OEDepict::OEImageTableOptions OEDepict::OELegendLayoutOptions OEDepict::OEPen OEDepict::OEPrepareDepictionOptions OEDepict::OEReportOptions OEDocking::OEBox OEDocking::OEBoxBase OEDocking::OECustomConstraints OEDocking::OEDockOptions OEDocking::OEFeature OEDocking::OEMakeReceptorOptions OEDocking::OEPoseOptimizer OEDocking::OEPoseOptimizerOptions OEDocking::OEPosit OEDocking::OEPositOptions OEDocking::OEPositProbability OEDocking::OEPositResults OEDocking::OEShapeFit OEDocking::OEShapeFitOptions OEDocking::OEShapeFitResults OEDocking::OESinglePoseResult OEDocking::OESphereBase OEEon::OEEonHit OEEon::OEEonHitlistOptions OEEon::OEEonOverlapScore OEEon::OEEonOverlayResults OEEon::OEEonOverlayScore OEEon::OEEonPBFunc OEEon::OEEonPBOptions OEEon::OEEonPBResults OEFastROCS::OEShapeDatabaseOptions OEFF::OEComplexEnergies OEFF::OEComplexFFParameter OEFF::OEFF14SBParsley OEFF::OEFF14SBParsleyParams OEFF::OEFF14SBSage OEFF::OEFF14SBSageParams OEFF::OEFF14SBSmirnoff OEFF::OEFF14SBSmirnoffParams OEFF::OEForceFieldParameter OEFF::OEMMFFIEFFOptions OEFF::OEMMFFSheffieldOptions OEGrapheme::OE2DActiveSiteDisplayOptions OEGrapheme::OE2DActiveSiteLegendDisplayOptions OEGrapheme::OE2DPropMap OEGrapheme::OEAlignedDepictionFrom3DOptions OEGrapheme::OEColorForceFieldDisplay OEGrapheme::OEColorForceFieldLegendDisplayOptions OEGrapheme::OEColorGradientDisplayOptions OEGrapheme::OEColorGradientLabel OEGrapheme::OEColorOverlapDisplayOptions OEGrapheme::OEComplexSurfaceArcFxnBase OEGrapheme::OEDepictionFrom3DOptions OEGrapheme::OEPeptideDisplayOptions OEGrapheme::OEPlotMarker OEGrapheme::OERamachandranPlot OEGrapheme::OEShapeOverlapDisplay OEGrapheme::OEShapeOverlapDisplayOptions OEGrapheme::OEShapeQueryDisplay OEGrapheme::OEShapeQueryDisplayOptions OEGrapheme::OESurfaceArc OEGraphSim::OEFingerPrint OEGraphSim::OEFPDatabaseOptions OEGraphSim::OEFPPattern OEMath::OEBox OEMath::OEKernelPLS OEMath::OEMatrix OEMath::OESphere OEMath::OESquareMatrix OEMedChem::OECreateMMPIndexStatus OEMedChem::OEMatchedPair OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMatchedPairTransform OEMedChem::OEMatchedPairTransformExtractOptions OEMedChem::OEMCSFragDatabaseOptions OEMedChem::OEMCSMolSimScore OEModels::OEROCSQueryModelBuilder OEModels::OEROCSQueryModelOptions OEMolAM1::OEAM1 OEMolAM1::OEAM1Options OEMolAM1::OEAM1Results OEMolAM1::OEOptimizedAM1 OEMolMMFF::OEMMFF OEMolMMFF::OEMMFFOutOfPlane OEMolMMFF::OEMMFFStretchBend OEMolPotential::OEBendParams OEMolPotential::OEInteraction OEMolPotential::OEOutOfPlaneParams OEMolPotential::OEStretchParams OEMolPotential::OETorsionParams OEMolPotential::OEVdwParams OEMolProp::OEFilter OEMolSmirnoff::OEParsley OEMolSmirnoff::OEParsleyParams OEMolSmirnoff::OESage OEMolSmirnoff::OESageParams OEMolSmirnoff::OESmirnoff OEMolSmirnoff::OESmirnoffParams OEOpt::OEBFGSOpt OEOpt::OEConjGradOpt OEOpt::OEDFPOpt OEOpt::OEFletcherReevesOpt OEOpt::OEHestenesStiefelOpt OEOpt::OEMaxStepLineMinimize OEOpt::OENewtonOpt OEOpt::OERibierePolakOpt OEPB::OEArea OEPB::OEBind OEPB::OEBindResults OEPB::OEET OEPB::OESimpleBindResults OEPB::OEZap OEPlatform::OEFile OEPlatform::oeisstream OEProton::OEChargeParameter OEProton::OEDesignUnitCharges OEProton::OEELF OEProton::OEELFOptions OEProton::OEFormalChargeOptions OEProton::OEMultistatepKaModel OEProton::OETautomerOptions OEShape::OEAnalyticColorFunc OEShape::OEAnalyticOptions OEShape::OEAnalyticShapeFunc OEShape::OEAsIsStarts OEShape::OEAtAtomStarts OEShape::OEBestOverlay OEShape::OEBestOverlayResults OEShape::OEBestOverlayScore OEShape::OECartesianStarts OEShape::OEColorFFParameter OEShape::OEColorForceField OEShape::OEColorOptions OEShape::OEColorOverlap OEShape::OEExactColorFunc OEShape::OEExactShapeFunc OEShape::OEFlexiOverlapOptions OEShape::OEFlexiOverlapResults OEShape::OEFlexiOverlay OEShape::OEFlexiOverlayOptions OEShape::OEGridColorFunc OEShape::OEGridShapeFunc OEShape::OEHermite OEShape::OEHermiteOptions OEShape::OEHermiteShapeFunc OEShape::OEInertialStarts OEShape::OEMultiRefOverlay OEShape::OEOverlap OEShape::OEOverlapFunc OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions OEShape::OEOverlapResults OEShape::OEOverlay OEShape::OEOverlayOptions OEShape::OEQuatStarts OEShape::OERandomStarts OEShape::OEROCS OEShape::OEROCSOptions OEShape::OEROCSResult OEShape::OEShapeGridOptions OEShape::OEShapeOptions OEShape::OEShapeQuery OEShape::OEShapeQueryPublic OEShape::OESubrocsStarts OESheff::OESheffield OESheff::OESheffieldOptions OESiteHopper::OESiteHopperDatabaseOptions OESiteHopper::OESiteHopperPatchOptions OESiteHopper::OESiteHopperResults OESiteHopper::OESiteHopperScore OESiteHopper::OESiteHopperSearchOptions OESpicoli::OESurface OESpruce::OEBioUnitExtractionOptions OESpruce::OECapBuilderOptions OESpruce::OEDesignUnitBuildOptions OESpruce::OEDesignUnitEnumerateSitesOptions OESpruce::OEDesignUnitMutationOptions OESpruce::OEDesignUnitPrepOptions OESpruce::OEDesignUnitSplitOptions OESpruce::OEHeterogenMetadata OESpruce::OELoopBuilderOptions OESpruce::OEMakeDesignUnitOptions OESpruce::OEPocket OESpruce::OEPocketOptions OESpruce::OEProtonateDesignUnitOptions OESpruce::OESecondaryStructureSuperposition OESpruce::OESequenceMetadata OESpruce::OESidechainBuilderOptions OESpruce::OESpruceFilter OESpruce::OESpruceFilterOptions OESpruce::OEStructuralSuperposition OESpruce::OEStructureMetadata OESpruce::OESuperpose OESpruce::OESuperposeOptions OESpruce::OESuperposeResults OESpruce::OESuperpositionOptions OESpruce::OEValidateDesignUnit OESystem::OEAnd OESystem::OEAnnotation OESystem::OEBase OESystem::OEBaseDataT OESystem::OEBinaryAnd OESystem::OEBinaryIOHandler OESystem::OEBinaryNot OESystem::OEBinaryOr OESystem::OEBitVector OESystem::OEBoolParameter OESystem::OEColorGradientBase OESystem::OEColorStop OESystem::OEConstParameter OESystem::OEContainer OESystem::OEDoubleParameter OESystem::OEErrorHandler OESystem::OEExponentColorGradient OESystem::OEExponentialColorGradient OESystem::OEFloatParameter OESystem::OEGaussian OESystem::OEGaussianContainer OESystem::OEGrid OESystem::OEInterface OESystem::OEIntParameter OESystem::OEIter OESystem::OELinearColorGradient OESystem::OELogarithmicColorGradient OESystem::OEMultiGrid OESystem::OEMultiParameter OESystem::OENot OESystem::OEOr OESystem::OEOwnedPtr OESystem::OEPredIter OESystem::OERole OESystem::OERoles OESystem::OEScalarGrid OESystem::OESkewGrid OESystem::OEStringParameter OESystem::OEUIntParameter OESystem::OEUnownedPtr OESz::OEBoundEntropyOptions OESz::OEEntropyResults OESz::OEFixedProteinLigandOptimizer OESz::OEFlexProteinLigandOptimizer OESz::OEFreeFormConf OESz::OEFreeFormConfAdvanced OESz::OEFreeFormConfOptions OESz::OEFreeFormConfResults OESz::OEFreeFormSolvOptions OESz::OEFreeFormSolvResults OESz::OELigandEntropyOptions OESz::OEProteinFlexOptions OESz::OEProteinLigandOptOptions OESz::OEProteinLigandOptResults OESz::OERestrictionEnergyResult OESz::OESingleConfResult OESz::OESzybkiEnsembleResults OESz::OESzybkiGeneralOptions OESz::OESzybkiOptions OESz::OESzybkiOptOptions OESz::OESzybkiProteinOptions OESz::OESzybkiResults OESz::OESzybkiSolventOptions OESz::OETorsionScanner OESz::OETorsionScanOptions OESz::OETorsionScanResult OESzmap::OESzmapEngine OESzmap::OESzmapEngineOptions OESzmap::OESzmapResults operator== OEBio::OEInteractionHintComponentTypeBase OEBio::OEInteractionHintTypeBase OEBio::OESplitMolComplexOptions OEChem::OE3DMolStyle OEChem::OEFuzzy OEChem::OEMolStyleColorer OEDepict::OEFont OEDepict::OEPen OEGrapheme::OEPlotMarker OEGraphSim::OEFingerPrint OEMedChem::OEMCSFragDatabaseOptions OEProton::OEChargeEngineBase OESystem::OEColor OESystem::OEIter OESystem::OERole operator>> OEPlatform::oeistream operator[] OESystem::OEBitVector OESystem::OEFixedGrid OESystem::OEFixedMultiGrid operator^= OESystem::OEBitVector operator|= OESystem::OEBitVector operator|| OEChem::OEFuzzy Optimize OEDocking::OEPoseOptimizer OESz::OEFixedProteinLigandOptimizer OESz::OEFlexProteinLigandOptimizer OESz::OEFreeFormConfAdvanced OptimizeRestraint OESz::OEFreeFormConfAdvanced Order OEChem::OEMolDatabase OrderAtoms OEChem::OEMolBase OrderBonds OEChem::OEAtomBase OEChem::OEMolBase OrderConfs OEChem::OEMCMolBase Orion back end Orion Platform Overlap OEEon::OEChargeFunc OEEon::OEEonPBFunc OEShape::OEFlexiOverlapFunc OEShape::OEOverlap OEShape::OEOverlapFuncBase overlapcolor.java Example Code overlapquery.java Example Code Overlay OEBioisostere::OEBroodOverlay OEBioisostere::OEBroodOverlayBase OEEon::OEEonOverlay OEShape::OEBestOverlay OEShape::OEFlexiOverlay OEShape::OEMultiRefOverlay OEShape::OEOverlay OEShape::OEROCS overlayallres.java Example Code overlaybestres.java Example Code overlaystruct.java Example Code

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package packages PAM250 Parent OESystem::OEInterface ParseNewRules OEMolProp::OEFilter ParseTitle OEChem::OETokenizerBase partial charge, [1] parts2mols.java Example Code pattern matching PDB data PDB Splitting Peek OESystem::OEBoundedBuffer OESystem::OEProtectedBuffer OESystem::OEUnboundedBuffer peekbyte OEChem::oemolistream OEPlatform::oeistream PeekMol OEChem::oemolthreadbase PlaceNewAtom OESzmap::OESzmapResults PlaceProbeMol OESzmap::OESzmapResults PlaceProbeSet OESzmap::OESzmapResults Pop OESystem::OEConsoleProgressTracer OESystem::OETracerBase PopActive OEChem::OEMCMolBase popcount PopGroup OEDepict::OEImageBase OEDepict::OEImageFileBase PoseEstimate OEDocking::OEPositProbability posemolecules.java Example Code pread OEPlatform::oeifstream OEPlatform::oeiofstream Predicate OESystem::OEPredIter predicate Predict OEMath::OEKernelPLS preliminary API PreOptimizeEnsemble OESz::OEFreeFormConfAdvanced Prep OEBioisostere::OEBroodFragPrep OEConfGen::OEMolBuilder OEShape::OEOverlapPrep PrepareEnsemble OESz::OEFreeFormConfAdvanced

PrepMol OEFF::OEFF14SBSmirnoff OEMolPotential::OEFFParams OEMolPotential::OEForceField PrevBit OESystem::OEBitVector Print OEPB::OEBindResults OEPB::OESimpleBindResults OESz::OESzybkiResults printatomnames.java Example Code PrintConfig OEMolProp::OEFilter PrintCsv OESz::OEFreeFormConfResults printinteractions.java Example Code PrintMemoryUsage OEFastROCS::OEShapeDatabase PrintTxt OESz::OEFreeFormConfResults ProcessMol OEMedChem::OEMCSFragDatabase project Project.sln proteinligandpb.java Example Code proteinmultipleoptions.java Example Code proteinprep.java Example Code proteinprep.txt Example Code Push OESystem::OEConcatIter OESystem::OEConsoleProgressTracer OESystem::OEIter OESystem::OEIterBase OESystem::OETracerBase PushActive OEChem::OEMCMolBase PushBack OEChem::OETrans PushFront OEChem::OETrans PushGroup OEDepict::OEImageBase OEDepict::OEImageFileBase Put OESystem::OEBoundedBuffer OESystem::OEProtectedBuffer OESystem::OEUnboundedBuffer put OEChem::oemolostream putbyte OEPlatform::oeostream PutMol OEChem::oemolthreadbase

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QMol OEChem::OEQMol

quietfilter.java Example Code

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randomizeatoms.java Example Code randomsample.java Example Code RankDesignUnits OEDocking::OEPosit RankReceptors OEDocking::OEPosit raster image reaction map index reaction molecule reaction role read OEChem::oemolistream OEPlatform::oeistream ReadConformers OEBioisostere::OEFragConfReader Ready OEShape::OEColorForceField receptor receptoroutercontourvolume.java Example Code receptors Refresh OEPlatform::OEFile OESystem::OEConsoleProgressTracer OESystem::OETracerBase Release OEPlatform::OECondition OEPlatform::OEMutex OEPlatform::OESpinlock OEPlatform::OETryMutex OESystem::OEOwnedPtr OESystem::OEUnownedPtr Remove OEChem::OEAtomBondSet RemoveAtom OEChem::OEAtomBondSet OEChem::OEConfBase RemoveAtoms OEChem::OEAtomBondSet RemoveBond OEChem::OEAtomBase OEChem::OEAtomBondSet OEChem::OEConfBase RemoveBonds OEChem::OEAtomBondSet RemoveDuplicates OESz::OEFreeFormConfAdvanced RemoveFromDB OEBio::OEResidueCategoryData RemoveMolFunc OEMolPotential::OEGenericFF OEMolPotential::OEGenericFF2 Render OEDepict::OEImage OEGrapheme::OE2DPropMap RenderGlyph OEGrapheme::OEAtomGlyphBase OEGrapheme::OEAtomGlyphCircle OEGrapheme::OEBondGlyphArrow OEGrapheme::OEBondGlyphBase OEGrapheme::OEBondGlyphCircle OEGrapheme::OEBondGlyphCross OEGrapheme::OEBondGlyphCurvedArrow OEGrapheme::OEBondGlyphScissors OEGrapheme::OEBondGlyphStitch OEGrapheme::OEBondGlyphZigZag

ReplaceReadFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase ReplaceWriteFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase rescore.java Example Code rescoreposes.java Example Code Reset OEProton::OETautomerMolFunction OEProton::OETyperMolFunction reset OEPlatform::oeisstream ResetFilters OEBio::OESplitMolComplexOptions ResetPerceived OEChem::OEMolBase ResetReadFailureCt OEChem::oemolistream ResetTorsionLibrary OEConfGen::OETorLib reshist.java Example Code Residue, [1] Resize OEMath::OEMatrix OEMath::OESquareMatrix rewind OEChem::oemolistream OEPlatform::oestream ring membership ring processing ring system identification ringdict2pdf.java Example Code ringdict2pdf.txt Example Code ringsubset.java Example Code rmsd.java Example Code ROC curve rocsmodeexample.java Example Code Rotamer rotatable bond, [1] rotorcount.java Example Code Run OEPlatform::OEThread running toolkit examples

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Save OEChem::OEMolDatabase SavePotentialGrid OESz::OESzybki Scan OESz::OETorsionScanner SCMol OEChem::OEGraphMol OEChem::OEMol OEChem::OEQMol ScoreAtom OEDocking::OEDock OEDocking::OEScore ScoreAtomComponent OEDocking::OEDock OEDocking::OEScore ScoreLigand OEDocking::OEDock OEDocking::OEPosit OEDocking::OEScore ScoreLigandComponent OEDocking::OEDock OEDocking::OEScore Screen OEBioisostere::OEDBBuilder script scripts SD data SDF sdf2csv.java Example Code sdfilter.java Example Code sdfmodprops.java Example Code sdfrename.java Example Code Search OEChem::OESubSearchDatabase OESiteHopper::OESiteHopperSearch OESiteHopper::OESiteHopperSearchBase searchfastfp.java Example Code searchfastfp.txt Example Code searchfp.java Example Code searchfp.txt Example Code Secondary Structure Seed OESystem::OERandom seek OEChem::oemolistream OEPlatform::oestream Select OEProton::OEELF SelectPart OEChem::OEPartPredT Sequence Alignment Set OEChem::OEIsMember OEChem::OEIsMemberPtr OEConstr::OEHarmonicPotential OEFF::OEComplexFF OEMedChem::OEMCSMolSimScore OEMolMMFF::OEMMFFOutOfPlane OEMolMMFF::OEMMFFStretchBend OEMolPotential::OEBendPotential OEMolPotential::OEFFPotential OEMolPotential::OEForceField OEMolPotential::OEInteractParams OEMolPotential::OEInterAdaptor OEMolPotential::OEInterNonBondPotBase OEMolPotential::OEMolFunc OEMolPotential::OENonBondPotBase OEMolPotential::OENumericMolFunc2 OEMolPotential::OEScaledMolFunc OEMolPotential::OEStretchPotential OEMolPotential::OESubsetAdaptor OEMolPotential::OETorAdaptor OEMolPotential::OETorQuatAdaptor OEMolPotential::OETorsionPotential OEPlatform::OEFile OESheff::OESheffield OESystem::OEColor set OEPlatform::oeisstream OEPlatform::oeistdstream OEPlatform::oeiwrapperstream OEPlatform::oeosstream OEPlatform::oeostdstream OEPlatform::oeowrapperstream Set_dc OEConstr::OEHarmonicPotential Set_kc OEConstr::OEHarmonicPotential SetA OEBio::OECrystalSymmetryParams OESheff::OESheffieldOptions OESystem::OEColor SetActive OEChem::OEMCMolBase SetAddCarbonSkeleton OEChem::OE2DRingDictionaryCreatorOptions SetAddCarbonSkeletonWithBondStereo OEChem::OE2DRingDictionaryCreatorOptions SetAddDepictionHydrogens OEDepict::OEAlignmentOptions OEDepict::OEPrepareDepictionOptions SetAddInteractionHints OESpruce::OEDesignUnitEnumerateSitesOptions SetAddMetadata OEBio::OEPlaceHydrogensOptions SetAddRGroup OEBio::OESplitMolComplexOptions SetAddStyle OESpruce::OEDesignUnitEnumerateSitesOptions SetAdjustHCount OEBio::OESplitMolComplexOptions SetAlignment OEDepict::OEFont SetAll OESystem::OEGrid SetAllAtomspKaData OEProton::OEMultistatepKaModel SetAllColor OEShape::OEColorOverlap SetAllowBuildDisulfideBridges OESpruce::OELoopBuilderOptions SetAllowedClashType OEDocking::OEPositOptions SetAllowTruncate OESpruce::OECapBuilderOptions SetAlpha OEBio::OECrystalSymmetryParams SetAlt OEBio::OEAltLocationFactory SetAltConfs OEBio::OEIridiumData SetAlteredTag OEChem::OEUniMolecularRxnOptions SetAlternateLocation OEBio::OEAtomMatchResidueID OEChem::OEResidue SetAlternateLocationHandling OESpruce::OEDesignUnitSplitOptions SetAltsMustBeCompatible OEBio::OEPlaceHydrogensOptions SetAminoAcidScale OEGrapheme::OEPeptideDisplayOptions SetAntiAliasing OEDepict::OEJavaImageBase SetApplyWarts OEProton::OETautomerOptions SetArg OEPlatform::OEThread SetAromatic OEChem::OEAtomBase OEChem::OEBondBase SetAromaticJCT OEBioisostere::OEIntrinsicPropOptions SetAromaticStyle OEDepict::OE2DMolDisplayOptions SetAsDensity OEBio::OEIridiumData SetAssignBondiRadii OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions SetAssignColor OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions SetAssignMapIdx OEChem::OELibraryGen SetAssignPartialChargesAndRadii OESpruce::OEDesignUnitPrepOptions SetAssumptions OEBio::OESplitMolComplexOptions SetAtom OEBio::OEReceptorProteinConstraint OEDocking::OEProteinConstraint SetAtomColor OEDepict::OE2DMolDisplayOptions SetAtomColorer OEChem::OE3DMolStyle SetAtomColorStyle OEDepict::OE2DMolDisplayOptions SetAtomDisplay OEGrapheme::OESurfaceArc SetAtomExpr OEConfGen::OEConfFixOptions SetAtomExternalHighlight OEDepict::OEHighlightByColor SetAtomExternalHighlightRatio OEDepict::OEHighlightByStick SetAtomicNum OEChem::OEAtomBase SetAtomicRadiiType OESz::OEFreeFormSolvOptions OESz::OESzybkiSolventOptions SetAtomLabelColorer OEChem::OE3DMolStyle SetAtomLabelDataTag OEChem::OE3DMolStyle SetAtomLabelFont OEDepict::OE2DMolDisplayOptions SetAtomLabelFontScale OEDepict::OE2DMolDisplayOptions SetAtomLabelMonochrome OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByLasso OEDepict::OEHighlightByStick OEDepict::OEHighlightOverlayByBallAndStick SetAtomLabelText OEChem::OE3DMolStyle SetAtomLabelType OEChem::OE3DMolStyle SetAtomPredicate OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions SetAtomPropertyFunctor OEDepict::OE2DMolDisplayOptions SetAtomPropLabelFont OEDepict::OE2DMolDisplayOptions SetAtomPropLabelFontScale OEDepict::OE2DMolDisplayOptions SetAtoms OESpicoli::OESurface SetAtomsElement OESpicoli::OESurface SetAtomStereoStyle OEDepict::OE2DMolDisplayOptions SetAtomStrength OEShape::OEShapeQuery SetAtomStyle OEChem::OE3DMolStyle SetAtomSVGMarkupFunctor OEDepict::OE2DMolDisplayOptions SetAtomVisibilityFunctor OEDepict::OE2DMolDisplayOptions SetAttachCutoff OEBioisostere::OEBroodScoreOptions SetAttachmentPoints OEMedChem::OEMatchedPairTransformExtractOptions SetAttachScale OEBioisostere::OEBroodGeneralOptions SetAuthor OESpruce::OEStructureMetadata SetAutoConstraints OEDocking::OEMakeReceptorOptions SetAxial OEChem::OEAtomBase SetB OEBio::OECrystalSymmetryParams OESheff::OESheffieldOptions OESystem::OEColor SetBackboneClashRejectThreshold OESpruce::OELoopBuilderOptions SetBackColor OEDepict::OEPen SetBackgroundColor OEDepict::OE2DMolDisplayOptions OEGrapheme::OE2DActiveSiteDisplayOptions SetBadClashOverlapDistance OEBio::OEPlaceHydrogensOptions SetBallRadiusScale OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightOverlayByBallAndStick SetBaseData OESystem::OEBase SetBaseFontSize OEDepict::OEImageTableOptions SetBaseWriteFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase SetBatchMaxRotors OEConfGen::OEThompsonOptions SetBestHits OEEon::OEEonHitlistOptions SetBestReceptorPoseOnly OEDocking::OEPositOptions SetBeta OEBio::OECrystalSymmetryParams SetBFactor OEChem::OEResidue SetBgn OEChem::OEBondBase SetBgnAngle OEGrapheme::OESurfaceArc SetBgnPen OEDepict::OE2DBondDisplay SetBigStep OESystem::OEDots SetBioUnitExtractionOptions OESpruce::OEMakeDesignUnitOptions SetBitOff OESystem::OEBitVector SetBitOn OESystem::OEBitVector SetBondColorStyle OEDepict::OE2DMolDisplayOptions SetBondExpr OEConfGen::OEConfFixOptions SetBondLineAtomLabelGapScale OEDepict::OE2DMolDisplayOptions SetBondLineGapScale OEDepict::OE2DMolDisplayOptions SetBondPredicate OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions SetBondPropertyFunctor OEDepict::OE2DMolDisplayOptions SetBondPropLabelFont OEDepict::OE2DMolDisplayOptions SetBondPropLabelFontScale OEDepict::OE2DMolDisplayOptions SetBondStereoStyle OEDepict::OE2DMolDisplayOptions SetBondSVGMarkupFunctor OEDepict::OE2DMolDisplayOptions SetBondWidthScaling OEDepict::OE2DMolDisplayOptions SetBoolData OESystem::OEBase SetBoundarySpacing OEPB::OEZap SetBoundingBoxPen OEDepict::OEHighlightLabel SetBoxExtension OEDocking::OEMakeReceptorOptions SetBoxMol OEDocking::OEMakeReceptorOptions SetBoxRange OEGrapheme::OEColorGradientDisplayOptions SetBoxRangePen OEGrapheme::OEColorGradientDisplayOptions SetBrief OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter SetBuildLoops OESpruce::OEDesignUnitBuildOptions SetBuildOptions OEBioisostere::OEBroodHitlistOptions OESpruce::OEDesignUnitPrepOptions SetBuildSidechains OESpruce::OEDesignUnitBuildOptions SetBuildTails OESpruce::OELoopBuilderOptions SetBuildType OEBioisostere::OEBroodBuildOptions SetBumpRadius OEBioisostere::OEBroodGeneralOptions SetBundleCofactors OEBio::OEMolComplexCategorizer SetBurialFactor OESpruce::OEPocketOptions SetButtonFont OEDepict::OELegendLayoutOptions SetButtonHeightScale OEDepict::OELegendLayoutOptions SetButtonPen OEDepict::OELegendLayoutOptions SetButtonWidthScale OEDepict::OELegendLayoutOptions SetBypassPredicate OEBio::OEPlaceHydrogensOptions SetC OEBio::OECrystalSymmetryParams OESheff::OESheffieldOptions SetCalculateFrozenTerms OESz::OESzybkiOptOptions SetCalculateGradients OESz::OESzybkiGeneralOptions SetCanon OEChem::OEParseSmilesOptions SetCanonOrder OEConfGen::OEMolBuilderOptions OEMolProp::OEFilter SetCapBuilderOptions OESpruce::OEDesignUnitBuildOptions SetCapCTermini OESpruce::OEDesignUnitBuildOptions SetCapNTermini OESpruce::OEDesignUnitBuildOptions SetCarbonHybridization OEProton::OETautomerOptions SetCarbonRadius OEShape::OEBestOverlay OEShape::OEOverlap OEShape::OEShapeOptions SetCategorizer OEBio::OESplitMolComplexOptions SetCategory OEBio::OEIridiumData SetCavitySolventParameter OESz::OESzybkiSolventOptions SetCellBorderPen OEDepict::OEImageTableOptions SetCellColor OEDepict::OEImageTableOptions SetCellFont OEDepict::OEImageTableOptions SetCellGap OEDepict::OEImageGrid OEDepict::OEReportOptions SetCenter OEDocking::OESphereBase OEGrapheme::OESurfaceArc OEMath::OESphere OESystem::OEGaussian OESystem::OEGaussianBase SetChainID OEBio::OEAtomMatchResidueID OEChem::OEResidue OESpruce::OESequenceMetadata SetCharge OEDepict::OE2DAtomDisplay SetChargeAliquot OEProton::OESpreadMetalCharges SetChargeEngine OESpruce::OEDesignUnitPrepOptions OESz::OESzybkiSolventOptions SetCharges OESheff::OESheffield SetChargeType OESz::OEFreeFormSolvOptions SetCheckBond OEBioisostere::OEBroodBuildOptions SetCheckGeometry OEBioisostere::OEBroodScoreOptions SetChiral OEChem::OEAtomBase OEChem::OEBondBase OEChem::OEInChIOptions SetClearBackground OEGrapheme::OEColorOverlapDisplayOptions OEGrapheme::OEShapeOverlapDisplayOptions OEGrapheme::OEShapeQueryDisplayOptions SetClearCoordinates OEChem::OELibraryGen OEChem::OEUniMolecularRxn OEChem::OEUniMolecularRxnOptions OEProton::OETautomerOptions SetClearCoords OEDepict::OEAlignmentOptions OEDepict::OEPrepareDepictionOptions OEGrapheme::OEAlignedDepictionFrom3DOptions SetClearMapping OEChem::OERxnAutomapperOptions SetClosed OEDepict::OE2DPath SetCoFactorChargeEngine OEProton::OEDesignUnitCharges SetCofactorCodes OESpruce::OEDesignUnitSplitOptions SetCollapseNonSiteAlts OESpruce::OEDesignUnitEnumerateSitesOptions SetCollectProteinByChain OEBio::OESplitMolComplexOptions SetColor OEDepict::OEFont OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByColor OEDepict::OEHighlightByLasso OEDepict::OEHighlightByStick OEGrapheme::OEColorForceFieldDisplay OESpicoli::OESurface OESystem::OEAnnotation OESystem::OEGaussian OESystem::OEGaussianBase SetColorAtomStyle OEGrapheme::OEShapeQueryDisplayOptions SetColorElement OESpicoli::OESurface SetColorForceField OEFastROCS::OEShapeDatabaseOptions OEModels::OEROCSQueryModelOptions OEShape::OEBestOverlay OEShape::OEColorOptions OEShape::OEColorOverlap OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions SetColorForceFieldType OEFastROCS::OEShapeDatabaseOptions SetColorFuncType OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions SetColorGridSpacing OEFastROCS::OEShapeDatabase SetColorOptimization OEFastROCS::OEShapeDatabaseOptions SetColorOptimize OEShape::OEBestOverlay SetColorOptions OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions SetColors OEDepict::OEHighlightOverlayBase SetColorScale OESiteHopper::OESiteHopperResults SetColorScoreScale OEFastROCS::OEShapeDatabaseOptions SetColorStopLabelFont OEGrapheme::OEColorGradientDisplayOptions SetColorStopLabelFontScale OEGrapheme::OEColorGradientDisplayOptions SetColorStopPrecision OEGrapheme::OEColorGradientDisplayOptions SetColorStopVisibility OEGrapheme::OEColorGradientDisplayOptions SetColorTanimoto OESiteHopper::OESiteHopperResults SetColumnWidths OEDepict::OEImageTableOptions SetCommandLine OESystem::OEHeader SetComment OESystem::OEHeader SetCommentEnergy OEConfGen::OETorDriveOptions SetComplexity OEBioisostere::OEExtrinsicPropOptions SetConfFixOptions OEConfGen::OEOmegaOptions SetConfGenRMS OESz::OEFreeFormSolvOptions SetConfsPerHit OEShape::OEROCSOptions SetConfTest OEChem::oemolistream SetConnectBufferDistance OESpruce::OELoopBuilderOptions SetConsiderAtomLabelBoundingBox OEDepict::OEHighlightByLasso SetContext OEMedChem::OEMatchedPairTransformExtractOptions OESzmap::OESzmapEngine SetContourStyle OEChem::OE3DMolStyle SetCoords OEChem::OEConfBase OEChem::OEMolBase OEDepict::OE2DAtomDisplay SetCoordsToInertialFrame OEGrapheme::OEDepictionFrom3DOptions SetCorrSolventOptions OESz::OEFreeFormConfOptions SetCropLength OESpruce::OELoopBuilderOptions SetCurvature OESpicoli::OESurface SetCurvatureElement OESpicoli::OESurface SetCustomConstraints OEBio::OEReceptor SetCutoff OEEon::OEEonHitlistOptions OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions OEMolPotential::OENonBondIntcsOptions SetCutoffGT OEFastROCS::OEShapeDatabaseOptions SetCutoffLT OEFastROCS::OEShapeDatabaseOptions SetCXSMILES OEChem::OEParseSmilesOptions SetData OESystem::OEBase OESystem::OEBaseDataT OESystem::OEBitVector SetDatabase OEShape::OEROCS SetDate OESystem::OEHeader SetDefault OEChem::OEPredicateParameter OESystem::OEMultiParameter OESystem::OETypedParameter SetDefaultBondPen OEDepict::OE2DMolDisplayOptions SetDefaultColor OEChem::OEMolStyleColorer SetDeleteClashingSolvent OESpruce::OECapBuilderOptions OESpruce::OESidechainBuilderOptions SetDeleteFloatingRes OESpruce::OESpruceFilterOptions SetDelta OESz::OETorsionScanOptions SetDepictOrientation OEDepict::OEPrepareDepictionOptions OEGrapheme::OEShapeQueryDisplayOptions SetDepth OEGrapheme::OEComplexSurfaceArcFxnBase SetDerivativeType OEShape::OEShapeGridOptions SetDescendingOrder OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions SetDesignUnit OESiteHopper::OESiteHopperScore SetDetails OEBio::OEInteractionHint SetDielectric OEEon::OEEonPBOptions OEFF::OEMMFFSheffieldOptions OEPB::OEET SetDielectricConst OEConfGen::OEMacrocycleBuilderOptions SetDielectricModel OEPB::OEZap SetDim OESystem::OEGrid OESystem::OEMultiGrid OESystem::OESkewGrid SetDimension OEChem::OEMolBase SetDimensions OEDepict::OE2DMolDisplayOptions OEGrapheme::OE2DActiveSiteDisplayOptions SetDirection OEMedChem::OEMatchedPairTransformExtractOptions SetDisplayPos OEDepict::OE2DBondDisplay SetDisplayType OEDepict::OE2DBondDisplay SetDist OESpruce::OESuperpositionOptions SetDistance OESpicoli::OESurface SetDistanceElement OESpicoli::OESurface SetDoubleData OESystem::OEBase SetDPI OEBio::OEIridiumData SetDuplicateDistance OEShape::OEOverlapPrepOptions SetDuplicateRemoval OESpruce::OEDesignUnitEnumerateSitesOptions SetEganEgg OEBioisostere::OEMolPropertyOptions SetElfLimit OEProton::OEELFOptions SetEnabled OEBio::OEReceptorConstraintFeature OEBio::OEReceptorProteinConstraint OEDocking::OEFeature OEDocking::OEProteinConstraint SetEnd OEChem::OEBondBase SetEndAngle OEGrapheme::OESurfaceArc SetEndPen OEDepict::OE2DBondDisplay SetEndResidueInsertCode OESpruce::OESequenceMetadata SetEndResidueNumber OESpruce::OESequenceMetadata SetEnergy OEChem::OEMolBase SetEnergyRange OEConfGen::OESliceEnsembleOptions SetEnergyWindow OEConfGen::OEFragOptions OEConfGen::OEMacrocycleOmegaOptions OEConfGen::OEOmegaOptions OEConfGen::OESliceEnsembleOptions SetEnhancedStereo OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions SetEntityID OEChem::OEResidue SetEnumAtoms OEConfGen::OEFlipperOptions SetEnumAtomSpecifiedStereo OEConfGen::OEFlipperOptions SetEnumBonds OEConfGen::OEFlipperOptions SetEnumBondSpecifiedStereo OEConfGen::OEFlipperOptions SetEnumBridgehead OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions SetEnumerateCofactorSites OESpruce::OEDesignUnitEnumerateSitesOptions SetEnumerateSitesOptions OESpruce::OEDesignUnitPrepOptions SetEnumEZ OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions SetEnumNitrogen OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions OEConfGen::OEMolBuilderOptions SetEnumRelativeAtomStereo OEConfGen::OEFlipperOptions SetEnumRing OEConfGen::OEMolBuilderOptions SetEnumRS OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions SetEnumSpecifiedStereo OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions SetEnvironment OESz::OELigandEntropyOptions SetError OEPB::OEZap SetErrorLevel OEMolProp::OEFilter SetExactVdWProteinLigand OESz::OESzybkiProteinOptions SetExcipientCodes OESpruce::OEDesignUnitSplitOptions SetExcipients OEBio::OEIridiumData SetExcludeSelf OEDocking::OEPositOptions SetExpectValidMol OEProton::OEChargeEngineBase SetExperimentDate OESpruce::OEStructureMetadata SetExperimentType OESpruce::OEStructureMetadata SetExplicitAtomLabelAngle OEDepict::OE2DMolDisplayOptions SetExplicitHydrogens OEChem::OELibraryGen SetExponent OEFF::OEMMFFSheffieldOptions OESystem::OEExponentColorGradient SetExpr OEChem::OEQBase SetExpType OEShape::OEAnalyticOptions SetExtChainID OEChem::OEResidue SetExtendMappedRegions OEChem::OERxnAutomapperOptions SetExtrinsicMaxOptions OEBioisostere::OEMolPropertyOptions SetExtrinsicMinOptions OEBioisostere::OEMolPropertyOptions SetFaceNormal OESpicoli::OESurface SetFaceNormals OESpicoli::OESurface SetFaceNormalsElement OESpicoli::OESurface SetFallbackChargeEngine OEProton::OEDesignUnitCharges SetFamily OEDepict::OEFont SetFastROCSMode OEFastROCS::OEShapeDatabaseOptions SetFeatureName OEBio::OEReceptorConstraintFeature OEDocking::OEFeature SetFill OEDepict::OEPen SetFilter OEChem::OESubSearchQuery SetFinalizationChargeEngine OEProton::OEDesignUnitCharges SetFitMol OEShape::OEColorOverlap OEShape::OEOverlap SetFixBackboneAtoms OESpruce::OESpruceFilterOptions SetFixBondOrder OESpruce::OESpruceFilterOptions SetFixBondsToMetals OESpruce::OESpruceFilterOptions SetFixDeleteH OEConfGen::OEConfFixOptions SetFixedCoords OEDepict::OEAlignmentOptions SetFixedHLayer OEChem::OEInChIOptions SetFixLigandState OESpruce::OESpruceFilterOptions SetFixMaxMatch OEConfGen::OEConfFixOptions SetFixMCS OEConfGen::OEConfFixOptions SetFixMol OEConfGen::OEConfFixOptions SetFixNames OESpruce::OESpruceFilterOptions SetFixPredicate OEConfGen::OEConfFixOptions SetFixRMS OEConfGen::OEConfFixOptions SetFixSmarts OEConfGen::OEConfFixOptions SetFixSubSearch OEConfGen::OEConfFixOptions SetFixUniqueMatch OEConfGen::OEConfFixOptions SetFixValence OEChem::OEUniMolecularRxnOptions SetFlagTableFailures OEMolProp::OEFilter SetFlavor OEChem::OEMolDatabaseSaveOptions OEChem::oemolistream OEChem::oemolithread OEChem::oemolostream OEChem::oemolothread OEChem::oemolstreambase SetFlexiOverlapOptions OEDocking::OEShapeFitOptions OEShape::OEFlexiOverlayOptions SetFlexiOverlayOptions OEDocking::OEPositOptions SetFlexRange OEDocking::OEPoseOptimizerOptions OESz::OEProteinFlexOptions SetFlipBiasScale OEBio::OEPlaceHydrogensOptions SetFlipPredicate OEBio::OEPlaceHydrogensOptions SetFloatData OESystem::OEBase SetFocusTarget OEPB::OEZap SetFont OEDepict::OEHighlightLabel SetFontScale OEDepict::OEHighlightLabel SetFooterHeight OEDepict::OEReportOptions SetForceCapping OESpruce::OECapBuilderOptions SetForceField OEConfGen::OEFragBuilderOptions OEConfGen::OETorDriveOptions OEConfGen::OETorDriver OEDocking::OEPoseOptimizerOptions OEShape::OEFlexiOverlapOptions OESz::OEBoundEntropyOptions OESz::OELigandEntropyOptions OESz::OEProteinLigandOptOptions OESz::OESzybkiGeneralOptions OESz::OETorsionScanOptions SetForceFieldType OEFF::OEMMFFSheffieldOptions OESz::OESzybkiGeneralOptions OESz::OETorsionScanOptions SetForeColor OEDepict::OEPen SetFormalCharge OEChem::OEAtomBase SetFormat OEChem::OEMolDatabaseSaveOptions OEChem::oemolistream OEChem::oemolithread OEChem::oemolostream OEChem::oemolothread OEChem::oemolstreambase SetFPTypeBase OEGraphSim::OEFingerPrint SetFragBuilderMode OEConfGen::OEMolBuilderOptions SetFragBuilderOptions OEConfGen::OEMolBuilderOptions SetFragGen OEConfGen::OEFragOptions SetFragKeep OEConfGen::OEFragOptions SetFragLimits OEMedChem::OEMCSFragDatabaseOptions SetFragmentationLimit OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions SetFragmentNumber OEBio::OEAtomMatchResidueID OEChem::OEResidue SetFrequency OEBioisostere::OEExtrinsicPropOptions SetFromCT OEConfGen::OEMolBuilderOptions SetFullConformationSearch OEDocking::OEPositOptions OEDocking::OEShapeFitOptions SetG OESystem::OEColor SetGamma OEBio::OECrystalSymmetryParams SetGeneralOptions OESz::OESzybkiOptions SetGenerateIdea OEBioisostere::OEBroodHitlistOptions SetGenerateTautomers OESpruce::OEProtonateDesignUnitOptions SetGradTolerance OESz::OEProteinLigandOptOptions OESz::OESzybkiOptOptions SetGridBuffer OEEon::OEEonPBOptions OEPB::OEET SetGridContourColorer OEChem::OE3DMolStyle SetGridSpacing OEEon::OEEonPBOptions OEPB::OEET OEPB::OEZap OEShape::OEOverlap OEShape::OEShapeGridOptions SetGridType OEChem::OE3DMolStyle SetGroupID OEBio::OEAltGroup SetGroupType OEChem::OEGroupBase Setgz OEChem::oemolistream OEChem::oemolostream SetHandlerImpl OESystem::OEErrorHandler SetHarmonic OEShape::OEFlexiOverlapOptions SetHarmonicConstraints OESz::OESzybki SetHasMTZ OEBio::OEIridiumData SetHCount OEDepict::OE2DAtomDisplay SetHeader OEDepict::OEImageTableOptions SetHeaderColor OEDepict::OEImageTableOptions SetHeaderFont OEDepict::OEImageTableOptions SetHeaderHeight OEDepict::OEReportOptions SetHeavyAtomCount OEBioisostere::OEIntrinsicPropOptions SetHeight OEDepict::OE2DMolDisplayOptions OEGrapheme::OE2DActiveSiteDisplayOptions SetHetAtom OEChem::OEResidue SetHetGroupNbrDist OESpruce::OEProtonateDesignUnitOptions SetHostFlex OEFF::OEComplexFF OEMolPotential::OEInterMolFunc1 SetHPosition OEDepict::OE2DAtomDisplay SetHyb OEChem::OEAtomBase SetHybridizationLevel OEProton::OETautomerOptions SetHydrogens OEChem::OEInChIOptions SetHydrogenStyle OEDepict::OE2DMolDisplayOptions SetHydrogenVisibility OEChem::OE3DMolStyle SetHyperlink OEDepict::OEFont SetID OESiteHopper::OESiteHopperScore OESpruce::OEHeterogenMetadata SetIdxFileName OEChem::OEMolDatabaseSaveOptions SetIEFFCluster OESz::OESzybkiGeneralOptions SetIEFFTerms OEFF::OEMMFFIEFFOptions SetIgnoreHydrogens OEChem::OEConfRMSDOptions SetIgnoreNitrogenStereo OEDocking::OEPositOptions SetIgnoreStereo OEConfGen::OEMolBuilderOptions SetIgnoreTerminalHeavy OEChem::OEConfRMSDOptions SetImpl OEChem::OELingoSim SetImplicitHCount OEChem::OEAtomBase SetIncludeInput OEConfGen::OEOmegaOptions SetIndexableFragmentRange OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions SetInFile OEChem::OERefInputAppOptions OEChem::OESimpleAppOptions SetInitialOrientation OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay SetInitialStep OEOpt::OESteepestDescentOpt SetInnerContour OEDepict::OEHighlightByCogwheel SetInnerContourLevel OEBio::OEReceptor SetInnerDielectric OEPB::OEET OEPB::OEZap SetInnerMask OEEon::OEEonPBOptions OEPB::OEET SetInRing OEChem::OEAtomBase OEChem::OEBondBase SetInsertCode OEBio::OEAtomMatchResidueID OEChem::OEResidue SetIntData OESystem::OEBase SetInteractionStyle OEChem::OE3DMolStyle SetInteractive OEGrapheme::OEPeptideDisplayOptions SetInterface OESystem::OEHeader SetIntermolecularVdWCutoff OESz::OESzybkiProteinOptions SetIntramolecularVdWCutoff OESz::OESzybkiGeneralOptions SetIntrinsicMaxOptions OEBioisostere::OEMolPropertyOptions SetIntrinsicMinOptions OEBioisostere::OEMolPropertyOptions SetIntType OEChem::OEAtomBase OEChem::OEBondBase SetIonicState OESz::OEFreeFormConfOptions OESz::OEFreeFormSolvOptions SetIridiumData OEBio::OEStructureQuality OESpruce::OEStructureMetadata SetIrrationalRFree OEBio::OEIridiumData SetIsList OESystem::OEParameter SetIsotope OEChem::OEAtomBase SetIsotopes OEMedChem::OEMatchedPairTransformExtractOptions SetIterations OEPB::OEZap SetIterCycleSize OEConfGen::OEMacrocycleOmegaOptions SetIterLimit OEOpt::OEOptimizer0 OEOpt::OEOptimizer1 OEOpt::OEOptimizer2 SetJoin OEPB::OEET SetKeepHessian OEOpt::OEBFGSOpt SetKeepTitle OEChem::OECreateSubSearchDatabaseOptions SetKekule OEProton::OETautomerOptions SetKeyless OESystem::OEParameter SetLabel OEDepict::OE2DAtomDisplay SetLabelFont OEDepict::OE2DAtomDisplay SetLabelStyle OEGrapheme::OEPeptideDisplayOptions SetLambdaX OEShape::OEHermiteOptions SetLambdaY OEShape::OEHermiteOptions SetLambdaZ OEShape::OEHermiteOptions SetLassoScale OEDepict::OEHighlightByLasso SetLegendBoxPen OEDepict::OELegendLayoutOptions SetLegendFont OEGrapheme::OE2DPropMap SetLegendFontScale OEGrapheme::OE2DPropMap SetLegendLocation OEGrapheme::OE2DPropMap SetLevel OEProton::OETautomerOptions OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase SetLigandCharge OESz::OEBoundEntropyOptions OESz::OELigandEntropyOptions OESz::OEProteinLigandOptOptions SetLigandChargeEngine OEProton::OEDesignUnitCharges SetLigandConstraints OESpruce::OESuperpositionOptions SetLigandDensity OEBio::OEIridiumData SetLigandFilter OEBio::OESplitMolComplexOptions SetLigandRMSDHeavy OESz::OESzybkiGeneralOptions SetLigands OEModels::OEROCSQueryModelBuilder SetLigandSubSearch OEBio::OEMolComplexCategorizer SetLimit OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabaseOptions OEProton::OEELFCharges SetLineCap OEDepict::OEPen SetLineJoin OEDepict::OEPen SetLineMinimize OEOpt::OEOptimizer1 SetLineStipple OEDepict::OEPen SetLineWidth OEDepict::OEPen SetLineWidthScale OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByColor OEDepict::OEHighlightByLasso SetLipidCodes OESpruce::OEDesignUnitSplitOptions SetLipinski OEBioisostere::OEExtrinsicPropOptions SetLipinskiAcc OEBioisostere::OEExtrinsicPropOptions SetLipinskiDon OEBioisostere::OEExtrinsicPropOptions SetList OEMolPotential::OEInteractParams SetLocationID OEBio::OEAltLocation SetLogP OEBioisostere::OEExtrinsicPropOptions SetLoopBuilderOptions OESpruce::OEDesignUnitBuildOptions SetLoopClashRejectThreshold OESpruce::OELoopBuilderOptions SetLoopDBFilename OESpruce::OELoopBuilderOptions SetMacrocycleBuilderOptions OEConfGen::OEMacrocycleOmegaOptions SetMacroCycOptions OEConfGen::OEFragBuilderOptions SetMakePackingResidues OESpruce::OEDesignUnitSplitOptions SetMapIdx OEChem::OEAtomBase SetMappingMethod OEChem::OERxnAutomapperOptions SetMargin OEDepict::OE2DMolDisplayOptions OEDepict::OEImageGrid OEDepict::OEImageTableOptions OEDepict::OELegendLayoutOptions SetMargins OEDepict::OE2DMolDisplayOptions OEDepict::OEImageGrid OEDepict::OEImageTableOptions OEDepict::OELegendLayoutOptions SetMarkedValuePen OEGrapheme::OEColorGradientDisplayOptions SetMarkedValuePrecision OEGrapheme::OEColorGradientDisplayOptions SetMarkedValues OEGrapheme::OEColorGradientDisplayOptions SetMartin OEBioisostere::OEExtrinsicPropOptions SetMaskCutoff OESzmap::OESzmapEngineOptions SetMass OEDepict::OE2DAtomDisplay SetMatchedPairData OEMedChem::OEMatchedPairTransformExtractOptions SetMatchedPairs OEMedChem::OEMatchedPairTransformExtractOptions SetMaxAcceptorAngle OEBio::OEPerceiveInteractionOptions SetMaxAllowedAtomPairClashes OEDepict::OEAlignmentOptions SetMaxAtomFilter OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMCSFragDatabaseOptions SetMaxAtoms OESpruce::OEBioUnitExtractionOptions SetMaxBindingSiteDist OEBio::OESplitMolComplexOptions SetMaxBondRotations OEDepict::OEAlignmentOptions OEGrapheme::OEAlignedDepictionFrom3DOptions OEGrapheme::OEDepictionFrom3DOptions SetMaxCationPiAngle OEBio::OEPerceiveInteractionOptions SetMaxCationPiDistance OEBio::OEPerceiveInteractionOptions SetMaxCenters OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions SetMaxChargeAidedHBondDistance OEBio::OEPerceiveInteractionOptions SetMaxChiral OEBioisostere::OEFragmentOptions SetMaxConfGen OESz::OEFreeFormSolvOptions SetMaxConfRange OEConfGen::OESliceEnsembleOptions SetMaxConfs OEConfGen::OEMacrocycleOmegaOptions OEConfGen::OEOmegaOptions OEConfGen::OESliceEnsembleOptions OEFastROCS::OEShapeDatabaseOptions SetMaxContactFraction OEBio::OEPerceiveInteractionOptions SetMaxCount OEProton::OEFormalChargeOptions SetMaxCovalentFraction OEBio::OEPerceiveInteractionOptions SetMaxDegree OEBioisostere::OEFragmentOptions SetMaxDonorAngle OEBio::OEPerceiveInteractionOptions SetMaxEnumConfs OEConfGen::OEMolBuilderOptions SetMaxHalogenAngle OEBio::OEPerceiveInteractionOptions SetMaxHalogenBondDistance OEBio::OEPerceiveInteractionOptions SetMaxHBondDistance OEBio::OEPerceiveInteractionOptions SetMaxHeavy OEBioisostere::OEFragmentOptions SetMaxHeavyAtom OEBio::OELigandInteractionHintComponent SetMaxHits OEBioisostere::OEBroodHitlistOptions OEEon::OEEonHitlistOptions OEShape::OEROCSOptions OESiteHopper::OESiteHopperSearchOptions SetMaxIter OEConfGen::OEMacrocycleOmegaOptions OESz::OEProteinLigandOptOptions OESz::OESzybkiOptOptions OESz::OETorsionScanOptions SetMaxLigAtoms OEBio::OEMolComplexCategorizer OESpruce::OEDesignUnitSplitOptions SetMaxLigResidues OEBio::OEMolComplexCategorizer OESpruce::OEDesignUnitSplitOptions SetMaxLocalStrain OEBioisostere::OEBroodBuildOptions OEDocking::OEShapeFitOptions SetMaxMatches OEChem::OECliqueSearch OEChem::OEConfRMSDOptions OEChem::OEMCSSearch OEChem::OESubSearch OEChem::OESubSearchQuery OEChem::OEUniMolecularRxnOptions SetMaxMetalBondDistance OEBio::OEPerceiveInteractionOptions SetMaxMoleculesPerModel OEModels::OEROCSQueryModelOptions SetMaxMolWt OEBioisostere::OEFragmentOptions SetMaxNbrDist OEProton::OESpreadMetalCharges SetMaxNonIdealAcceptorAngle OEBio::OEPerceiveInteractionOptions SetMaxNonIdealDonorAngle OEBio::OEPerceiveInteractionOptions SetMaxNonIdealHBondDistance OEBio::OEPerceiveInteractionOptions SetMaxNumMicrostates OEProton::OEMultistatepKaModelOptions SetMaxOptIterations OEFastROCS::OEShapeDatabase SetMaxOptSteps OEDocking::OEShapeFitOptions OEShape::OEFlexiOverlayOptions OEShape::OEOverlayOptions SetMaxOverlays OEFastROCS::OEShapeDatabaseOptions SetMaxParts OESpruce::OEBioUnitExtractionOptions SetMaxPatternMatches OEDepict::OEAlignmentOptions SetMaxPeptideResidues OEBio::OEMolComplexCategorizer SetMaxPiStackAngle OEBio::OEPerceiveInteractionOptions SetMaxPiStackDistance OEBio::OEPerceiveInteractionOptions SetMaxProteinAtoms OEBio::OEMolComplexCategorizer SetMaxRandomTranslation OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay OEShape::OERandomStarts SetMaxRecord OEMedChem::OECreateMMPIndexOptions SetMaxRotors OEConfGen::OETorDriveOptions SetMaxSaltBridgeDistance OEBio::OEPerceiveInteractionOptions SetMaxScfIter OEMolAM1::OEAM1Options SetMaxSearchTime OEConfGen::OETorDriveOptions OEProton::OETautomerOptions SetMaxStep OEOpt::OELineMinimize SetMaxSubstateCutoff OEBio::OEPlaceHydrogensOptions SetMaxSubstituentLimitSkip OEMedChem::OEMatchedPairTransformExtractOptions

SetMaxSurfaceArea OESpruce::OEPocketOptions SetMaxSurfaceWaterDist OEBio::OESplitMolComplexOptions SetMaxSystemAtoms OESpruce::OEDesignUnitSplitOptions SetMaxTautomericAtoms OEProton::OETautomerOptions SetMaxTautomersGenerated OEProton::OETautomerOptions SetMaxTautomersToReturn OEProton::OETautomerOptions SetMaxTerminalHeavy OEConfGen::OESliceEnsembleOptions SetMaxTrials OEConfGen::OEThompsonOptions SetMaxTrialsRange OEConfGen::OEThompsonOptions SetMaxTStackAngle OEBio::OEPerceiveInteractionOptions SetMaxTStackDistance OEBio::OEPerceiveInteractionOptions SetMaxUnpairedAngle OEBio::OEPerceiveInteractionOptions SetMaxUnpairedDistance OEBio::OEPerceiveInteractionOptions SetMaxValue OEGrapheme::OE2DPropMap SetMaxZoneSize OEProton::OETautomerOptions SetMCSCorrespondence OEMedChem::OEMatchedPairTransformExtractOptions SetMCSExhaustiveMode OEChem::OERxnAutomapperOptions SetMCSFunc OEChem::OECliqueSearch OEChem::OEMCSSearch OEConfGen::OEConfFixOptions SetMCSMinAtoms OEConfGen::OEConfFixOptions SetMCSType OEConfGen::OEConfFixOptions SetMergeColorAtoms OEModels::OEROCSQueryModelOptions SetMetalChargeEngine OEProton::OEDesignUnitCharges SetMethod OEPB::OEArea OEShape::OEBestOverlay OEShape::OEOverlap OESpruce::OESuperpose OESpruce::OESuperposeOptions SetMid OESystem::OEGrid OESystem::OEMultiGrid OESystem::OESkewGrid SetMinAtoms OEChem::OECliqueSearch OEChem::OEMCSSearch SetMinContactFraction OEBio::OEPerceiveInteractionOptions SetMinCovalentFraction OEBio::OEPerceiveInteractionOptions SetMinDegree OEBioisostere::OEFragmentOptions SetMinFontSize OEDepict::OEImageBase SetMinFreqHeavy OEBioisostere::OEDBScreenOptions SetMinFrequency OEBioisostere::OEDBScreenOptions SetMinHBondContactFraction OEBio::OEPerceiveInteractionOptions SetMinHeavy OEBioisostere::OEFragmentOptions SetMinimizeSidechains OESpruce::OESidechainBuilderOptions SetMinimizeSidechainsShell OESpruce::OESidechainBuilderOptions SetMinimizeType OEShape::OEBestOverlay SetMinLigAtoms OEBio::OEMolComplexCategorizer OESpruce::OEDesignUnitSplitOptions SetMinProbability OEDocking::OEPositOptions SetMinScore OESpruce::OEBioUnitExtractionOptions SetMinSurfaceArea OESpruce::OEPocketOptions SetMinValue OEGrapheme::OE2DPropMap SetMMFFTerms OEFF::OEMMFFIEFFOptions SetMMFFTypeCheck OEMolProp::OEFilter SetMMPLimit OEMedChem::OEMatchedPairTransformExtractOptions SetModelNumber OEChem::OEResidue SetMolBuilderOptions OEConfGen::OEOmegaOptions SetMolecule OEPB::OEZap OEShape::OEShapeQuery SetMoleculeTitle OEMedChem::OEMatchedPairTransform SetMolFunc OEMolPotential::OEMolAdaptor SetMolFunc2 OEMolPotential::OEMolAdaptor2 SetMolWt OEBioisostere::OEIntrinsicPropOptions SetMultiplier OEShape::OEColorOptions SetMutations OESpruce::OEDesignUnitMutationOptions SetName OEBio::OEAtomMatchResidueID OEBio::OEReceptorProteinConstraint OEChem::OEAtomBase OEChem::OEResidue OEDocking::OEProteinConstraint OEGrapheme::OEColorForceFieldDisplay OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter SetNCPU OESiteHopper::OESiteHopperSearchOptions SetNegativeColor OEGrapheme::OE2DPropMap SetNegativeImageType OEDocking::OEMakeReceptorOptions SetNeutralPH OEBioisostere::OEBroodBuildOptions SetNoFlipPredicate OEBio::OEPlaceHydrogensOptions SetNonBondCutoff OEDocking::OEPoseOptimizerOptions OEFF::OEComplexFF OEMolPotential::OEForceField OEMolPotential::OEInterNonBondPotBase OESz::OEProteinLigandOptOptions SetNonPolymerPseudoAtoms OEChem::OEInChIOptions SetNonRingOptions OEConfGen::OEFragBuilderOptions SetNormal OESpicoli::OESurface SetNormalizeAndRescore OESiteHopper::OESiteHopperSearchOptions SetNormals OESpicoli::OESurface SetNormalsElement OESpicoli::OESurface SetNPolyMax OEShape::OEHermiteOptions SetNucleicChargeEngine OEProton::OEDesignUnitCharges SetNumBestHits OEShape::OEROCSOptions SetNumDevices OEFastROCS::OEShapeDatabase SetNumericGradDelta OEMolAM1::OEAM1Options SetNumGrids OESystem::OEFixedMultiGrid SetNumInertialStarts OEFastROCS::OEShapeDatabaseOptions SetNumMatchedPairs OEMedChem::OECreateMMPIndexStatus SetNumModels OEModels::OEROCSQueryModelOptions SetNumMols OEMedChem::OECreateMMPIndexStatus SetNumOpenThreads OEFastROCS::OEShapeDatabase SetNumProcessors OEChem::OECreateSubSearchDatabaseOptions OEGraphSim::OECreateFastFPDatabaseOptions OEGraphSim::OEFPDatabaseOptions SetNumRandomStarts OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay OEShape::OERandomStarts SetNumStarts OESz::OETorsionScanOptions SetNumThreads OEMedChem::OECreateMMPIndexOptions SetNumTriangles OESpicoli::OESurface SetNumVertices OESpicoli::OESurface SetOccupancy OEChem::OEResidue SetOERelease OESystem::OEHeader SetOEVersion OESystem::OEHeader SetOmegaOptions OESz::OEFreeFormConfOptions SetOptimizationInclSurfaceAreaTerm OESpruce::OELoopBuilderOptions SetOptimizationMaxLoops OESpruce::OELoopBuilderOptions SetOptimizationShell OESpruce::OELoopBuilderOptions SetOptimizationStage1IterMultiplier OESpruce::OELoopBuilderOptions SetOptimizationStage2IterMultiplier OESpruce::OELoopBuilderOptions SetOptimizationTolerance OESpruce::OELoopBuilderOptions SetOptimizationType OESz::OEProteinLigandOptOptions SetOptimizationUseSolventModel OESpruce::OELoopBuilderOptions SetOptimize OEProton::OEAM1BCCCharges OEProton::OEAM1Charges SetOptimizeExpProtons OESpruce::OEProtonateDesignUnitOptions SetOptimizeOptions OESz::OEFreeFormConfOptions SetOptimizerType OESz::OESzybkiOptOptions SetOptions OEConfGen::OEFragBuilder OEConfGen::OEMacrocycleBuilder OEConfGen::OEMacrocycleOmega OEConfGen::OEMolBuilder OEConfGen::OEOmega OEMedChem::OEMatchedPairAnalyzerOptions OEMedChem::OEMatchedPairTransformExtractOptions OEMedChem::OEMCSFragDatabaseOptions OESpruce::OESuperpose SetOptOptions OESz::OESzybkiOptions SetOrder OEChem::OEBondBase SetOrderPriority OESystem::OEInterface OESystem::OEOptions OESystem::OEParameter SetOtherChargeEngine OEProton::OEDesignUnitCharges SetOuterContourLevel OEBio::OEReceptor setoutercontourvolume.java Example Code SetOuterDielectric OEPB::OEZap SetOuterMask OEEon::OEEonPBOptions OEPB::OEET SetOutFile OEChem::OERefInputAppOptions OEChem::OESimpleAppOptions SetOutputStream OESystem::OEErrorHandler SetOverlapColor OEGrapheme::OEShapeOverlapDisplayOptions SetOverlapDisplayStyle OEGrapheme::OEShapeOverlapDisplayOptions SetOverlapDiv OESz::OETorsionScanOptions SetOverlapFunc OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions SetOverlayOptions OEShape::OEROCSOptions SetPackedColor OESystem::OEColor SetPackingResidues OEBio::OEIridiumData SetPageHeight OEDepict::OEReportOptions SetPageMargin OEDepict::OEReportOptions SetPageMargins OEDepict::OEReportOptions SetPageOrientation OEDepict::OEReportOptions SetPageSize OEDepict::OEReportOptions SetPageWidth OEDepict::OEReportOptions SetParameterVisibility OESystem::OEOptions SetPartialCharge OEChem::OEAtomBase SetPartOccupancyLigand OEBio::OEIridiumData SetPartOccupancyProtein OEBio::OEIridiumData SetPatchOptions OESiteHopper::OESiteHopperDatabaseOptions SetPen OEDepict::OEHighlightByLasso SetPenaltyForceConstant OESz::OETorsionScanOptions SetPerceiveBondStereo OEDepict::OEPrepareDepictionOptions SetPerceived OEChem::OEMolBase SetPercent OEProton::OEELFOptions SetPercentage OEProton::OEELFCharges SetPerformPrep OEShape::OEROCSOptions SetPermissiveBCCs OEProton::OEAM1BCCCharges SetpH OEProton::OEMultistatepKaModelOptions SetPhi OEChem::OEEuler SetpKaNormalize OEMolProp::OEFilter SetPlaceHydrogensOptions OESpruce::OEProtonateDesignUnitOptions SetPlatform OESystem::OEHeader SetPoserCacheCount OEDocking::OEPositOptions SetPoseRelaxMode OEDocking::OEPositOptions SetPoseRelaxOptions OEDocking::OEPositOptions SetPosition OEDepict::OEHighlightByLasso SetPositiveColor OEGrapheme::OE2DPropMap SetPositMethods OEDocking::OEPositOptions SetPossibleCovalent OEBio::OEIridiumData SetPotential OESpicoli::OESurface SetPotentialElement OESpicoli::OESurface SetPotentialName OESpicoli::OESurface SetPrefactor OESystem::OEGaussian OESystem::OEGaussianBase SetPreferAuthorRecord OESpruce::OEBioUnitExtractionOptions SetPreOptimizeOptions OESz::OEFreeFormConfOptions SetPrepOptions OESpruce::OEMakeDesignUnitOptions SetPrimaryAlt OEBio::OEAltLocationFactory SetPriorTemperature OEConfGen::OEThompsonOptions SetProbe OESzmap::OESzmapEngineOptions SetProbeRadius OEPB::OEZap SetProcessCarbons OEProton::OEMultistatepKaModelOptions SetProcessorType OEMedChem::OEMatchedPairAnalyzerOptions SetProgram OESystem::OEHeader SetProgress OESystem::OEConsoleProgressTracer OESystem::OETracerBase SetPromoteUnknowns OEBio::OESplitMolComplexOptions SetProperty OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay SetPropertyFont OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay SetPropertyOffset OEDepict::OE2DAtomDisplay OEDepict::OE2DBondDisplay SetPropertyOptions OEBioisostere::OEBroodScoreOptions SetProtectiveGroupLabelFont OEDepict::OE2DMolDisplayOptions SetProtectiveGroupStyle OEDepict::OE2DMolDisplayOptions SetProtein OEPB::OEBind OESz::OEFixedProteinLigandOptimizer OESz::OESzybki SetProteinChargeEngine OEProton::OEDesignUnitCharges SetProteinColorer OEChem::OE3DMolStyle SetProteinDielectric OESz::OESzybkiProteinOptions SetProteinElectrostaticModel OESz::OESzybkiProteinOptions SetProteinFilter OEBio::OESplitMolComplexOptions SetProteinFlexibilityRange OESz::OESzybkiProteinOptions SetProteinFlexibilityType OESz::OESzybkiProteinOptions SetProteinNonStandardChargeEngine OEProton::OEDesignUnitCharges SetProteinOptions OESz::OESzybkiOptions SetProteinStyle OEChem::OE3DMolStyle SetProtonate OESpruce::OEDesignUnitPrepOptions SetProtonateOptions OESpruce::OEDesignUnitPrepOptions SetProxyGridCutoff OEShape::OEAnalyticOptions SetPsi OEChem::OEEuler SetQuerySurfaceArcFxn OEGrapheme::OEColorOverlapDisplayOptions OEGrapheme::OEShapeOverlapDisplayOptions SetQuiet OEChem::OEParseSmilesOptions SetR OESystem::OEColor SetRacemicStereo OEChem::OEInChIOptions SetRacemicType OEProton::OETautomerOptions SetRad OEDocking::OESphereBase OEMath::OESphere SetRadical OEDepict::OE2DAtomDisplay SetRadii OESheff::OESheffield SetRadiiApproximation OEShape::OEBestOverlay OEShape::OEOverlap OEShape::OEShapeOptions SetRadius OEChem::OEAtomBase OEGrapheme::OESurfaceArc SetRadiusMargin OEProton::OESpreadMetalCharges SetRadiusRatio OEGrapheme::OE2DPropMap SetRandomSeed OEConfGen::OEMacrocycleBuilderOptions OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay OEShape::OERandomStarts SetRangeIncrement OEConfGen::OESliceEnsembleOptions SetRangeOff OESystem::OEBitVector SetRangeOn OESystem::OEBitVector SetRank OESiteHopper::OESiteHopperResults SetRankPredicate OEShape::OEROCSOptions SetRankTautomers OEProton::OETautomerOptions SetReadFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase setreasonablechargestate.java Example Code SetReconnectedMetals OEChem::OEInChIOptions SetReentrant OESystem::OESkewGrid SetRefFile OEChem::OERefInputAppOptions SetRefGrid OEShape::OEBestOverlay OEShape::OEOverlap SetRefMol OEPB::OEET OEShape::OEBestOverlay OEShape::OEColorOverlap OEShape::OEOverlap SetRefTolerance OEConfGen::OEMacrocycleBuilderOptions SetRegionType OEMedChem::OEBemisMurckoOptions SetRelativeStereo OEChem::OEInChIOptions SetRemoveAttractiveVdWForces OESz::OESzybkiGeneralOptions SetRemoveCoulombTerms OESz::OESzybkiGeneralOptions SetRemoveDuplicate OEShape::OEOverlapPrepOptions SetRemoveUnmappedFragments OEChem::OELibraryGen SetRenderHint OESystem::OEAnnotation SetRenderInteractiveLegend OEGrapheme::OE2DActiveSiteDisplayOptions SetRepairRequestedHint OEProton::OEChargeEngineBase SetRequired OESystem::OEParameter SetResidueCategoryData OEBio::OEMolComplexCategorizer SetResidueCutoff OESiteHopper::OESiteHopperPatchOptions SetResidueID OESz::OEProteinFlexOptions SetResidueNumber OEBio::OEAtomMatchResidueID OEChem::OEResidue SetResidueSVGMarkupFunctor OEGrapheme::OE2DActiveSiteDisplayOptions SetResolution OEBio::OEIridiumData OEDocking::OEDockOptions OEGrapheme::OE2DPropMap SetRestrictToRefSite OESpruce::OEDesignUnitEnumerateSitesOptions SetResults OESz::OEEntropyResults SetRetainBondStereo OEChem::OEExtractRingTemplateOptions SetRetainExistingBuiltInTemplates OEChem::OE2DRingDictionaryCreatorOptions SetRetainExistingTemplates OEChem::OE2DRingDictionaryCreatorOptions OEChem::OEExtractRingTemplateOptions SetReturn OEPlatform::OEThread SetReturnSelectedConfs OEProton::OEELFCharges SetRevision OESpruce::OEStructureMetadata SetRevisionDate OESpruce::OEStructureMetadata SetRFree OEBio::OEIridiumData SetRGBA OESystem::OEColor SetRigidOverlay OEShape::OEFlexiOverlayOptions SetRigidOverlayOptions OEDocking::OEShapeFitOptions OEShape::OEFlexiOverlayOptions SetRingFragLimit OEMedChem::OEMCSFragDatabaseOptions SetRingOnly OEBioisostere::OEBroodScoreOptions SetRingOptions OEConfGen::OEFragBuilderOptions SetRMS OEConfGen::OEFragOptions SetRMSDCutoff OEDepict::OEAlignmentOptions SetRMSRange OEConfGen::OESliceEnsembleOptions SetRMSThreshold OEConfGen::OESliceEnsembleOptions SetRotamerCoverage OESpruce::OESidechainBuilderOptions SetRotamerLibrary OESpruce::OESidechainBuilderOptions SetRotateAroundBonds OEDepict::OEAlignmentOptions SetRotateTo2DReference OEGrapheme::OEDepictionFrom3DOptions SetRotationAngle OEDepict::OEFont SetRotorCount OEBioisostere::OEIntrinsicPropOptions SetRotorOffset OEConfGen::OETorDriveOptions SetRotorPredicate OEConfGen::OETorDriveOptions SetRowData OEMath::OEMatrix SetRowHeights OEDepict::OEImageTableOptions SetRunType OESz::OESzybkiOptions SetRxn OEChem::OEMolBase SetRxnRole OEChem::OEAtomBase SetSaltConcentration OEEon::OEEonPBOptions OEPB::OEET OEPB::OEZap OESz::OESzybkiSolventOptions SetSampleHydrogens OEConfGen::OEMolBuilderOptions SetSaveRange OEChem::OECliqueSearch SetSaveStereo OEProton::OETautomerOptions SetScale OEDepict::OE2DMolDisplayOptions OEGrapheme::OE2DActiveSiteDisplayOptions SetScaleFactor OESiteHopper::OESiteHopperPatchOptions SetSCFTolerance OEMolAM1::OEAM1Options SetScoreCutoff OESiteHopper::OESiteHopperSearchOptions SetScoreMethod OEDocking::OEDockOptions SetScoreType OEBioisostere::OEBroodGeneralOptions OEFastROCS::OEShapeDatabaseOptions OEShape::OEColorOptions OEShape::OEShapeOptions SetSDEnergy OEConfGen::OETorDriveOptions SetSDTag OEMolProp::OEFilter SetSecondaryStructure OEChem::OEResidue SetSemiMethod OEMolAM1::OEAM1Options SetSeparateResidues OEBio::OESplitMolComplexOptions SetSeqAlignExtendPenalty OESpruce::OELoopBuilderOptions SetSeqAlignGapPenalty OESpruce::OELoopBuilderOptions SetSeqAlignMethod OESpruce::OELoopBuilderOptions SetSequence OESpruce::OESequenceMetadata SetSequenceCutoff OESiteHopper::OESiteHopperSearchOptions SetSequenceID OEChem::OEResidue SetSequenceSimilarity OESiteHopper::OESiteHopperResults SetSerialNumber OEChem::OEResidue SetShapeCutoff OEBioisostere::OEBroodScoreOptions SetShapeFuncType OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions SetShapeGrid OEShape::OEShapeQuery SetShapeGridSpacing OEFastROCS::OEShapeDatabase SetShapeOptions OEShape::OEFlexiOverlapOptions OEShape::OEOverlayOptions SetShapeScoreScale OEFastROCS::OEShapeDatabaseOptions SetShapeTanimoto OESiteHopper::OESiteHopperResults SetSheffieldParameters OESz::OESzybki SetSidechainBuilderOptions OESpruce::OEDesignUnitBuildOptions SetSimFunc OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabase OEGraphSim::OEFPDatabaseOptions SetSingleSourceMol OEBioisostere::OEFragmentOptions SetSiteResidues OESpruce::OESuperpositionOptions SetSiteSize OESiteHopper::OESiteHopperPatchOptions OESpruce::OEDesignUnitEnumerateSitesOptions SetSize OEDepict::OEFont OESystem::OEBitVector SetSizeLimit OEProton::OEAM1BCCCharges OEProton::OEAM1Charges SetSkipRefinement OEConfGen::OEMacrocycleBuilderOptions SetSliceEnsembleOptions OEConfGen::OEMacrocycleOmegaOptions OEConfGen::OEOmegaOptions OEConfGen::OETorDriver SetSmallStep OESystem::OEDots SetSMARTS OEMedChem::OEMatchedPairTransformExtractOptions SetSmarts OEBioisostere::OEFragmentOptions SetSmartsFile OEBioisostere::OEFragmentOptions SetSmiles OESpruce::OEHeterogenMetadata SetSoluteDielectric OESz::OESzybkiGeneralOptions SetSoluteDielectricConstant OESheff::OESheffieldOptions SetSolvationType OESz::OETorsionScanOptions SetSolventChargeEngine OEProton::OEDesignUnitCharges SetSolventDielectric OESz::OESzybkiSolventOptions SetSolventDielectricConstant OESheff::OESheffieldOptions SetSolventModel OESz::OEProteinLigandOptOptions OESz::OESzybkiSolventOptions SetSolventOptions OESz::OEFreeFormConfOptions OESz::OESzybkiOptions SetSortByBitCounts OEChem::OECreateSubSearchDatabaseOptions SetSp3CFrac OEBioisostere::OEIntrinsicPropOptions SetSpaceGroup OEBio::OECrystalSymmetryParams OESystem::OESkewGrid SetSpacing OESystem::OEGrid OESystem::OEMultiGrid OESystem::OESkewGrid SetSplitCovalent OEBio::OESplitMolComplexOptions SetSplitCovalentCofactors OEBio::OESplitMolComplexOptions SetSplitOptions OESpruce::OEMakeDesignUnitOptions SetStackSize OEPlatform::OEThread SetStandardizeBondLen OEBio::OEPlaceHydrogensOptions SetStartFactor OEConfGen::OERingFragOptions SetStartingMaterial OEChem::OELibraryGen SetStartPoints OEShape::OECartesianStarts SetStartResidueInsertCode OESpruce::OESequenceMetadata SetStartResidueNumber OESpruce::OESequenceMetadata SetStarts OEShape::OEOverlayOptions OEShape::OEQuatStarts SetState OEBio::OEAltLocationFactory SetStereo OEChem::OEAtomBase OEChem::OEBondBase OEChem::OEInChIOptions SetStickWidthScale OEDepict::OEHighlightByBallAndStick OEDepict::OEHighlightByCogwheel OEDepict::OEHighlightByStick OEDepict::OEHighlightOverlayByBallAndStick SetStippleFactor OEDepict::OEPen SetStrict OEChem::OEParseSmilesOptions OESystem::OEErrorHandler OESystem::OEErrorHandlerImplBase SetStrictAtomTypes OEConfGen::OEMolBuilderOptions SetStrictMapping OEChem::OERxnAutomapperOptions SetStrictMode OESpruce::OESidechainBuilderOptions SetStrictProlineMatch OESpruce::OELoopBuilderOptions SetStrictProtonationMode OESpruce::OEDesignUnitPrepOptions SetStrictSmirks OEChem::OEUniMolecularRxnOptions SetStrictStereo OEConfGen::OEOmegaOptions SetString OEChem::oemolostream SetStringData OESystem::OEBase SetStringDefault OESystem::OEParameter SetStringValue OESystem::OEParameter SetStructureID OESpruce::OEStructureMetadata SetStubColumn OEDepict::OEImageTableOptions SetStubColumnColor OEDepict::OEImageTableOptions SetStubColumnFont OEDepict::OEImageTableOptions SetStyle OEDepict::OEFont SetSubChainID OEChem::OEResidue SetSubstituentLimit OEMedChem::OEMatchedPairTransformExtractOptions SetSubstituentSearch OEMedChem::OEBemisMurckoOptions SetSuperAtomLabelFont OEDepict::OE2DMolDisplayOptions SetSuperAtomStyle OEDepict::OE2DMolDisplayOptions OEGrapheme::OE2DActiveSiteDisplayOptions SetSuperpose OESpruce::OEBioUnitExtractionOptions OESpruce::OEMakeDesignUnitOptions SetSuperpositionMethod OESpruce::OEMakeDesignUnitOptions SetSuperpositionType OESpruce::OESuperpositionOptions SetSuppressHydrogens OEDepict::OEAlignmentOptions OEDepict::OEPrepareDepictionOptions OEGrapheme::OEAlignedDepictionFrom3DOptions OEGrapheme::OEDepictionFrom3DOptions SetSurfaceAlpha OEChem::OE3DMolStyle SetSurfaceArcFxn OEGrapheme::OEShapeQueryDisplayOptions SetSurfaceColorer OEChem::OE3DMolStyle SetSurfaceCutoff OESiteHopper::OESiteHopperPatchOptions SetSurfaceStyle OEChem::OE3DMolStyle SetSurfaceType OEChem::OE3DMolStyle SetSVGMagnifyResidueInHover OEGrapheme::OE2DActiveSiteDisplayOptions SetSymmetrize OEProton::OEAM1BCCCharges OEProton::OEAM1Charges SetSymmetryClass OEChem::OEAtomBase SetSymmetryThreshold OEShape::OEBestOverlay OEShape::OEInertialStarts SetSzybkiGeneralOptions OESz::OEFreeFormConfOptions SetTable OEMolProp::OEFilter SetTag OEChem::OESDDataPair SetTargetComponentID OESpruce::OEDesignUnitSplitOptions SetTargetMask OEDocking::OEMakeReceptorOptions SetTargetPred OEDocking::OEMakeReceptorOptions SetTask OESystem::OEConsoleProgressTracer OESystem::OETracerBase SetTautomers OEBioisostere::OEBroodBuildOptions SetTemperature OESz::OESzybkiGeneralOptions SetText OESystem::OEColor SetTheta OEChem::OEEuler SetThompsonOptions OEConfGen::OETorDriveOptions SetTimeLimit OEConfGen::OEFragOptions SetTimeout OEChem::OEInChIOptions SetTitle OEBio::OEDesignUnit OEBio::OEInteractionHintContainer OEChem::OEMolBase OEMolPotential::OEForceField OEShape::OEColorForceField OEShape::OEShapeQueryBase OESiteHopper::OESiteHopperScore OESpicoli::OESurface OESpruce::OEHeterogenMetadata OESystem::OEAnnotation OESystem::OEGridAbstractBase OESystem::OEGridBase OESystem::OESkewGrid SetTitleFont OEDepict::OE2DMolDisplayOptions SetTitleFontScale OEDepict::OE2DMolDisplayOptions SetTitleHeight OEDepict::OE2DMolDisplayOptions SetTitleLocation OEDepict::OE2DMolDisplayOptions SetTitleSeparator OEChem::OELibraryGen SetTolerance OEOpt::OEOptimizer1 OEOpt::OEOptimizer2 OESz::OETorsionScanOptions SetTorDriveOptions OEConfGen::OEOmegaOptions OEConfGen::OETorDriver SetTorLib OEConfGen::OETorDriveOptions OEDocking::OEPositOptions OEDocking::OEShapeFitOptions SetTorsion OEChem::OEConfBase SetTorsionConstraint OESz::OESzybki SetTorsionDrive OEConfGen::OEOmegaOptions SetTorsionLibrary OEConfGen::OETorLib SetTotal OEFastROCS::OEDBTracer OEFastROCS::OEDBTracerBase SetTPSA OEBioisostere::OEIntrinsicPropOptions SetTracer OEChem::oemolistream OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OECreateFastFPDatabaseOptions OEMedChem::OECreateMMPIndexOptions OESystem::oeprogressstream SetTransform OEMedChem::OEMatchedPairTransform OESiteHopper::OESiteHopperScore SetTransformThreshold OESpruce::OELoopBuilderOptions SetTrialsRangeIncrement OEConfGen::OEThompsonOptions SetTriangle OESpicoli::OESurface SetTriangles OESpicoli::OESurface SetTrianglesElement OESpicoli::OESurface SetTverskyCoeffs OEFastROCS::OEShapeDatabaseOptions OEGraphSim::OEFPDatabaseOptions SetType OEBio::OEReceptorProteinConstraint OEChem::OEAtomBase OEChem::OEBondBase OEDocking::OEProteinConstraint OESpruce::OEHeterogenMetadata OESystem::OEAnnotation OESystem::OEScalarGrid OESystem::OESkewGrid SetTypeCheck OEMolProp::OEFilter SetU11 OEChem::OEAnisoUij SetU12 OEChem::OEAnisoUij SetU13 OEChem::OEAnisoUij SetU22 OEChem::OEAnisoUij SetU23 OEChem::OEAnisoUij SetU33 OEChem::OEAnisoUij SetUndefinedStereo OEChem::OEInChIOptions SetUnindexedMols OEMedChem::OECreateMMPIndexStatus SetUnitCell OESystem::OESkewGrid SetUnsaturatedHeteroBonds OEMedChem::OEBemisMurckoOptions Setup OEBioisostere::OEBroodDBFilter OEDocking::OEBox OEDocking::OEBoxBase OEEon::OEChargeFunc OEMath::OEBox OEMolPotential::OEMolFunc OEShape::OEHermite OEShape::OEStarts SetupFlex OEShape::OEOverlapFuncBase SetupHost OEFF::OEComplexFF OEMolPotential::OEInterMolFunc1 SetupRef OEBioisostere::OEBroodOverlay OEBioisostere::OEFragOverlay OEDocking::OEPositProbability OEDocking::OEShapeFit OEEon::OEChargeFunc OEEon::OEEonPBOverlay OEShape::OEFlexiOverlapFunc OEShape::OEFlexiOverlay OEShape::OEMultiRefOverlay OEShape::OEOverlapFuncBase OEShape::OEOverlay OEShape::OEStarts OESpruce::OESuperpose SetupTarget OEDocking::OEAlignReceptorFunction SetUseBondOrder OEBioisostere::OEBroodScoreOptions SetUseConstraints OESpruce::OESuperposeOptions SetUseCoulomb OEMolPotential::OENonBondIntcsOptions SetUseCurrentCharges OESz::OESzybkiSolventOptions SetUseGPU OEConfGen::OETorDriveOptions SetUseHydrogens OEPB::OEArea OEShape::OEBestOverlay OEShape::OEOverlap OEShape::OEOverlapPrep OEShape::OEOverlapPrepOptions SetUseInput3D OESz::OEFreeFormSolvOptions SetUseInputEnsemble OESz::OEFreeFormConfOptions OESz::OEFreeFormSolvOptions SetUseInternalCoord OESz::OETorsionScanOptions SetUseMaxHits OEShape::OEROCSOptions SetUseMMFF94s OEFF::OEMMFFIEFFOptions SetUseOptimalLambdas OEShape::OEHermiteOptions SetUsePackingResidues OESpruce::OELoopBuilderOptions SetUseProperty OEBioisostere::OEBroodScoreOptions SetUseProxyGrid OEShape::OEAnalyticOptions SetUserDefinedAngles OESz::OETorsionScanOptions SetUserStarts OEFastROCS::OEShapeDatabaseOptions OEShape::OEBestOverlay SetUserStartsScaleFactor OESiteHopper::OESiteHopperPatchOptions SetUseSinglePointPB OESz::OETorsionScanOptions SetUseSolventCorr OESz::OEFreeFormConfOptions SetUseThompson OEConfGen::OETorDriveOptions SetUseVdW OEMolPotential::OENonBondIntcsOptions SetValenceCorrection OEChem::OELibraryGen SetValid OEMedChem::OECreateMMPIndexStatus SetValidateKekule OEChem::OELibraryGen OEChem::OEUniMolecularRxn OEChem::OEUniMolecularRxnOptions SetValidRMSD OESpruce::OESuperposeOptions SetValidSeqScore OESpruce::OESuperposeOptions SetValidTanimoto OESpruce::OESuperposeOptions SetValue OEChem::OEMolParameter OEChem::OEPredicateParameter OEChem::OESDDataPair OESystem::OEMultiParameter OESystem::OETypedParameter SetValues OESystem::OEFixedGrid OESystem::OEMultiGrid OESystem::OESkewGrid SetVeber OEBioisostere::OEMolPropertyOptions SetVerbose OEMedChem::OECreateMMPIndexOptions OEPB::OEZap OEProton::OEFormalChargeOptions OESz::OESzybkiGeneralOptions SetVersion OESystem::OEHeader SetVertex OESpicoli::OESurface SetVertexClique OESpicoli::OESurface SetVertexCliqueElement OESpicoli::OESurface SetVertices OESpicoli::OESurface SetVerticesElement OESpicoli::OESurface SetVisibility OESystem::OEParameter SetVisible OEDepict::OEAtomDisplayBase OEDepict::OEBondDisplayBase SetWarnNoLigand OEBio::OESplitMolComplexOptions SetWarts OEConfGen::OEFlipperClassicOptions OEConfGen::OEFlipperOptions OEConfGen::OEOmegaOptions OEProton::OEFormalChargeOptions SetWaterFilter OEBio::OESplitMolComplexOptions SetWaterProcessing OEBio::OEPlaceHydrogensOptions SetWeight OEBio::OEInteractionHint SetWidth OEDepict::OE2DMolDisplayOptions OEGrapheme::OE2DActiveSiteDisplayOptions OESystem::OEGaussian OESystem::OEGaussianBase SetWriteFxn OESystem::OEBinaryIOHandler OESystem::OEBinaryIOHandlerBase SetWriteIdx OEChem::OEMolDatabaseSaveOptions SetX OEDepict::OE2DPoint OESystem::OEGaussian OESystem::OEGaussianBase SetXDim OESystem::OEGrid OESystem::OEMultiGrid SetXMid OESystem::OEGrid OESystem::OEMultiGrid SetY OEDepict::OE2DPoint OESystem::OEGaussian OESystem::OEGaussianBase SetYDim OESystem::OEGrid OESystem::OEMultiGrid SetYMid OESystem::OEGrid OESystem::OEMultiGrid SetZ OESystem::OEGaussian OESystem::OEGaussianBase SetZap OEPB::OEBind SetZDim OESystem::OEGrid OESystem::OEMultiGrid SetZMid OESystem::OEGrid OESystem::OEMultiGrid SetZValue OEBio::OECrystalSymmetryParams shapedatabasechunker.java Example Code shapedatabaseprep.java Example Code ShapeDatabaseServer::GetBestOverlays ShapeDatabaseServer::GetName ShapeDatabaseServer::GetVersion ShapeDatabaseServer::IsLoaded ShapeDatabaseServer::OEThrowSetLevel ShapeDatabaseServer::QueryHistogram ShapeDatabaseServer::QueryResults ShapeDatabaseServer::QueryStatus ShapeDatabaseServer::SetName ShapeDatabaseServer::SubmitQuery shapedistancematrix.java Example Code shapeoverlap2pdf.java Example Code shapeoverlap2pdf.txt Example Code shapeprops.java Example Code shard Sidechain Rotamer Signal OEPlatform::OECondition Similarity OEChem::OELingoSim similarity measure Cosine Dice Euclidean Manhattan Tanimoto Tversky SimpleBind OEPB::OEBind simpleconformer.java Example Code simplefastrocssearch.java Example Code simplenewton.java Example Code simpleomega.java Example Code simpleoverlap.java Example Code simpleprepscript.java Example Code simpleprotein.java Example Code simplesmirnoff.java Example Code simplevacuum.java Example Code single atom index singleconformer.java Example Code singleconformermacrocycle.java Example Code SingleMatch OEChem::OESubSearch Size OEBio::OEResidueCategoryData OEPlatform::OEFile OESystem::OEBoundedBuffer OESystem::OEUnboundedBuffer size OEChem::oemolistream OEPlatform::oestream sizefilter.java Example Code skip OEChem::oemolistream OEPlatform::oeistream skipbyte OEChem::oemolistream OEPlatform::oeistream skipline OEChem::oemolistream OEPlatform::oeistream Slice OEConfGen::OEConfSlicer smallest ring membership smallest set of smallest rings SMARTS, [1], [2] SMARTS atom primitives SMARTS bond primitives SMARTS logical operations smartsalign.java Example Code smartsalign2d.java Example Code smartsalign2d.txt Example Code SMILES, [1], [2] SMIRKS Sort OESystem::OEIter SortedOverlay OEEon::OEEonOverlay OEShape::OEFlexiOverlay OEShape::OEOverlay SortedSearch OEGraphSim::OEFastFPDatabase Space Group SpatialCoordToElement OESystem::OEGridBase SpatialCoordToGridIdx OESystem::OEGridBase specificmolprop.java Example Code sphereexclusionclustering.java Example Code splitmolcomplex.java Example Code splitmolcomplex.txt Example Code splitmolcomplexfrags.java Example Code splitmolcomplexfrags.txt Example Code splitmolcomplexlowlevel.java Example Code splitmolcomplexlowlevel.txt Example Code SSSR, [1] stable API StandardizeAndFilter OESpruce::OESpruceFilter Start OEPlatform::OEThread OESystem::OECycleTimer OESystem::OEStopwatch OESystem::OEWallTimer Std OEGraphSim::OEFPHistogram stereo atom stereo bond stereoandtorsion.java Example Code str OEPlatform::oeosstream stream OEPlatform::oeistdstream OEPlatform::oeiwrapperstream OEPlatform::oeostdstream OEPlatform::oeowrapperstream stripsalts.java Example Code structural key substructure search Superpose OESpruce::OESuperpose SVG Swap Ambiguous SwapEnds OEChem::OEBondBase Sweep OEChem::OEAtomBase OEChem::OEAtomBondSet OEChem::OEBondBase OEChem::OEGroupBase OEChem::OEMolBase SweepConfs OEChem::OEMCMolBase Symmetry SystematicSolidBodyOptimize OEDocking::OEScore szmapbestorientations.java Example Code szmapenergies.java Example Code

T

Tanimoto OEPB::OEET similarity measure tar, [1] tell OEChem::oemolistream OEChem::oemolostream OEPlatform::oestream TimeSeed OESystem::OERandom ToFirst OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEPredIter ToggleBit OESystem::OEBitVector toggleinnercontour.java Example Code ToHexString OEBio::OEAltLocationState OESystem::OEBitVector ToIndex OEMedChem::OEMatchedPair ToLast OESystem::OEConcatIter OESystem::OEIter OESystem::OEIterBase OESystem::OEPredIter toolkit directory structure toolkit examples tophits.java Example Code tophitsconf.java Example Code tophitsquery.java Example Code ToRecord OEBioisostere::OEBroodDBPacket OEBioisostere::OEBroodScore OEEon::OEEonHit

Torsion torsiondrive.java Example Code ToSmiles OEMedChem::OEMatchedPair Total OESystem::OEDots OESystem::OEThreadedDots total hydrogen count TransferCharge OEProton::OEChargeEngineBase OEProton::OEDesignUnitCharges Transform OEBioisostere::OEBroodOverlayBase OEChem::OEConfBase OEChem::OETrans OEChem::OETransBase OEFastROCS::OEShapeDatabaseScore OEShape::OEBestOverlayScore OESpruce::OESecondaryStructureSuperposition OESpruce::OEStructuralSuperposition OESpruce::OESuperposeResults TransformValue OESystem::OEColorGradientBase OESystem::OEExponentColorGradient OESystem::OEExponentialColorGradient OESystem::OELinearColorGradient OESystem::OELogarithmicColorGradient Translate OEChem::OEAtomBondSet translate_example.java Example Code translate_example.txt Example Code Transpose OEMath::OEMatrix Try OEPlatform::OETryMutex Tversky similarity measure

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UnCompress OEChem::OEMolBase unimolrxn.java Example Code uniqinchi.java Example Code uniqmol.java Example Code Unit Cell UnsetProtein OESz::OESzybki Update OEFastROCS::OEDBTracer OEFastROCS::OEDBTracerBase OEFastROCS::OEFastROCSHistogram OESystem::OEDots OESystem::OEThreadedDots

UpdateColorCoords OEShape::OEFlexiOverlapFunc UpdateValues OESystem::OEOptions Usage OESystem::OEErrorHandler usercolor.java Example Code userinertialstartsexample.java Example Code, [1] UseSavedHessian OEOpt::OEBFGSOpt UseSZMAPWaterModel OEProton::OEDesignUnitCharges UsingExplicitLigandName OEBio::OEMolComplexCategorizer OEBio::OEMolComplexCategorizerBase

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valence models MDL valence model OpenEye charge valence model OpenEye hydrogen count valence model Validate OEMedChem::OEBemisMurckoOptions OEShape::OEFlexiOverlapOptions OESpruce::OEValidateDesignUnit

vector image Verbose OESystem::OEErrorHandler viewmdlsearch.java Example Code viewmdlsearch.txt Example Code Visual Studio, [1]

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Wait OEPlatform::OECondition Warning OESystem::OEErrorHandler what OEChem::OEMolDBException wibergbondorders.java Example Code Windows

WinZip, [1] Write OEBioisostere::OEDBWriter OEDepict::OEImageFileBase OEShape::OEColorForceField write OEChem::oemolostream OEPlatform::oeostream WriteMolecule OEChem::OEMolDatabase

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zapatoms1.java Example Code zapbind.java Example Code zapfocussing.java Example Code zapforces.java Example Code zapgrid1.java Example Code

zapgrid2.java Example Code zapgrid3.java Example Code zapsolv1.java Example Code zaptransfer.java Example Code zwitterion zwitterionic