rdkit package¶
Subpackages¶
- rdkit.Avalon package
- Submodules
- rdkit.Avalon.pyAvalonTools module
CheckMolecule()CheckMoleculeString()CloseCheckMolFiles()Generate2DCoords()GetAvalonCountFP()GetAvalonFP()GetAvalonFPAsWords()GetCanonSmiles()GetCheckMolLog()InitializeCheckMol()StruChkFlagStruChkFlag.alias_conversion_failedStruChkFlag.atom_check_failedStruChkFlag.atom_clashStruChkFlag.bad_moleculeStruChkFlag.dubious_stereo_removedStruChkFlag.either_warningStruChkFlag.fragments_foundStruChkFlag.namesStruChkFlag.rechargedStruChkFlag.size_check_failedStruChkFlag.stereo_errorStruChkFlag.stereo_forced_badStruChkFlag.stereo_transformedStruChkFlag.template_transformedStruChkFlag.transformedStruChkFlag.values
StruChkResult
- rdkit.Avalon.pyAvalonTools module
- Module contents
- Submodules
- rdkit.Chem package
- Subpackages
- rdkit.Chem.AtomPairs package
- rdkit.Chem.ChemUtils package
- rdkit.Chem.Draw package
- Submodules
- rdkit.Chem.Draw.IPythonConsole module
- rdkit.Chem.Draw.MolDrawing module
DrawingOptionsDrawingOptions.atomLabelDeuteriumTritiumDrawingOptions.atomLabelFontFaceDrawingOptions.atomLabelFontSizeDrawingOptions.atomLabelMinFontSizeDrawingOptions.atomNumberOffsetDrawingOptions.bgColorDrawingOptions.bondLineWidthDrawingOptions.colorBondsDrawingOptions.coordScaleDrawingOptions.dashDrawingOptions.dblBondLengthFracDrawingOptions.dblBondOffsetDrawingOptions.defaultColorDrawingOptions.dotsPerAngstromDrawingOptions.elemDictDrawingOptions.includeAtomNumbersDrawingOptions.noCarbonSymbolsDrawingOptions.radicalSymbolDrawingOptions.selectColorDrawingOptions.showUnknownDoubleBondsDrawingOptions.useFractionDrawingOptions.wedgeDashedBonds
FontMolDrawingcmp()
- rdkit.Chem.Draw.SimilarityMaps module
- rdkit.Chem.Draw.rdMolDraw2D module
ContourAndDrawGaussians()ContourAndDrawGrid()ContourParamsContourParams.contourWidthContourParams.coordScaleForQuantizationContourParams.dashNegativeContourParams.drawAsLinesContourParams.extraGridPaddingContourParams.fillGridContourParams.gridResolutionContourParams.isovalScaleForQuantizationContourParams.setColourMap()ContourParams.setContourColour()ContourParams.setScale
DrawMoleculeACS1996()IntStringMapMeanBondLength()MolDraw2DMolDraw2D.ClearDrawing()MolDraw2D.DrawArc()MolDraw2D.DrawArrow()MolDraw2D.DrawAttachmentLine()MolDraw2D.DrawEllipse()MolDraw2D.DrawLine()MolDraw2D.DrawMolecule()MolDraw2D.DrawMoleculeWithHighlights()MolDraw2D.DrawMolecules()MolDraw2D.DrawPolygon()MolDraw2D.DrawReaction()MolDraw2D.DrawRect()MolDraw2D.DrawString()MolDraw2D.DrawTriangle()MolDraw2D.DrawWavyLine()MolDraw2D.FillPolys()MolDraw2D.FlexiMode()MolDraw2D.FontSize()MolDraw2D.GetDrawCoords()MolDraw2D.GetMolSize()MolDraw2D.Height()MolDraw2D.LineWidth()MolDraw2D.Offset()MolDraw2D.SetColour()MolDraw2D.SetDrawOptions()MolDraw2D.SetFillPolys()MolDraw2D.SetFlexiMode()MolDraw2D.SetFontSize()MolDraw2D.SetLineWidth()MolDraw2D.SetOffset()MolDraw2D.SetScale()MolDraw2D.Width()MolDraw2D.drawOptions()
MolDraw2DCairoMolDraw2DSVGMolDrawOptionsMolDrawOptions.addAtomIndicesMolDrawOptions.addBondIndicesMolDrawOptions.addStereoAnnotationMolDrawOptions.additionalAtomLabelPaddingMolDrawOptions.annotationFontScaleMolDrawOptions.atomHighlightsAreCirclesMolDrawOptions.atomLabelDeuteriumTritiumMolDrawOptions.atomLabelsMolDrawOptions.atomRegionsMolDrawOptions.baseFontSizeMolDrawOptions.bondLineWidthMolDrawOptions.centreMoleculesBeforeDrawingMolDrawOptions.circleAtomsMolDrawOptions.clearBackgroundMolDrawOptions.comicModeMolDrawOptions.continuousHighlightMolDrawOptions.drawMolsSameScaleMolDrawOptions.dummiesAreAttachmentsMolDrawOptions.dummyIsotopeLabelsMolDrawOptions.explicitMethylMolDrawOptions.fillHighlightsMolDrawOptions.fixedBondLengthMolDrawOptions.fixedFontSizeMolDrawOptions.fixedScaleMolDrawOptions.flagCloseContactsDistMolDrawOptions.fontFileMolDrawOptions.getAnnotationColour()MolDrawOptions.getBackgroundColour()MolDrawOptions.getHighlightColour()MolDrawOptions.getLegendColour()MolDrawOptions.getQueryColour()MolDrawOptions.getSymbolColour()MolDrawOptions.getVariableAttachmentColour()MolDrawOptions.highlightBondWidthMultiplierMolDrawOptions.highlightRadiusMolDrawOptions.includeAtomTagsMolDrawOptions.includeChiralFlagLabelMolDrawOptions.includeMetadataMolDrawOptions.includeRadicalsMolDrawOptions.isotopeLabelsMolDrawOptions.legendFontSizeMolDrawOptions.legendFractionMolDrawOptions.maxFontSizeMolDrawOptions.minFontSizeMolDrawOptions.multiColourHighlightStyleMolDrawOptions.multipleBondOffsetMolDrawOptions.noAtomLabelsMolDrawOptions.paddingMolDrawOptions.prepareMolsBeforeDrawingMolDrawOptions.rotateMolDrawOptions.scaleBondWidthMolDrawOptions.scaleHighlightBondWidthMolDrawOptions.scalingFactorMolDrawOptions.setAnnotationColour()MolDrawOptions.setAtomPalette()MolDrawOptions.setBackgroundColour()MolDrawOptions.setHighlightColour()MolDrawOptions.setLegendColour()MolDrawOptions.setQueryColour()MolDrawOptions.setSymbolColour()MolDrawOptions.setVariableAttachmentColour()MolDrawOptions.simplifiedStereoGroupLabelMolDrawOptions.singleColourWedgeBondsMolDrawOptions.splitBondsMolDrawOptions.unspecifiedStereoIsUnknownMolDrawOptions.updateAtomPalette()MolDrawOptions.useAvalonAtomPalette()MolDrawOptions.useBWAtomPalette()MolDrawOptions.useCDKAtomPalette()MolDrawOptions.useComplexQueryAtomSymbolsMolDrawOptions.useDefaultAtomPalette()MolDrawOptions.useMolBlockWedgingMolDrawOptions.variableAtomRadiusMolDrawOptions.variableBondWidthMultiplier
MolToACS1996SVG()MolToSVG()MultiColourHighlightStylePrepareAndDrawMolecule()PrepareMolForDrawing()SetACS1996Mode()SetDarkMode()SetMonochromeMode()UpdateDrawerParamsFromJSON()UpdateMolDrawOptionsFromJSON()map_indexing_suite_IntStringMap_entry
- rdkit.Chem.Draw.rdMolDraw2DQt module
- rdkit.Chem.Draw.aggCanvas module
- rdkit.Chem.Draw.cairoCanvas module
- rdkit.Chem.Draw.canvasbase module
- rdkit.Chem.Draw.mplCanvas module
- rdkit.Chem.Draw.qtCanvas module
- Module contents
DebugDraw()DrawMorganBit()DrawMorganBits()DrawMorganEnv()DrawMorganEnvs()DrawRDKitBit()DrawRDKitBits()DrawRDKitEnv()DrawRDKitEnvs()FingerprintEnvMolToFile()MolToImage()MolsMatrixToGridImage()MolsToGridImage()MolsToImage()ReactionToImage()SetComicMode()ShowMol()calcAtomGaussians()shouldKekulize()
- Submodules
- rdkit.Chem.EState package
- Submodules
- rdkit.Chem.EState.AtomTypes module
- rdkit.Chem.EState.EState module
- rdkit.Chem.EState.EState_VSA module
EState_VSA1()EState_VSA10()EState_VSA11()EState_VSA2()EState_VSA3()EState_VSA4()EState_VSA5()EState_VSA6()EState_VSA7()EState_VSA8()EState_VSA9()EState_VSA_()VSA_EState1()VSA_EState10()VSA_EState2()VSA_EState3()VSA_EState4()VSA_EState5()VSA_EState6()VSA_EState7()VSA_EState8()VSA_EState9()VSA_EState_()
- rdkit.Chem.EState.Fingerprinter module
- Module contents
- Submodules
- rdkit.Chem.FeatMaps package
- Submodules
- rdkit.Chem.FeatMaps.FeatMapParser module
- rdkit.Chem.FeatMaps.FeatMapPoint module
- rdkit.Chem.FeatMaps.FeatMapUtils module
- rdkit.Chem.FeatMaps.FeatMaps module
- Module contents
- Submodules
- rdkit.Chem.Features package
- rdkit.Chem.Fingerprints package
- Submodules
- rdkit.Chem.Fingerprints.ClusterMols module
- rdkit.Chem.Fingerprints.DbFpSupplier module
- rdkit.Chem.Fingerprints.FingerprintMols module
- rdkit.Chem.Fingerprints.MolSimilarity module
- rdkit.Chem.Fingerprints.SimilarityScreener module
- Module contents
- Submodules
- rdkit.Chem.Fraggle package
- rdkit.Chem.MolDb package
- Submodules
- Module contents
- rdkit.Chem.MolKey package
- rdkit.Chem.Pharm2D package
- Submodules
- rdkit.Chem.Pharm2D.Generate module
- rdkit.Chem.Pharm2D.Gobbi_Pharm2D module
- rdkit.Chem.Pharm2D.Matcher module
- rdkit.Chem.Pharm2D.SigFactory module
SigFactorySigFactory.GetBins()SigFactory.GetBitDescription()SigFactory.GetBitDescriptionAsText()SigFactory.GetBitIdx()SigFactory.GetBitInfo()SigFactory.GetFeatFamilies()SigFactory.GetMolFeats()SigFactory.GetNumBins()SigFactory.GetSigSize()SigFactory.GetSignature()SigFactory.Init()SigFactory.SetBins()
- rdkit.Chem.Pharm2D.Utils module
- Module contents
- Submodules
- rdkit.Chem.Pharm3D package
- Submodules
- rdkit.Chem.Pharm3D.EmbedLib module
AddExcludedVolumes()Check2DBounds()CoarseScreenPharmacophore()CombiEnum()ComputeChiralVolume()ConstrainedEnum()DownsampleBoundsMatrix()EmbedMol()EmbedOne()EmbedPharmacophore()GetAllPharmacophoreMatches()GetAtomHeavyNeighbors()MatchFeatsToMol()MatchPharmacophore()MatchPharmacophoreToMol()OptimizeMol()ReplaceGroup()UpdatePharmacophoreBounds()isNaN()
- rdkit.Chem.Pharm3D.ExcludedVolume module
- rdkit.Chem.Pharm3D.Pharmacophore module
ExplicitPharmacophorePharmacophorePharmacophore.getFeature()Pharmacophore.getFeatures()Pharmacophore.getLowerBound()Pharmacophore.getLowerBound2D()Pharmacophore.getUpperBound()Pharmacophore.getUpperBound2D()Pharmacophore.setLowerBound()Pharmacophore.setLowerBound2D()Pharmacophore.setUpperBound()Pharmacophore.setUpperBound2D()
- rdkit.Chem.Pharm3D.EmbedLib module
- Module contents
- Submodules
- rdkit.Chem.Scaffolds package
- Submodules
- rdkit.Chem.Scaffolds.MurckoScaffold module
- rdkit.Chem.Scaffolds.rdScaffoldNetwork module
BRICSScaffoldParams()CreateScaffoldNetwork()EdgeTypeNetworkEdgeNetworkEdge_VECTScaffoldNetworkScaffoldNetworkParamsScaffoldNetworkParams.collectMolCountsScaffoldNetworkParams.flattenChiralityScaffoldNetworkParams.flattenIsotopesScaffoldNetworkParams.flattenKeepLargestScaffoldNetworkParams.includeGenericBondScaffoldsScaffoldNetworkParams.includeGenericScaffoldsScaffoldNetworkParams.includeScaffoldsWithAttachmentsScaffoldNetworkParams.includeScaffoldsWithoutAttachmentsScaffoldNetworkParams.keepOnlyFirstFragmentScaffoldNetworkParams.pruneBeforeFragmenting
UpdateScaffoldNetwork()
- Module contents
- Submodules
- rdkit.Chem.SimpleEnum package
- rdkit.Chem.Subshape package
- Submodules
- rdkit.Chem.Subshape.BuilderUtils module
AppendSkeletonPoints()AssignMolFeatsToPoints()CalculateDirectionsAtPoint()ClusterTerminalPts()ComputeGridIndices()ComputeShapeGridCentroid()ExpandTerminalPts()FindFarthestGridPoint()FindGridPointBetweenPoints()FindTerminalPtsFromConformer()FindTerminalPtsFromShape()GetMoreTerminalPoints()
- rdkit.Chem.Subshape.SubshapeAligner module
ClusterAlignments()GetShapeShapeDistance()SubshapeAlignerSubshapeAligner.GetSubshapeAlignments()SubshapeAligner.GetTriangleMatches()SubshapeAligner.PruneMatchesUsingDirection()SubshapeAligner.PruneMatchesUsingFeatures()SubshapeAligner.PruneMatchesUsingShape()SubshapeAligner.coarseGridToleranceMultSubshapeAligner.dirThreshSubshapeAligner.distMetricSubshapeAligner.edgeTolSubshapeAligner.medGridToleranceMultSubshapeAligner.numFeatThreshSubshapeAligner.shapeDistTolSubshapeAligner.triangleRMSTol
SubshapeAlignmentSubshapeDistanceMetricTransformMol()
- rdkit.Chem.Subshape.SubshapeBuilder module
SubshapeBuilderSubshapeBuilder.CombineSubshapes()SubshapeBuilder.GenerateSubshapeShape()SubshapeBuilder.GenerateSubshapeSkeleton()SubshapeBuilder.SampleSubshape()SubshapeBuilder.featFactorySubshapeBuilder.fractionSubshapeBuilder.gridDimsSubshapeBuilder.gridSpacingSubshapeBuilder.nbrCountSubshapeBuilder.stepSizeSubshapeBuilder.terminalPtRadScaleSubshapeBuilder.winRad
SubshapeCombineOperations
- rdkit.Chem.Subshape.SubshapeObjects module
- rdkit.Chem.Subshape.BuilderUtils module
- Module contents
- Submodules
- rdkit.Chem.Suppliers package
- rdkit.Chem.fmcs package
- Submodules
- rdkit.Chem.fmcs.fmcs module
AtomAtomSmartsNoAromaticityBondCachingTargetsMatcherCangenNodeDefaultDirectedEdgeEnumerationMoleculeFragmentedTypedMoleculeMATCH()MCSResultOutgoingEdgeSingleBestAtomsSingleBestAtomsCompleteRingsOnlySingleBestBondsSingleBestBondsCompleteRingsOnlySubgraphTimerTypedFragmentTypedMoleculeUniquerVerboseCachingTargetsMatcherVerboseHeapOpsall_subgraph_extensions()assign_isotopes_from_class_tag()atom_typer_any()atom_typer_elements()atom_typer_isotopes()bond_typer_any()bond_typer_bondtypes()canon()check_completeRingsOnly()compute_mcs()convert_input_to_typed_molecules()default_atom_typer()default_bond_typer()enumerate_subgraphs()find_duplicates()find_extension_size()find_extensions()find_upper_fragment_size_limits()fmcs()fragmented_mol_to_enumeration_mols()gen_primes()generate_smarts()get_canonical_bondtype_counts()get_canonical_bondtypes()get_closure_label()get_counts()get_initial_cangen_nodes()get_isotopes()get_selected_atom_classes()get_specified_types()get_typed_fragment()get_typed_molecule()intersect_counts()main()make_arbitrary_smarts()make_canonical_smarts()make_complete_sdf()make_fragment_sdf()make_fragment_smiles()make_structure_format()nonempty_powerset()parse_num_atoms()parse_select()parse_threshold()parse_timeout()powerset()prune_maximize_atoms()prune_maximize_bonds()remove_unknown_bondtypes()rerank()restore_isotopes()save_atom_classes()save_isotopes()set_isotopes()starting_fromsubgraph_to_fragment()tiebreaker()
- rdkit.Chem.fmcs.fmcs module
- Module contents
- Submodules
- Submodules
- rdkit.Chem.AllChem module
- rdkit.Chem.BRICS module
- rdkit.Chem.BuildFragmentCatalog module
BuildCatalog()CalcGains()CalcGainsFromFps()OutputGainsData()ParseArgs()ProcessGainsData()RunDetailsRunDetails.actColRunDetails.biasListRunDetails.catalogNameRunDetails.dbNameRunDetails.delimRunDetails.detailsNameRunDetails.doBuildRunDetails.doDetailsRunDetails.doGainsRunDetails.doScoreRunDetails.doSigsRunDetails.fpNameRunDetails.gainsNameRunDetails.hasTitleRunDetails.inFileNameRunDetails.maxPathRunDetails.minPathRunDetails.nActsRunDetails.nBitsRunDetails.nameColRunDetails.numMolsRunDetails.onBitsNameRunDetails.scoresNameRunDetails.smiColRunDetails.tableNameRunDetails.topN
ScoreFromLists()ScoreMolecules()ShowDetails()SupplierFromDetails()Usage()message()
- rdkit.Chem.ChemicalFeatures module
- rdkit.Chem.ChemicalForceFields module
- rdkit.Chem.Crippen module
- rdkit.Chem.Descriptors module
- rdkit.Chem.Descriptors3D module
- rdkit.Chem.EnumerateHeterocycles module
- rdkit.Chem.EnumerateStereoisomers module
- rdkit.Chem.FastSDMolSupplier module
- rdkit.Chem.FeatFinderCLI module
- rdkit.Chem.FilterCatalog module
- rdkit.Chem.FragmentCatalog module
- rdkit.Chem.FragmentMatcher module
- rdkit.Chem.Fragments module
fr_Al_COO()fr_Al_OH()fr_Al_OH_noTert()fr_ArN()fr_Ar_COO()fr_Ar_N()fr_Ar_NH()fr_Ar_OH()fr_COO()fr_COO2()fr_C_O()fr_C_O_noCOO()fr_C_S()fr_HOCCN()fr_Imine()fr_NH0()fr_NH1()fr_NH2()fr_N_O()fr_Ndealkylation1()fr_Ndealkylation2()fr_Nhpyrrole()fr_SH()fr_aldehyde()fr_alkyl_carbamate()fr_alkyl_halide()fr_allylic_oxid()fr_amide()fr_amidine()fr_aniline()fr_aryl_methyl()fr_azide()fr_azo()fr_barbitur()fr_benzene()fr_benzodiazepine()fr_bicyclic()fr_diazo()fr_dihydropyridine()fr_epoxide()fr_ester()fr_ether()fr_furan()fr_guanido()fr_halogen()fr_hdrzine()fr_hdrzone()fr_imidazole()fr_imide()fr_isocyan()fr_isothiocyan()fr_ketone()fr_ketone_Topliss()fr_lactam()fr_lactone()fr_methoxy()fr_morpholine()fr_nitrile()fr_nitro()fr_nitro_arom()fr_nitro_arom_nonortho()fr_nitroso()fr_oxazole()fr_oxime()fr_para_hydroxylation()fr_phenol()fr_phenol_noOrthoHbond()fr_phos_acid()fr_phos_ester()fr_piperdine()fr_piperzine()fr_priamide()fr_prisulfonamd()fr_pyridine()fr_quatN()fr_sulfide()fr_sulfonamd()fr_sulfone()fr_term_acetylene()fr_tetrazole()fr_thiazole()fr_thiocyan()fr_thiophene()fr_unbrch_alkane()fr_urea()
- rdkit.Chem.FunctionalGroups module
- rdkit.Chem.GraphDescriptors module
- rdkit.Chem.Graphs module
- rdkit.Chem.Lipinski module
FractionCSP3()HeavyAtomCount()NHOHCount()NOCount()NumAliphaticCarbocycles()NumAliphaticHeterocycles()NumAliphaticRings()NumAromaticCarbocycles()NumAromaticHeterocycles()NumAromaticRings()NumHAcceptors()NumHDonors()NumHeteroatoms()NumRotatableBonds()NumSaturatedCarbocycles()NumSaturatedHeterocycles()NumSaturatedRings()RingCount()
- rdkit.Chem.MACCSkeys module
- rdkit.Chem.MCS module
- rdkit.Chem.MolCatalog module
- rdkit.Chem.MolStandardize module
- Submodules
- rdkit.Chem.MolStandardize.rdMolStandardize module
AllowedAtomsValidationCHARGE_CORRECTIONS()CanonicalTautomer()ChargeCorrectionChargeParent()ChargeParentInPlace()Cleanup()CleanupInPlace()CleanupParametersCleanupParameters.acidbaseFileCleanupParameters.doCanonicalCleanupParameters.fragmentFileCleanupParameters.largestFragmentChooserCountHeavyAtomsOnlyCleanupParameters.largestFragmentChooserUseAtomCountCleanupParameters.maxRestartsCleanupParameters.maxTautomersCleanupParameters.maxTransformsCleanupParameters.normalizationsFileCleanupParameters.preferOrganicCleanupParameters.tautomerReassignStereoCleanupParameters.tautomerRemoveBondStereoCleanupParameters.tautomerRemoveIsotopicHsCleanupParameters.tautomerRemoveSp3StereoCleanupParameters.tautomerTransformsFile
DisallowedAtomsValidationDisallowedRadicalValidationDisconnectOrganometallics()DisconnectOrganometallicsInPlace()FeaturesValidationFragmentParent()FragmentParentInPlace()FragmentRemoverFragmentRemoverFromData()FragmentValidationGetV1TautomerEnumerator()Is2DValidationIsotopeParent()IsotopeParentInPlace()IsotopeValidationLargestFragmentChooserLayout2DValidationMetalDisconnectorMetalDisconnectorOptionsMolVSValidationNeutralValidationNoAtomValidationNormalize()NormalizeInPlace()NormalizerNormalizerFromData()NormalizerFromParams()PipelinePipelineLogPipelineLogEntryPipelineOptionsPipelineOptions.allowAromaticBondTypePipelineOptions.allowAtomBondClashExemptionPipelineOptions.allowDativeBondTypePipelineOptions.allowEmptyMoleculesPipelineOptions.allowEnhancedStereoPipelineOptions.allowLongBondsInRingsPipelineOptions.atomClashLimitPipelineOptions.bondLengthLimitPipelineOptions.is2DZeroThresholdPipelineOptions.metalNofPipelineOptions.metalNonPipelineOptions.minMedianBondLengthPipelineOptions.normalizerDataPipelineOptions.normalizerMaxRestartsPipelineOptions.outputV2000PipelineOptions.reportAllFailuresPipelineOptions.scaledMedianBondLengthPipelineOptions.strictParsing
PipelineResultPipelineStagePipelineStatusPipelineStatus.BASIC_VALIDATION_ERRORPipelineStatus.CHARGE_STANDARDIZATION_ERRORPipelineStatus.FEATURES_VALIDATION_ERRORPipelineStatus.FRAGMENTS_REMOVEDPipelineStatus.FRAGMENT_STANDARDIZATION_ERRORPipelineStatus.INPUT_ERRORPipelineStatus.IS2D_VALIDATION_ERRORPipelineStatus.LAYOUT2D_VALIDATION_ERRORPipelineStatus.METALS_DISCONNECTEDPipelineStatus.METAL_STANDARDIZATION_ERRORPipelineStatus.NORMALIZATION_APPLIEDPipelineStatus.NORMALIZER_STANDARDIZATION_ERRORPipelineStatus.NO_EVENTPipelineStatus.OUTPUT_ERRORPipelineStatus.PIPELINE_ERRORPipelineStatus.PREPARE_FOR_STANDARDIZATION_ERRORPipelineStatus.PREPARE_FOR_VALIDATION_ERRORPipelineStatus.PROTONATION_CHANGEDPipelineStatus.STANDARDIZATION_ERRORPipelineStatus.STEREO_VALIDATION_ERRORPipelineStatus.STRUCTURE_MODIFICATIONPipelineStatus.VALIDATION_ERRORPipelineStatus.namesPipelineStatus.values
RDKitValidationReionize()ReionizeInPlace()ReionizerReionizerFromData()RemoveFragments()RemoveFragmentsInPlace()SmilesTautomerMapStandardizeSmiles()StereoParent()StereoParentInPlace()StereoValidationSuperParent()SuperParentInPlace()TautomerTautomerEnumeratorTautomerEnumerator.Canonicalize()TautomerEnumerator.Enumerate()TautomerEnumerator.GetCallback()TautomerEnumerator.GetMaxTautomers()TautomerEnumerator.GetMaxTransforms()TautomerEnumerator.GetReassignStereo()TautomerEnumerator.GetRemoveBondStereo()TautomerEnumerator.GetRemoveSp3Stereo()TautomerEnumerator.PickCanonical()TautomerEnumerator.ScoreTautomer()TautomerEnumerator.SetCallback()TautomerEnumerator.SetMaxTautomers()TautomerEnumerator.SetMaxTransforms()TautomerEnumerator.SetReassignStereo()TautomerEnumerator.SetRemoveBondStereo()TautomerEnumerator.SetRemoveSp3Stereo()TautomerEnumerator.tautomerScoreVersion
TautomerEnumeratorCallbackTautomerEnumeratorResultTautomerEnumeratorStatusTautomerParent()TautomerParentInPlace()UnchargerUpdateParamsFromJSON()ValidateSmiles()ValidationMethodmap_indexing_suite_SmilesTautomerMap_entry
- rdkit.Chem.MolStandardize.rdMolStandardize module
- Submodules
- rdkit.Chem.MolSurf module
LabuteASA()PEOE_VSA1()PEOE_VSA10()PEOE_VSA11()PEOE_VSA12()PEOE_VSA13()PEOE_VSA14()PEOE_VSA2()PEOE_VSA3()PEOE_VSA4()PEOE_VSA5()PEOE_VSA6()PEOE_VSA7()PEOE_VSA8()PEOE_VSA9()SMR_VSA1()SMR_VSA10()SMR_VSA2()SMR_VSA3()SMR_VSA4()SMR_VSA5()SMR_VSA6()SMR_VSA7()SMR_VSA8()SMR_VSA9()SlogP_VSA1()SlogP_VSA10()SlogP_VSA11()SlogP_VSA12()SlogP_VSA2()SlogP_VSA3()SlogP_VSA4()SlogP_VSA5()SlogP_VSA6()SlogP_VSA7()SlogP_VSA8()SlogP_VSA9()TPSA()pyLabuteASA()pyPEOE_VSA_()pySMR_VSA_()pySlogP_VSA_()
- rdkit.Chem.PandasTools module
AddMoleculeColumnToFrame()AddMurckoToFrame()AlignMol()AlignToScaffold()ChangeMoleculeRendering()FrameToGridImage()InstallPandasTools()LoadSDF()PrintAsImageString()RGroupDecompositionToFrame()RemoveSaltsFromFrame()RenderImagesInAllDataFrames()SaveSMILESFromFrame()SaveXlsxFromFrame()TestCaseUninstallPandasTools()WriteSDF()
- rdkit.Chem.PeriodicTable module
- rdkit.Chem.PropertyMol module
- rdkit.Chem.PyMol module
MolViewerMolViewer.AddPharmacophore()MolViewer.DeleteAll()MolViewer.DeleteAllExcept()MolViewer.DisplayCollisions()MolViewer.DisplayHBonds()MolViewer.DisplayObject()MolViewer.GetAtomCoords()MolViewer.GetPNG()MolViewer.GetSelectedAtoms()MolViewer.HideAll()MolViewer.HideObject()MolViewer.HighlightAtoms()MolViewer.InitializePyMol()MolViewer.LoadFile()MolViewer.Redraw()MolViewer.SaveFile()MolViewer.SelectAtoms()MolViewer.SelectProteinNeighborhood()MolViewer.SetDisplayStyle()MolViewer.SetDisplayUpdate()MolViewer.ShowMol()MolViewer.Zoom()
- rdkit.Chem.QED module
- rdkit.Chem.Randomize module
- rdkit.Chem.Recap module
RecapDecompose()RecapHierarchyNodeTestCaseTestCase.test1()TestCase.test2()TestCase.test3()TestCase.testAmideRxn()TestCase.testAmineRxn()TestCase.testAromCAromCRxn()TestCase.testAromNAliphCRxn()TestCase.testAromNAromCRxn()TestCase.testEsterRxn()TestCase.testEtherRxn()TestCase.testLactamNAliphCRxn()TestCase.testMinFragmentSize()TestCase.testOlefinRxn()TestCase.testSFNetIssue1801871()TestCase.testSFNetIssue1804418()TestCase.testSFNetIssue1881803()TestCase.testSulfonamideRxn()TestCase.testUreaRxn()
- rdkit.Chem.ReducedGraphs module
- rdkit.Chem.RegistrationHash module
- rdkit.Chem.SATIS module
- rdkit.Chem.SaltRemover module
- rdkit.Chem.ShowMols module
- rdkit.Chem.TemplateAlign module
- rdkit.Chem.TorsionFingerprints module
- rdkit.Chem.inchi module
- rdkit.Chem.rdchem module
AddMolSubstanceGroup()AtomAtom.ClearProp()Atom.DescribeQuery()Atom.GetAtomMapNum()Atom.GetAtomicNum()Atom.GetBonds()Atom.GetBoolProp()Atom.GetChiralTag()Atom.GetDegree()Atom.GetDoubleProp()Atom.GetExplicitBitVectProp()Atom.GetExplicitValence()Atom.GetFormalCharge()Atom.GetHybridization()Atom.GetIdx()Atom.GetImplicitValence()Atom.GetIntProp()Atom.GetIsAromatic()Atom.GetIsotope()Atom.GetMass()Atom.GetMonomerInfo()Atom.GetNeighbors()Atom.GetNoImplicit()Atom.GetNumExplicitHs()Atom.GetNumImplicitHs()Atom.GetNumRadicalElectrons()Atom.GetOwningMol()Atom.GetPDBResidueInfo()Atom.GetProp()Atom.GetPropNames()Atom.GetPropsAsDict()Atom.GetQueryType()Atom.GetSmarts()Atom.GetSymbol()Atom.GetTotalDegree()Atom.GetTotalNumHs()Atom.GetTotalValence()Atom.GetUnsignedProp()Atom.HasOwningMol()Atom.HasProp()Atom.HasQuery()Atom.HasValenceViolation()Atom.InvertChirality()Atom.IsInRing()Atom.IsInRingSize()Atom.Match()Atom.NeedsUpdatePropertyCache()Atom.SetAtomMapNum()Atom.SetAtomicNum()Atom.SetBoolProp()Atom.SetChiralTag()Atom.SetDoubleProp()Atom.SetExplicitBitVectProp()Atom.SetFormalCharge()Atom.SetHybridization()Atom.SetIntProp()Atom.SetIsAromatic()Atom.SetIsotope()Atom.SetMonomerInfo()Atom.SetNoImplicit()Atom.SetNumExplicitHs()Atom.SetNumRadicalElectrons()Atom.SetPDBResidueInfo()Atom.SetProp()Atom.SetUnsignedProp()Atom.UpdatePropertyCache()
AtomKekulizeExceptionAtomMonomerInfoAtomMonomerTypeAtomPDBResidueInfoAtomPDBResidueInfo.GetAltLoc()AtomPDBResidueInfo.GetChainId()AtomPDBResidueInfo.GetInsertionCode()AtomPDBResidueInfo.GetIsHeteroAtom()AtomPDBResidueInfo.GetOccupancy()AtomPDBResidueInfo.GetResidueName()AtomPDBResidueInfo.GetResidueNumber()AtomPDBResidueInfo.GetSecondaryStructure()AtomPDBResidueInfo.GetSegmentNumber()AtomPDBResidueInfo.GetSerialNumber()AtomPDBResidueInfo.GetTempFactor()AtomPDBResidueInfo.SetAltLoc()AtomPDBResidueInfo.SetChainId()AtomPDBResidueInfo.SetInsertionCode()AtomPDBResidueInfo.SetIsHeteroAtom()AtomPDBResidueInfo.SetOccupancy()AtomPDBResidueInfo.SetResidueName()AtomPDBResidueInfo.SetResidueNumber()AtomPDBResidueInfo.SetSecondaryStructure()AtomPDBResidueInfo.SetSegmentNumber()AtomPDBResidueInfo.SetSerialNumber()AtomPDBResidueInfo.SetTempFactor()
AtomSanitizeExceptionAtomValenceExceptionBondBond.ClearProp()Bond.DescribeQuery()Bond.GetBeginAtom()Bond.GetBeginAtomIdx()Bond.GetBondDir()Bond.GetBondType()Bond.GetBondTypeAsDouble()Bond.GetBoolProp()Bond.GetDoubleProp()Bond.GetEndAtom()Bond.GetEndAtomIdx()Bond.GetIdx()Bond.GetIntProp()Bond.GetIsAromatic()Bond.GetIsConjugated()Bond.GetOtherAtom()Bond.GetOtherAtomIdx()Bond.GetOwningMol()Bond.GetProp()Bond.GetPropNames()Bond.GetPropsAsDict()Bond.GetSmarts()Bond.GetStereo()Bond.GetStereoAtoms()Bond.GetUnsignedProp()Bond.GetValenceContrib()Bond.HasOwningMol()Bond.HasProp()Bond.HasQuery()Bond.IsInRing()Bond.IsInRingSize()Bond.Match()Bond.SetBondDir()Bond.SetBondType()Bond.SetBoolProp()Bond.SetDoubleProp()Bond.SetIntProp()Bond.SetIsAromatic()Bond.SetIsConjugated()Bond.SetProp()Bond.SetStereo()Bond.SetStereoAtoms()Bond.SetUnsignedProp()
BondDirBondStereoBondTypeBondType.AROMATICBondType.DATIVEBondType.DATIVELBondType.DATIVEONEBondType.DATIVERBondType.DOUBLEBondType.FIVEANDAHALFBondType.FOURANDAHALFBondType.HEXTUPLEBondType.HYDROGENBondType.IONICBondType.ONEANDAHALFBondType.OTHERBondType.QUADRUPLEBondType.QUINTUPLEBondType.SINGLEBondType.THREEANDAHALFBondType.THREECENTERBondType.TRIPLEBondType.TWOANDAHALFBondType.UNSPECIFIEDBondType.ZEROBondType.namesBondType.values
ChiralTypeClearMolSubstanceGroups()CompositeQueryTypeConformerConformer.ClearComputedProps()Conformer.ClearProp()Conformer.GetAtomPosition()Conformer.GetBoolProp()Conformer.GetDoubleProp()Conformer.GetId()Conformer.GetIntProp()Conformer.GetNumAtoms()Conformer.GetOwningMol()Conformer.GetPositions()Conformer.GetProp()Conformer.GetPropNames()Conformer.GetPropsAsDict()Conformer.GetUnsignedProp()Conformer.HasOwningMol()Conformer.HasProp()Conformer.Is3D()Conformer.Set3D()Conformer.SetAtomPosition()Conformer.SetBoolProp()Conformer.SetDoubleProp()Conformer.SetId()Conformer.SetIntProp()Conformer.SetPositions()Conformer.SetProp()Conformer.SetUnsignedProp()
CreateMolDataSubstanceGroup()CreateMolSubstanceGroup()CreateStereoGroup()EditableMolFixedMolSizeMolBundleForwardStereoGroupIds()GetAtomAlias()GetAtomRLabel()GetAtomValue()GetDefaultPickleProperties()GetMolSubstanceGroupWithIdx()GetMolSubstanceGroups()GetNumPiElectrons()GetPeriodicTable()GetSupplementalSmilesLabel()HybridizationTypeKekulizeExceptionMolMol.AddConformer()Mol.ClearComputedProps()Mol.ClearProp()Mol.Compute2DCoords()Mol.ComputeGasteigerCharges()Mol.Debug()Mol.GetAromaticAtoms()Mol.GetAtomWithIdx()Mol.GetAtoms()Mol.GetAtomsMatchingQuery()Mol.GetBondBetweenAtoms()Mol.GetBondWithIdx()Mol.GetBonds()Mol.GetBoolProp()Mol.GetConformer()Mol.GetConformers()Mol.GetDoubleProp()Mol.GetIntProp()Mol.GetNumAtoms()Mol.GetNumBonds()Mol.GetNumConformers()Mol.GetNumHeavyAtoms()Mol.GetProp()Mol.GetPropNames()Mol.GetPropsAsDict()Mol.GetRingInfo()Mol.GetStereoGroups()Mol.GetSubstructMatch()Mol.GetSubstructMatches()Mol.GetUnsignedProp()Mol.HasProp()Mol.HasQuery()Mol.HasSubstructMatch()Mol.NeedsUpdatePropertyCache()Mol.RemoveAllConformers()Mol.RemoveConformer()Mol.SetBoolProp()Mol.SetDoubleProp()Mol.SetIntProp()Mol.SetProp()Mol.SetUnsignedProp()Mol.ToBinary()Mol.UpdatePropertyCache()
MolBundleMolBundleCanSerialize()MolSanitizeExceptionPeriodicTablePeriodicTable.GetAbundanceForIsotope()PeriodicTable.GetAtomicNumber()PeriodicTable.GetAtomicWeight()PeriodicTable.GetDefaultValence()PeriodicTable.GetElementName()PeriodicTable.GetElementSymbol()PeriodicTable.GetMassForIsotope()PeriodicTable.GetMaxAtomicNumber()PeriodicTable.GetMostCommonIsotope()PeriodicTable.GetMostCommonIsotopeMass()PeriodicTable.GetNOuterElecs()PeriodicTable.GetRb0()PeriodicTable.GetRcovalent()PeriodicTable.GetRow()PeriodicTable.GetRvdw()PeriodicTable.GetValenceList()
PropertyPickleOptionsPropertyPickleOptions.AllPropsPropertyPickleOptions.AtomPropsPropertyPickleOptions.BondPropsPropertyPickleOptions.ComputedPropsPropertyPickleOptions.CoordsAsDoublePropertyPickleOptions.MolPropsPropertyPickleOptions.NoConformersPropertyPickleOptions.NoPropsPropertyPickleOptions.PrivatePropsPropertyPickleOptions.QueryAtomDataPropertyPickleOptions.namesPropertyPickleOptions.values
QueryAtomQueryBondRWMolResonanceFlagsResonanceMolSupplierResonanceMolSupplier.Enumerate()ResonanceMolSupplier.GetAtomConjGrpIdx()ResonanceMolSupplier.GetBondConjGrpIdx()ResonanceMolSupplier.GetIsEnumerated()ResonanceMolSupplier.GetNumConjGrps()ResonanceMolSupplier.GetProgressCallback()ResonanceMolSupplier.GetSubstructMatch()ResonanceMolSupplier.GetSubstructMatches()ResonanceMolSupplier.SetNumThreads()ResonanceMolSupplier.SetProgressCallback()ResonanceMolSupplier.WasCanceled()ResonanceMolSupplier.atEnd()ResonanceMolSupplier.reset()
ResonanceMolSupplierCallbackRingInfoRingInfo.AddRing()RingInfo.AreAtomsInSameRing()RingInfo.AreAtomsInSameRingOfSize()RingInfo.AreBondsInSameRing()RingInfo.AreBondsInSameRingOfSize()RingInfo.AreRingFamiliesInitialized()RingInfo.AreRingsFused()RingInfo.AtomMembers()RingInfo.AtomRingFamilies()RingInfo.AtomRingSizes()RingInfo.AtomRings()RingInfo.BondMembers()RingInfo.BondRingFamilies()RingInfo.BondRingSizes()RingInfo.BondRings()RingInfo.IsAtomInRingOfSize()RingInfo.IsBondInRingOfSize()RingInfo.IsRingFused()RingInfo.MinAtomRingSize()RingInfo.MinBondRingSize()RingInfo.NumAtomRings()RingInfo.NumBondRings()RingInfo.NumFusedBonds()RingInfo.NumRelevantCycles()RingInfo.NumRingFamilies()RingInfo.NumRings()
SetAtomAlias()SetAtomRLabel()SetAtomValue()SetDefaultPickleProperties()SetSupplementalSmilesLabel()StereoDescriptorStereoGroupStereoGroupTypeStereoGroup_vectStereoInfoStereoSpecifiedStereoTypeSubstanceGroupSubstanceGroup.AddAtomWithBookmark()SubstanceGroup.AddAtomWithIdx()SubstanceGroup.AddAttachPoint()SubstanceGroup.AddBondWithBookmark()SubstanceGroup.AddBondWithIdx()SubstanceGroup.AddBracket()SubstanceGroup.AddCState()SubstanceGroup.AddParentAtomWithBookmark()SubstanceGroup.AddParentAtomWithIdx()SubstanceGroup.ClearAttachPoints()SubstanceGroup.ClearBrackets()SubstanceGroup.ClearCStates()SubstanceGroup.ClearProp()SubstanceGroup.GetAtoms()SubstanceGroup.GetAttachPoints()SubstanceGroup.GetBonds()SubstanceGroup.GetBoolProp()SubstanceGroup.GetBrackets()SubstanceGroup.GetCStates()SubstanceGroup.GetDoubleProp()SubstanceGroup.GetIndexInMol()SubstanceGroup.GetIntProp()SubstanceGroup.GetOwningMol()SubstanceGroup.GetParentAtoms()SubstanceGroup.GetProp()SubstanceGroup.GetPropNames()SubstanceGroup.GetPropsAsDict()SubstanceGroup.GetStringVectProp()SubstanceGroup.GetUnsignedProp()SubstanceGroup.GetUnsignedVectProp()SubstanceGroup.HasProp()SubstanceGroup.SetAtoms()SubstanceGroup.SetBonds()SubstanceGroup.SetBoolProp()SubstanceGroup.SetDoubleProp()SubstanceGroup.SetIntProp()SubstanceGroup.SetParentAtoms()SubstanceGroup.SetProp()SubstanceGroup.SetUnsignedProp()
SubstanceGroupAttachSubstanceGroupCStateSubstanceGroup_VECTSubstructMatchParametersSubstructMatchParameters.aromaticMatchesConjugatedSubstructMatchParameters.atomPropertiesSubstructMatchParameters.bondPropertiesSubstructMatchParameters.maxMatchesSubstructMatchParameters.maxRecursiveMatchesSubstructMatchParameters.numThreadsSubstructMatchParameters.recursionPossibleSubstructMatchParameters.setExtraFinalCheck()SubstructMatchParameters.uniquifySubstructMatchParameters.useChiralitySubstructMatchParameters.useEnhancedStereoSubstructMatchParameters.useGenericMatchersSubstructMatchParameters.useQueryQueryMatches
tossit()
- rdkit.Chem.rdDistGeom module
ETDG()ETKDG()ETKDGv2()ETKDGv3()EmbedFailureCausesEmbedFailureCauses.BAD_DOUBLE_BOND_STEREOEmbedFailureCauses.CHECK_CHIRAL_CENTERSEmbedFailureCauses.CHECK_CHIRAL_CENTERS2EmbedFailureCauses.CHECK_TETRAHEDRAL_CENTERSEmbedFailureCauses.ETK_MINIMIZATIONEmbedFailureCauses.FINAL_CENTER_IN_VOLUMEEmbedFailureCauses.FINAL_CHIRAL_BOUNDSEmbedFailureCauses.FIRST_MINIMIZATIONEmbedFailureCauses.INITIAL_COORDSEmbedFailureCauses.LINEAR_DOUBLE_BONDEmbedFailureCauses.MINIMIZE_FOURTH_DIMENSIONEmbedFailureCauses.namesEmbedFailureCauses.values
EmbedMolecule()EmbedMultipleConfs()EmbedParametersEmbedParameters.ETversionEmbedParameters.GetFailureCounts()EmbedParameters.SetBoundsMat()EmbedParameters.SetCPCI()EmbedParameters.SetCoordMap()EmbedParameters.boundsMatForceScalingEmbedParameters.boxSizeMultEmbedParameters.clearConfsEmbedParameters.embedFragmentsSeparatelyEmbedParameters.enableSequentialRandomSeedsEmbedParameters.enforceChiralityEmbedParameters.forceTransAmidesEmbedParameters.ignoreSmoothingFailuresEmbedParameters.maxIterationsEmbedParameters.numThreadsEmbedParameters.numZeroFailEmbedParameters.onlyHeavyAtomsForRMSEmbedParameters.optimizerForceTolEmbedParameters.pruneRmsThreshEmbedParameters.randNegEigEmbedParameters.randomSeedEmbedParameters.symmetrizeConjugatedTerminalGroupsForPruningEmbedParameters.trackFailuresEmbedParameters.useBasicKnowledgeEmbedParameters.useExpTorsionAnglePrefsEmbedParameters.useMacrocycle14configEmbedParameters.useMacrocycleTorsionsEmbedParameters.useRandomCoordsEmbedParameters.useSmallRingTorsionsEmbedParameters.useSymmetryForPruningEmbedParameters.verbose
GetExperimentalTorsions()GetMoleculeBoundsMatrix()KDG()srETKDGv3()
- rdkit.Chem.rdqueries module
AAtomQueryAtom()AHAtomQueryAtom()AtomNumEqualsQueryAtom()AtomNumGreaterQueryAtom()AtomNumLessQueryAtom()ExplicitDegreeEqualsQueryAtom()ExplicitDegreeGreaterQueryAtom()ExplicitDegreeLessQueryAtom()ExplicitValenceEqualsQueryAtom()ExplicitValenceGreaterQueryAtom()ExplicitValenceLessQueryAtom()FormalChargeEqualsQueryAtom()FormalChargeGreaterQueryAtom()FormalChargeLessQueryAtom()HCountEqualsQueryAtom()HCountGreaterQueryAtom()HCountLessQueryAtom()HasBitVectPropWithValueQueryAtom()HasBoolPropWithValueQueryAtom()HasBoolPropWithValueQueryBond()HasChiralTagQueryAtom()HasDoublePropWithValueQueryAtom()HasDoublePropWithValueQueryBond()HasIntPropWithValueQueryAtom()HasIntPropWithValueQueryBond()HasPropQueryAtom()HasPropQueryBond()HasStringPropWithValueQueryAtom()HasStringPropWithValueQueryBond()HybridizationEqualsQueryAtom()HybridizationGreaterQueryAtom()HybridizationLessQueryAtom()InNRingsEqualsQueryAtom()InNRingsGreaterQueryAtom()InNRingsLessQueryAtom()IsAliphaticQueryAtom()IsAromaticQueryAtom()IsBridgeheadQueryAtom()IsInRingQueryAtom()IsUnsaturatedQueryAtom()IsotopeEqualsQueryAtom()IsotopeGreaterQueryAtom()IsotopeLessQueryAtom()MAtomQueryAtom()MHAtomQueryAtom()MassEqualsQueryAtom()MassGreaterQueryAtom()MassLessQueryAtom()MinRingSizeEqualsQueryAtom()MinRingSizeGreaterQueryAtom()MinRingSizeLessQueryAtom()MissingChiralTagQueryAtom()NonHydrogenDegreeEqualsQueryAtom()NonHydrogenDegreeGreaterQueryAtom()NonHydrogenDegreeLessQueryAtom()NumAliphaticHeteroatomNeighborsEqualsQueryAtom()NumAliphaticHeteroatomNeighborsGreaterQueryAtom()NumAliphaticHeteroatomNeighborsLessQueryAtom()NumHeteroatomNeighborsEqualsQueryAtom()NumHeteroatomNeighborsGreaterQueryAtom()NumHeteroatomNeighborsLessQueryAtom()NumRadicalElectronsEqualsQueryAtom()NumRadicalElectronsGreaterQueryAtom()NumRadicalElectronsLessQueryAtom()QAtomQueryAtom()QHAtomQueryAtom()ReplaceAtomWithQueryAtom()RingBondCountEqualsQueryAtom()RingBondCountGreaterQueryAtom()RingBondCountLessQueryAtom()TotalDegreeEqualsQueryAtom()TotalDegreeGreaterQueryAtom()TotalDegreeLessQueryAtom()TotalValenceEqualsQueryAtom()TotalValenceGreaterQueryAtom()TotalValenceLessQueryAtom()XAtomQueryAtom()XHAtomQueryAtom()
- rdkit.Chem.rdFMCS module
AtomCompareBondCompareFindMCS()MCSAcceptanceMCSAtomCompareMCSAtomCompareParametersMCSBondCompareMCSBondCompareParametersMCSFinalMatchCheckMCSParametersMCSParameters.AtomCompareParametersMCSParameters.AtomTyperMCSParameters.BondCompareParametersMCSParameters.BondTyperMCSParameters.FinalMatchCheckerMCSParameters.InitialSeedMCSParameters.MaximizeBondsMCSParameters.ProgressCallbackMCSParameters.ShouldAcceptMCSMCSParameters.StoreAllMCSParameters.ThresholdMCSParameters.TimeoutMCSParameters.Verbose
MCSProgressMCSProgressDataMCSResultRingCompare
- rdkit.Chem.rdMolAlign module
- rdkit.Chem.rdMolHash module
HashFunctionHashFunction.AnonymousGraphHashFunction.ArthorSubstructureOrderHashFunction.AtomBondCountsHashFunction.CanonicalSmilesHashFunction.DegreeVectorHashFunction.ElementGraphHashFunction.ExtendedMurckoHashFunction.HetAtomProtomerHashFunction.HetAtomProtomerv2HashFunction.HetAtomTautomerHashFunction.HetAtomTautomerv2HashFunction.MesomerHashFunction.MolFormulaHashFunction.MurckoScaffoldHashFunction.NetChargeHashFunction.RedoxPairHashFunction.RegioisomerHashFunction.SmallWorldIndexBRHashFunction.SmallWorldIndexBRLHashFunction.namesHashFunction.values
MolHash()
- rdkit.Chem.rdReducedGraphs module
- rdkit.Chem.rdtrajectory module
- rdkit.Chem.rdMolTransforms module
CanonicalizeConformer()CanonicalizeMol()ComputeCanonicalTransform()ComputeCentroid()ComputePrincipalAxesAndMoments()ComputePrincipalAxesAndMomentsFromGyrationMatrix()GetAngleDeg()GetAngleRad()GetBondLength()GetDihedralDeg()GetDihedralRad()SetAngleDeg()SetAngleRad()SetBondLength()SetDihedralDeg()SetDihedralRad()TransformConformer()
- rdkit.Chem.rdmolfiles module
AddMetadataToPNGFile()AddMetadataToPNGString()AtomFromSmarts()AtomFromSmiles()BondFromSmarts()BondFromSmiles()CXSmilesFieldsCXSmilesFields.CX_ALLCXSmilesFields.CX_ALL_BUT_COORDSCXSmilesFields.CX_ATOM_LABELSCXSmilesFields.CX_ATOM_PROPSCXSmilesFields.CX_BOND_ATROPISOMERCXSmilesFields.CX_BOND_CFGCXSmilesFields.CX_COORDINATE_BONDSCXSmilesFields.CX_COORDSCXSmilesFields.CX_ENHANCEDSTEREOCXSmilesFields.CX_LINKNODESCXSmilesFields.CX_MOLFILE_VALUESCXSmilesFields.CX_NONECXSmilesFields.CX_POLYMERCXSmilesFields.CX_RADICALSCXSmilesFields.CX_SGROUPSCXSmilesFields.namesCXSmilesFields.values
CanonicalRankAtoms()CanonicalRankAtomsInFragment()CanonicalizeEnhancedStereo()CreateAtomBoolPropertyList()CreateAtomDoublePropertyList()CreateAtomIntPropertyList()CreateAtomStringPropertyList()ForwardSDMolSupplierMaeMolSupplierMaeWriterMetadataFromPNGFile()MetadataFromPNGString()MolFragmentToCXSmarts()MolFragmentToCXSmiles()MolFragmentToSmarts()MolFragmentToSmiles()MolFromFASTA()MolFromHELM()MolFromMol2Block()MolFromMol2File()MolFromMolBlock()MolFromMolFile()MolFromMrvBlock()MolFromMrvFile()MolFromPDBBlock()MolFromPDBFile()MolFromPNGFile()MolFromPNGString()MolFromRDKitSVG()MolFromSequence()MolFromSmarts()MolFromSmiles()MolFromTPLBlock()MolFromTPLFile()MolFromXYZBlock()MolFromXYZFile()MolMetadataToPNGFile()MolMetadataToPNGString()MolToCMLBlock()MolToCMLFile()MolToCXSmarts()MolToCXSmiles()MolToFASTA()MolToHELM()MolToMolBlock()MolToMolFile()MolToMrvBlock()MolToMrvFile()MolToPDBBlock()MolToPDBFile()MolToRandomSmilesVect()MolToSequence()MolToSmarts()MolToSmiles()MolToTPLBlock()MolToTPLFile()MolToV2KMolBlock()MolToV3KMolBlock()MolToV3KMolFile()MolToXYZBlock()MolToXYZFile()MolWriterParamsMolsFromCDXML()MolsFromCDXMLFile()MolsFromPNGFile()MolsFromPNGString()MultithreadedSDMolSupplierMultithreadedSmilesMolSupplierPDBWriterRestoreBondDirOptionSDMolSupplierSDWriterSmartsParserParamsSmilesMolSupplierSmilesMolSupplierFromText()SmilesParserParamsSmilesWriteParamsSmilesWriterTDTMolSupplierTDTWriter
- rdkit.Chem.rdPartialCharges module
- rdkit.Chem.rdMolCatalog module
- rdkit.Chem.rdCoordGen module
AddCoords()CoordGenParamsCoordGenParams.SetCoordMap()CoordGenParams.SetTemplateMol()CoordGenParams.coordgenScalingCoordGenParams.dbg_useConstrainedCoordGenParams.dbg_useFixedCoordGenParams.minimizerPrecisionCoordGenParams.sketcherBestPrecisionCoordGenParams.sketcherCoarsePrecisionCoordGenParams.sketcherQuickPrecisionCoordGenParams.sketcherStandardPrecisionCoordGenParams.templateFileDirCoordGenParams.treatNonterminalBondsToMetalAsZOBs
SetDefaultTemplateFileDir()
- rdkit.Chem.rdMolChemicalFeatures module
BuildFeatureFactory()BuildFeatureFactoryFromString()GetAtomMatch()MolChemicalFeatureMolChemicalFeature.ClearCache()MolChemicalFeature.GetActiveConformer()MolChemicalFeature.GetAtomIds()MolChemicalFeature.GetFactory()MolChemicalFeature.GetFamily()MolChemicalFeature.GetId()MolChemicalFeature.GetMol()MolChemicalFeature.GetPos()MolChemicalFeature.GetType()MolChemicalFeature.SetActiveConformer()
MolChemicalFeatureFactory
- rdkit.Chem.rdMMPA module
- rdkit.Chem.rdRGroupDecomposition module
RGroupCoreAlignmentRGroupDecompose()RGroupDecompositionRGroupDecompositionParametersRGroupDecompositionParameters.alignmentRGroupDecompositionParameters.allowMultipleRGroupsOnUnlabelledRGroupDecompositionParameters.allowNonTerminalRGroupsRGroupDecompositionParameters.chunkSizeRGroupDecompositionParameters.doEnumerationRGroupDecompositionParameters.doTautomersRGroupDecompositionParameters.gaMaximumOperationsRGroupDecompositionParameters.gaNumberOperationsWithoutImprovementRGroupDecompositionParameters.gaNumberRunsRGroupDecompositionParameters.gaParallelRunsRGroupDecompositionParameters.gaPopulationSizeRGroupDecompositionParameters.gaRandomSeedRGroupDecompositionParameters.includeTargetMolInResultsRGroupDecompositionParameters.labelsRGroupDecompositionParameters.matchingStrategyRGroupDecompositionParameters.onlyMatchAtRGroupsRGroupDecompositionParameters.removeAllHydrogenRGroupsRGroupDecompositionParameters.removeAllHydrogenRGroupsAndLabelsRGroupDecompositionParameters.removeHydrogensPostMatchRGroupDecompositionParameters.rgroupLabellingRGroupDecompositionParameters.scoreMethodRGroupDecompositionParameters.substructMatchParamsRGroupDecompositionParameters.timeout
RGroupLabellingRGroupLabelsRGroupMatchingRGroupScoreRelabelMappedDummies()
- rdkit.Chem.rdForceFieldHelpers module
CreateEmptyForceFieldForMol()GetUFFAngleBendParams()GetUFFBondStretchParams()GetUFFInversionParams()GetUFFTorsionParams()GetUFFVdWParams()MMFFGetMoleculeForceField()MMFFGetMoleculeProperties()MMFFHasAllMoleculeParams()MMFFOptimizeMolecule()MMFFOptimizeMoleculeConfs()MMFFSanitizeMolecule()OptimizeMolecule()OptimizeMoleculeConfs()UFFGetMoleculeForceField()UFFHasAllMoleculeParams()UFFOptimizeMolecule()UFFOptimizeMoleculeConfs()
- rdkit.Chem.rdDepictor module
AddRingSystemTemplates()Compute2DCoords()Compute2DCoordsMimicDistmat()ConstrainedDepictionParamsGenerateDepictionMatching2DStructure()GenerateDepictionMatching3DStructure()GetPreferCoordGen()IsCoordGenSupportAvailable()LoadDefaultRingSystemTemplates()NormalizeDepiction()SetPreferCoordGen()SetRingSystemTemplates()StraightenDepiction()UsingCoordGen
- rdkit.Chem.rdChemicalFeatures module
- rdkit.Chem.rdmolops module
AddHs()AddRecursiveQuery()AddStereoAnnotations()AddWavyBondsForStereoAny()AdjustQueryParametersAdjustQueryParameters.NoAdjustments()AdjustQueryParameters.adjustConjugatedFiveRingsAdjustQueryParameters.adjustDegreeAdjustQueryParameters.adjustDegreeFlagsAdjustQueryParameters.adjustHeavyDegreeAdjustQueryParameters.adjustHeavyDegreeFlagsAdjustQueryParameters.adjustRingChainAdjustQueryParameters.adjustRingChainFlagsAdjustQueryParameters.adjustRingCountAdjustQueryParameters.adjustRingCountFlagsAdjustQueryParameters.adjustSingleBondsBetweenAromaticAtomsAdjustQueryParameters.adjustSingleBondsToDegreeOneNeighborsAdjustQueryParameters.aromatizeIfPossibleAdjustQueryParameters.makeAtomsGenericAdjustQueryParameters.makeAtomsGenericFlagsAdjustQueryParameters.makeBondsGenericAdjustQueryParameters.makeBondsGenericFlagsAdjustQueryParameters.makeDummiesQueriesAdjustQueryParameters.setMDLFiveRingAromaticityAdjustQueryParameters.useStereoCareForBonds
AdjustQueryProperties()AdjustQueryPropertiesWithGenericGroups()AdjustQueryWhichFlagsAdjustQueryWhichFlags.ADJUST_IGNOREALLAdjustQueryWhichFlags.ADJUST_IGNORECHAINSAdjustQueryWhichFlags.ADJUST_IGNOREDUMMIESAdjustQueryWhichFlags.ADJUST_IGNOREMAPPEDAdjustQueryWhichFlags.ADJUST_IGNORENONDUMMIESAdjustQueryWhichFlags.ADJUST_IGNORENONEAdjustQueryWhichFlags.ADJUST_IGNORERINGSAdjustQueryWhichFlags.namesAdjustQueryWhichFlags.values
AromaticityModelAssignAtomChiralTagsFromMolParity()AssignAtomChiralTagsFromStructure()AssignChiralTypesFromBondDirs()AssignRadicals()AssignStereochemistry()AssignStereochemistryFrom3D()AtomHasConjugatedBond()BondWedgingParametersCleanup()CleanupAtropisomers()CleanupChirality()CleanupOrganometallics()CollapseAttachmentPoints()CombineMols()ConvertGenericQueriesToSubstanceGroups()CountAtomElec()DativeBondsToHaptic()DeleteSubstructs()DetectBondStereoChemistry()DetectBondStereochemistry()DetectChemistryProblems()ExpandAttachmentPoints()FastFindRings()FindAllPathsOfLengthN()FindAllSubgraphsOfLengthMToN()FindAllSubgraphsOfLengthN()FindAtomEnvironmentOfRadiusN()FindMesoCenters()FindPotentialStereo()FindPotentialStereoBonds()FindRingFamilies()FindUniqueSubgraphsOfLengthN()FragmentOnBRICSBonds()FragmentOnBonds()FragmentOnSomeBonds()Get3DDistanceMatrix()GetAdjacencyMatrix()GetAllowNontetrahedralChirality()GetDistanceMatrix()GetFormalCharge()GetMolFrags()GetMostSubstitutedCoreMatch()GetSSSR()GetShortestPath()GetSymmSSSR()GetUseLegacyStereoPerception()HapticBondsToDative()HasQueryHs()Kekulize()KekulizeIfPossible()LayeredFingerprint()MergeQueryHs()MolAddRecursiveQueries()MolzipLabelMolzipParamsMurckoDecompose()NeedsHs()ParseMolQueryDefFile()PathToSubmol()PatternFingerprint()RDKFingerprint()ReapplyMolBlockWedging()RemoveAllHs()RemoveHs()RemoveHsParametersRemoveHsParameters.removeAndTrackIsotopesRemoveHsParameters.removeDefiningBondStereoRemoveHsParameters.removeDegreeZeroRemoveHsParameters.removeDummyNeighborsRemoveHsParameters.removeHigherDegreesRemoveHsParameters.removeHydridesRemoveHsParameters.removeInSGroupsRemoveHsParameters.removeIsotopesRemoveHsParameters.removeMappedRemoveHsParameters.removeNonimplicitRemoveHsParameters.removeNontetrahedralNeighborsRemoveHsParameters.removeOnlyHNeighborsRemoveHsParameters.removeWithQueryRemoveHsParameters.removeWithWedgedBondRemoveHsParameters.showWarningsRemoveHsParameters.updateExplicitCount
RemoveNonExplicit3DChirality()RemoveStereochemistry()RenumberAtoms()ReplaceCore()ReplaceSidechains()ReplaceSubstructs()SanitizeFlagsSanitizeFlags.SANITIZE_ADJUSTHSSanitizeFlags.SANITIZE_ALLSanitizeFlags.SANITIZE_CLEANUPSanitizeFlags.SANITIZE_CLEANUPATROPISOMERSSanitizeFlags.SANITIZE_CLEANUPCHIRALITYSanitizeFlags.SANITIZE_CLEANUP_ORGANOMETALLICSSanitizeFlags.SANITIZE_FINDRADICALSSanitizeFlags.SANITIZE_KEKULIZESanitizeFlags.SANITIZE_NONESanitizeFlags.SANITIZE_PROPERTIESSanitizeFlags.SANITIZE_SETAROMATICITYSanitizeFlags.SANITIZE_SETCONJUGATIONSanitizeFlags.SANITIZE_SETHYBRIDIZATIONSanitizeFlags.SANITIZE_SYMMRINGSSanitizeFlags.namesSanitizeFlags.values
SanitizeMol()SetAllowNontetrahedralChirality()SetAromaticity()SetBondStereoFromDirections()SetConjugation()SetDoubleBondNeighborDirections()SetGenericQueriesFromProperties()SetHybridization()SetTerminalAtomCoords()SetUseLegacyStereoPerception()SimplifyEnhancedStereo()SortMatchesByDegreeOfCoreSubstitution()SplitMolByPDBChainId()SplitMolByPDBResidues()StereoBondThresholdsTranslateChiralFlagToStereoGroups()UnfoldedRDKFingerprintCountBased()WedgeBond()WedgeMolBonds()molzip()molzipFragments()
- rdkit.Chem.rdFreeSASA module
- rdkit.Chem.rdMolInterchange module
- rdkit.Chem.rdShapeHelpers module
- rdkit.Chem.rdinchi module
- rdkit.Chem.rdChemReactions module
CartesianProductStrategyChemicalReactionChemicalReaction.AddAgentTemplate()ChemicalReaction.AddProductTemplate()ChemicalReaction.AddReactantTemplate()ChemicalReaction.AddRecursiveQueriesToReaction()ChemicalReaction.ClearComputedProps()ChemicalReaction.ClearProp()ChemicalReaction.GetAgentTemplate()ChemicalReaction.GetAgents()ChemicalReaction.GetBoolProp()ChemicalReaction.GetDoubleProp()ChemicalReaction.GetIntProp()ChemicalReaction.GetNumAgentTemplates()ChemicalReaction.GetNumProductTemplates()ChemicalReaction.GetNumReactantTemplates()ChemicalReaction.GetProductTemplate()ChemicalReaction.GetProducts()ChemicalReaction.GetProp()ChemicalReaction.GetPropNames()ChemicalReaction.GetPropsAsDict()ChemicalReaction.GetReactantTemplate()ChemicalReaction.GetReactants()ChemicalReaction.GetReactingAtoms()ChemicalReaction.GetSubstructParams()ChemicalReaction.GetUnsignedProp()ChemicalReaction.HasProp()ChemicalReaction.Initialize()ChemicalReaction.IsInitialized()ChemicalReaction.IsMoleculeAgent()ChemicalReaction.IsMoleculeProduct()ChemicalReaction.IsMoleculeReactant()ChemicalReaction.RemoveAgentTemplates()ChemicalReaction.RemoveUnmappedProductTemplates()ChemicalReaction.RemoveUnmappedReactantTemplates()ChemicalReaction.RunReactant()ChemicalReaction.RunReactantInPlace()ChemicalReaction.RunReactants()ChemicalReaction.SetBoolProp()ChemicalReaction.SetDoubleProp()ChemicalReaction.SetIntProp()ChemicalReaction.SetProp()ChemicalReaction.SetUnsignedProp()ChemicalReaction.ToBinary()ChemicalReaction.Validate()
Compute2DCoordsForReaction()CreateDifferenceFingerprintForReaction()CreateStructuralFingerprintForReaction()EnumerateLibraryEnumerateLibraryBaseEnumerateLibraryBase.GetEnumerator()EnumerateLibraryBase.GetPosition()EnumerateLibraryBase.GetReaction()EnumerateLibraryBase.GetState()EnumerateLibraryBase.InitFromString()EnumerateLibraryBase.ResetState()EnumerateLibraryBase.Serialize()EnumerateLibraryBase.SetState()EnumerateLibraryBase.next()EnumerateLibraryBase.nextSmiles()
EnumerateLibraryCanSerialize()EnumerationParamsEnumerationStrategyBaseEvenSamplePairsStrategyFingerprintTypeGetChemDrawRxnAdjustParams()GetDefaultAdjustParams()HasAgentTemplateSubstructMatch()HasProductTemplateSubstructMatch()HasReactantTemplateSubstructMatch()HasReactionAtomMapping()HasReactionSubstructMatch()IsReactionTemplateMoleculeAgent()MOL_SPTR_VECTMatchOnlyAtRgroupsAdjustParams()MrvBlockIsReaction()MrvFileIsReaction()PreprocessReaction()RandomSampleAllBBsStrategyRandomSampleStrategyReactionFingerprintParamsReactionFromMolecule()ReactionFromMrvBlock()ReactionFromMrvFile()ReactionFromPNGFile()ReactionFromPNGString()ReactionFromRxnBlock()ReactionFromRxnFile()ReactionFromSmarts()ReactionMetadataToPNGFile()ReactionMetadataToPNGString()ReactionToMolecule()ReactionToMrvBlock()ReactionToMrvFile()ReactionToRxnBlock()ReactionToSmarts()ReactionToSmiles()ReactionToV3KRxnBlock()ReactionsFromCDXMLBlock()ReactionsFromCDXMLFile()ReduceProductToSideChains()RemoveMappingNumbersFromReactions()SanitizeFlagsSanitizeRxn()SanitizeRxnAsMols()UpdateProductsStereochemistry()VectMolVect
- rdkit.Chem.rdSubstructLibrary module
AddPatterns()CachedMolHolderCachedSmilesMolHolderCachedTrustedSmilesMolHolderFPHolderBaseKeyFromPropHolderKeyHolderBaseMolHolderMolHolderBasePatternHolderSubstructLibrarySubstructLibrary.AddMol()SubstructLibrary.CountMatches()SubstructLibrary.GetFpHolder()SubstructLibrary.GetKeyHolder()SubstructLibrary.GetMatches()SubstructLibrary.GetMol()SubstructLibrary.GetMolHolder()SubstructLibrary.GetSearchOrder()SubstructLibrary.HasMatch()SubstructLibrary.InitFromStream()SubstructLibrary.Serialize()SubstructLibrary.SetSearchOrder()SubstructLibrary.ToStream()
SubstructLibraryCanSerialize()TautomerPatternHolder
- rdkit.Chem.rdfiltercatalog module
ExclusionListFilterCatalogFilterCatalogCanSerialize()FilterCatalogEntryFilterCatalogEntry.ClearProp()FilterCatalogEntry.GetDescription()FilterCatalogEntry.GetFilterMatches()FilterCatalogEntry.GetProp()FilterCatalogEntry.GetPropList()FilterCatalogEntry.HasFilterMatch()FilterCatalogEntry.IsValid()FilterCatalogEntry.Serialize()FilterCatalogEntry.SetDescription()FilterCatalogEntry.SetProp()
FilterCatalogEntryListFilterCatalogListOfEntryListFilterCatalogParamsFilterCatalogParams.AddCatalog()FilterCatalogParams.FilterCatalogsFilterCatalogParams.FilterCatalogs.ALLFilterCatalogParams.FilterCatalogs.BRENKFilterCatalogParams.FilterCatalogs.CHEMBLFilterCatalogParams.FilterCatalogs.CHEMBL_BMSFilterCatalogParams.FilterCatalogs.CHEMBL_DundeeFilterCatalogParams.FilterCatalogs.CHEMBL_GlaxoFilterCatalogParams.FilterCatalogs.CHEMBL_InpharmaticaFilterCatalogParams.FilterCatalogs.CHEMBL_LINTFilterCatalogParams.FilterCatalogs.CHEMBL_MLSMRFilterCatalogParams.FilterCatalogs.CHEMBL_SureChEMBLFilterCatalogParams.FilterCatalogs.NIHFilterCatalogParams.FilterCatalogs.PAINSFilterCatalogParams.FilterCatalogs.PAINS_AFilterCatalogParams.FilterCatalogs.PAINS_BFilterCatalogParams.FilterCatalogs.PAINS_CFilterCatalogParams.FilterCatalogs.ZINCFilterCatalogParams.FilterCatalogs.namesFilterCatalogParams.FilterCatalogs.values
FilterHierarchyMatcherFilterMatchFilterMatcherBaseGetFlattenedFunctionalGroupHierarchy()GetFunctionalGroupHierarchy()IntPairMolListPythonFilterMatcherRunFilterCatalog()SmartsMatcherVectFilterMatch
- rdkit.Chem.rdfragcatalog module
FragCatGeneratorFragCatParamsFragCatalogFragCatalog.GetBitDescription()FragCatalog.GetBitDiscrims()FragCatalog.GetBitEntryId()FragCatalog.GetBitFuncGroupIds()FragCatalog.GetBitOrder()FragCatalog.GetCatalogParams()FragCatalog.GetEntryBitId()FragCatalog.GetEntryDescription()FragCatalog.GetEntryDownIds()FragCatalog.GetEntryFuncGroupIds()FragCatalog.GetEntryOrder()FragCatalog.GetFPLength()FragCatalog.GetNumEntries()FragCatalog.Serialize()
FragFPGenerator
- rdkit.Chem.rdMolDescriptors module
AtomPairsParametersBCUT2D()CalcAUTOCORR2D()CalcAUTOCORR3D()CalcAsphericity()CalcChi0n()CalcChi0v()CalcChi1n()CalcChi1v()CalcChi2n()CalcChi2v()CalcChi3n()CalcChi3v()CalcChi4n()CalcChi4v()CalcChiNn()CalcChiNv()CalcCoulombMat()CalcCrippenDescriptors()CalcEEMcharges()CalcEccentricity()CalcExactMolWt()CalcFractionCSP3()CalcGETAWAY()CalcHallKierAlpha()CalcInertialShapeFactor()CalcKappa1()CalcKappa2()CalcKappa3()CalcLabuteASA()CalcMORSE()CalcMolFormula()CalcNPR1()CalcNPR2()CalcNumAliphaticCarbocycles()CalcNumAliphaticHeterocycles()CalcNumAliphaticRings()CalcNumAmideBonds()CalcNumAromaticCarbocycles()CalcNumAromaticHeterocycles()CalcNumAromaticRings()CalcNumAtomStereoCenters()CalcNumAtoms()CalcNumBridgeheadAtoms()CalcNumHBA()CalcNumHBD()CalcNumHeavyAtoms()CalcNumHeteroatoms()CalcNumHeterocycles()CalcNumLipinskiHBA()CalcNumLipinskiHBD()CalcNumRings()CalcNumRotatableBonds()CalcNumSaturatedCarbocycles()CalcNumSaturatedHeterocycles()CalcNumSaturatedRings()CalcNumSpiroAtoms()CalcNumUnspecifiedAtomStereoCenters()CalcOxidationNumbers()CalcPBF()CalcPMI1()CalcPMI2()CalcPMI3()CalcPhi()CalcRDF()CalcRadiusOfGyration()CalcSpherocityIndex()CalcTPSA()CalcWHIM()CustomProp_VSA_()DoubleCubicLatticeVolumeGetAtomFeatures()GetAtomPairAtomCode()GetAtomPairCode()GetAtomPairFingerprint()GetConnectivityInvariants()GetFeatureInvariants()GetHashedAtomPairFingerprint()GetHashedAtomPairFingerprintAsBitVect()GetHashedMorganFingerprint()GetHashedTopologicalTorsionFingerprint()GetHashedTopologicalTorsionFingerprintAsBitVect()GetMACCSKeysFingerprint()GetMorganFingerprint()GetMorganFingerprintAsBitVect()GetTopologicalTorsionFingerprint()GetUSR()GetUSRCAT()GetUSRDistributions()GetUSRDistributionsFromPoints()GetUSRFromDistributions()GetUSRScore()MQNs_()MakePropertyRangeQuery()NumRotatableBondsOptionsPEOE_VSA_()PropertiesPropertyFunctorPropertyRangeQueryPythonPropertyFunctorSMR_VSA_()SlogP_VSA_()
- rdkit.Chem.rdFingerprintGenerator module
AdditionalOutputAdditionalOutput.AllocateAtomCounts()AdditionalOutput.AllocateAtomToBits()AdditionalOutput.AllocateBitInfoMap()AdditionalOutput.AllocateBitPaths()AdditionalOutput.CollectAtomCounts()AdditionalOutput.CollectAtomToBits()AdditionalOutput.CollectBitInfoMap()AdditionalOutput.CollectBitPaths()AdditionalOutput.GetAtomCounts()AdditionalOutput.GetAtomToBits()AdditionalOutput.GetBitInfoMap()AdditionalOutput.GetBitPaths()
AtomInvariantsGeneratorAtomPairFingerprintOptionsBondInvariantsGeneratorFPTypeFingerprintGenerator32FingerprintGenerator32.GetCountFingerprint()FingerprintGenerator32.GetCountFingerprintAsNumPy()FingerprintGenerator32.GetCountFingerprints()FingerprintGenerator32.GetFingerprint()FingerprintGenerator32.GetFingerprintAsNumPy()FingerprintGenerator32.GetFingerprints()FingerprintGenerator32.GetInfoString()FingerprintGenerator32.GetOptions()FingerprintGenerator32.GetSparseCountFingerprint()FingerprintGenerator32.GetSparseCountFingerprints()FingerprintGenerator32.GetSparseFingerprint()FingerprintGenerator32.GetSparseFingerprints()
FingerprintGenerator64FingerprintGenerator64.GetCountFingerprint()FingerprintGenerator64.GetCountFingerprintAsNumPy()FingerprintGenerator64.GetCountFingerprints()FingerprintGenerator64.GetFingerprint()FingerprintGenerator64.GetFingerprintAsNumPy()FingerprintGenerator64.GetFingerprints()FingerprintGenerator64.GetInfoString()FingerprintGenerator64.GetOptions()FingerprintGenerator64.GetSparseCountFingerprint()FingerprintGenerator64.GetSparseCountFingerprints()FingerprintGenerator64.GetSparseFingerprint()FingerprintGenerator64.GetSparseFingerprints()
FingerprintOptionsGetAtomPairAtomInvGen()GetAtomPairGenerator()GetCountFPs()GetFPs()GetMorganAtomInvGen()GetMorganBondInvGen()GetMorganFeatureAtomInvGen()GetMorganGenerator()GetRDKitAtomInvGen()GetRDKitFPGenerator()GetSparseCountFPs()GetSparseFPs()GetTopologicalTorsionGenerator()MorganFingerprintOptionsRDKitFingerprintOptionsTopologicalTorsionFingerprintOptions
- rdkit.Chem.rdMHFPFingerprint module
MHFPEncoderMHFPEncoder.CreateShinglingFromMol()MHFPEncoder.CreateShinglingFromSmiles()MHFPEncoder.Distance()MHFPEncoder.EncodeMol()MHFPEncoder.EncodeMolsBulk()MHFPEncoder.EncodeSECFPMol()MHFPEncoder.EncodeSECFPMolsBulk()MHFPEncoder.EncodeSECFPSmiles()MHFPEncoder.EncodeSECFPSmilesBulk()MHFPEncoder.EncodeSmiles()MHFPEncoder.EncodeSmilesBulk()MHFPEncoder.FromArray()MHFPEncoder.FromStringArray()
- rdkit.Chem.rdSLNParse module
- rdkit.Chem.rdAbbreviations module
- rdkit.Chem.rdDeprotect module
- rdkit.Chem.rdMolEnumerator module
- rdkit.Chem.rdCIPLabeler module
- rdkit.Chem.rdTautomerQuery module
PatternFingerprintTautomerTarget()TautomerQueryTautomerQuery.GetModifiedAtoms()TautomerQuery.GetModifiedBonds()TautomerQuery.GetSubstructMatch()TautomerQuery.GetSubstructMatches()TautomerQuery.GetSubstructMatchesWithTautomers()TautomerQuery.GetTautomers()TautomerQuery.GetTemplateMolecule()TautomerQuery.IsSubstructOf()TautomerQuery.PatternFingerprintTemplate()TautomerQuery.ToBinary()
TautomerQueryCanSerialize()
- rdkit.Chem.rdEHTTools module
- rdkit.Chem.rdDetermineBonds module
- Module contents
- Subpackages
- rdkit.DataManip package
- rdkit.DataStructs package
- Submodules
- rdkit.DataStructs.BitEnsemble module
- rdkit.DataStructs.BitEnsembleDb module
- rdkit.DataStructs.BitUtils module
- rdkit.DataStructs.LazySignature module
- rdkit.DataStructs.TopNContainer module
- rdkit.DataStructs.VectCollection module
VectCollectionVectCollection.AddVect()VectCollection.DetachVectsMatchingBit()VectCollection.DetachVectsNotMatchingBit()VectCollection.GetBit()VectCollection.GetChildren()VectCollection.GetNumBits()VectCollection.GetOnBits()VectCollection.GetOrVect()VectCollection.NumChildren()VectCollection.Reset()VectCollection.Uniquify()VectCollection.orVect
- rdkit.DataStructs.cDataStructs module
AllBitSimilarity()AllProbeBitsMatch()AsymmetricSimilarity()AsymmetricSimilarityNeighbors()AsymmetricSimilarityNeighbors_sparse()BitVectToBinaryText()BitVectToFPSText()BitVectToText()BraunBlanquetSimilarity()BraunBlanquetSimilarityNeighbors()BraunBlanquetSimilarityNeighbors_sparse()BulkAllBitSimilarity()BulkAsymmetricSimilarity()BulkBraunBlanquetSimilarity()BulkCosineSimilarity()BulkDiceSimilarity()BulkKulczynskiSimilarity()BulkMcConnaugheySimilarity()BulkOnBitSimilarity()BulkRogotGoldbergSimilarity()BulkRusselSimilarity()BulkSokalSimilarity()BulkTanimotoSimilarity()BulkTverskySimilarity()ComputeL1Norm()ConvertToExplicit()ConvertToNumpyArray()CosineSimilarity()CosineSimilarityNeighbors()CosineSimilarityNeighbors_sparse()CreateFromBinaryText()CreateFromBitString()CreateFromFPSText()DiceSimilarity()DiceSimilarityNeighbors()DiceSimilarityNeighbors_sparse()DiscreteValueTypeDiscreteValueVectExplicitBitVectExplicitBitVect.FromBase64()ExplicitBitVect.GetBit()ExplicitBitVect.GetNumBits()ExplicitBitVect.GetNumOffBits()ExplicitBitVect.GetNumOnBits()ExplicitBitVect.GetOnBits()ExplicitBitVect.SetBit()ExplicitBitVect.SetBitsFromList()ExplicitBitVect.ToBase64()ExplicitBitVect.ToBinary()ExplicitBitVect.ToBitString()ExplicitBitVect.ToList()ExplicitBitVect.UnSetBit()ExplicitBitVect.UnSetBitsFromList()
FPBReaderFoldFingerprint()InitFromDaylightString()IntSparseIntVectKulczynskiSimilarity()KulczynskiSimilarityNeighbors()KulczynskiSimilarityNeighbors_sparse()LongSparseIntVectMcConnaugheySimilarity()McConnaugheySimilarityNeighbors()McConnaugheySimilarityNeighbors_sparse()MultiFPBReaderNumBitsInCommon()OffBitProjSimilarity()OffBitsInCommon()OnBitProjSimilarity()OnBitSimilarity()OnBitsInCommon()RogotGoldbergSimilarity()RogotGoldbergSimilarityNeighbors()RogotGoldbergSimilarityNeighbors_sparse()RusselSimilarity()RusselSimilarityNeighbors()RusselSimilarityNeighbors_sparse()SokalSimilarity()SokalSimilarityNeighbors()SokalSimilarityNeighbors_sparse()SparseBitVectSparseBitVect.FromBase64()SparseBitVect.GetBit()SparseBitVect.GetNumBits()SparseBitVect.GetNumOffBits()SparseBitVect.GetNumOnBits()SparseBitVect.GetOnBits()SparseBitVect.SetBit()SparseBitVect.SetBitsFromList()SparseBitVect.ToBase64()SparseBitVect.ToBinary()SparseBitVect.ToBitString()SparseBitVect.ToList()SparseBitVect.UnSetBit()SparseBitVect.UnSetBitsFromList()
TanimotoSimilarity()TanimotoSimilarityNeighbors()TanimotoSimilarityNeighbors_sparse()TverskySimilarity()UIntSparseIntVectULongSparseIntVect
- Module contents
- Submodules
- rdkit.Dbase package
- Submodules
- rdkit.Dbase.DbConnection module
DbConnectDbConnect.AddColumn()DbConnect.AddTable()DbConnect.Commit()DbConnect.GetColumnNames()DbConnect.GetColumnNamesAndTypes()DbConnect.GetColumns()DbConnect.GetCursor()DbConnect.GetData()DbConnect.GetDataCount()DbConnect.GetTableNames()DbConnect.InsertColumnData()DbConnect.InsertData()DbConnect.KillCursor()
DbError
- rdkit.Dbase.DbInfo module
- rdkit.Dbase.DbModule module
- rdkit.Dbase.DbReport module
- rdkit.Dbase.DbResultSet module
- rdkit.Dbase.DbUtils module
- rdkit.Dbase.StorageUtils module
- rdkit.Dbase.DbConnection module
- Module contents
- Submodules
- rdkit.DistanceGeometry package
- rdkit.ForceField package
- rdkit.ForceField.rdForceField module
ForceFieldForceField.AddDistanceConstraint()ForceField.AddExtraPoint()ForceField.AddFixedPoint()ForceField.CalcEnergy()ForceField.CalcGrad()ForceField.Dimension()ForceField.GetExtraPointPos()ForceField.Initialize()ForceField.MMFFAddAngleConstraint()ForceField.MMFFAddDistanceConstraint()ForceField.MMFFAddPositionConstraint()ForceField.MMFFAddTorsionConstraint()ForceField.Minimize()ForceField.MinimizeTrajectory()ForceField.NumPoints()ForceField.Positions()ForceField.UFFAddAngleConstraint()ForceField.UFFAddDistanceConstraint()ForceField.UFFAddPositionConstraint()ForceField.UFFAddTorsionConstraint()
MMFFMolPropertiesMMFFMolProperties.GetMMFFAngleBendParams()MMFFMolProperties.GetMMFFAtomType()MMFFMolProperties.GetMMFFBondStretchParams()MMFFMolProperties.GetMMFFFormalCharge()MMFFMolProperties.GetMMFFOopBendParams()MMFFMolProperties.GetMMFFPartialCharge()MMFFMolProperties.GetMMFFStretchBendParams()MMFFMolProperties.GetMMFFTorsionParams()MMFFMolProperties.GetMMFFVdWParams()MMFFMolProperties.SetMMFFAngleTerm()MMFFMolProperties.SetMMFFBondTerm()MMFFMolProperties.SetMMFFDielectricConstant()MMFFMolProperties.SetMMFFDielectricModel()MMFFMolProperties.SetMMFFEleTerm()MMFFMolProperties.SetMMFFOopTerm()MMFFMolProperties.SetMMFFStretchBendTerm()MMFFMolProperties.SetMMFFTorsionTerm()MMFFMolProperties.SetMMFFVariant()MMFFMolProperties.SetMMFFVdWTerm()MMFFMolProperties.SetMMFFVerbosity()
- Module contents
- rdkit.ForceField.rdForceField module
- rdkit.Geometry package
- Submodules
- rdkit.Geometry.rdGeometry module
ComputeDihedralAngle()ComputeGridCentroid()ComputeSignedDihedralAngle()FindGridTerminalPoints()Point2DPoint3DPointNDProtrudeDistance()TanimotoDistance()TverskyIndex()UniformGrid3D()UniformGrid3D_UniformGrid3D_.CompareParams()UniformGrid3D_.GetGridIndex()UniformGrid3D_.GetGridIndices()UniformGrid3D_.GetGridPointIndex()UniformGrid3D_.GetGridPointLoc()UniformGrid3D_.GetNumX()UniformGrid3D_.GetNumY()UniformGrid3D_.GetNumZ()UniformGrid3D_.GetOccupancyVect()UniformGrid3D_.GetOffset()UniformGrid3D_.GetSize()UniformGrid3D_.GetSpacing()UniformGrid3D_.GetVal()UniformGrid3D_.GetValPoint()UniformGrid3D_.SetSphereOccupancy()UniformGrid3D_.SetVal()UniformGrid3D_.SetValPoint()
WriteGridToFile()
- rdkit.Geometry.rdGeometry module
- Module contents
- Submodules
- rdkit.ML package
- Subpackages
- rdkit.ML.Cluster package
- Submodules
- rdkit.ML.Cluster.Butina module
- rdkit.ML.Cluster.ClusterUtils module
- rdkit.ML.Cluster.ClusterVis module
- rdkit.ML.Cluster.Clusters module
ClusterCluster.AddChild()Cluster.AddChildren()Cluster.Compare()Cluster.FindSubtree()Cluster.GetChildren()Cluster.GetData()Cluster.GetIndex()Cluster.GetMetric()Cluster.GetName()Cluster.GetPoints()Cluster.GetPointsPositions()Cluster.GetPosition()Cluster.IsTerminal()Cluster.Print()Cluster.RemoveChild()Cluster.SetData()Cluster.SetIndex()Cluster.SetMetric()Cluster.SetName()Cluster.SetPosition()
cmp()
- rdkit.ML.Cluster.Murtagh module
- rdkit.ML.Cluster.Resemblance module
- rdkit.ML.Cluster.Standardize module
- rdkit.ML.Cluster.Clustering module
- Module contents
- Submodules
- rdkit.ML.Composite package
- rdkit.ML.Data package
- Submodules
- rdkit.ML.Data.DataUtils module
- rdkit.ML.Data.FindQuantBounds module
- rdkit.ML.Data.MLData module
MLDataSetMLDataSet.AddPoint()MLDataSet.AddPoints()MLDataSet.GetAllData()MLDataSet.GetInputData()MLDataSet.GetNPossibleVals()MLDataSet.GetNPts()MLDataSet.GetNResults()MLDataSet.GetNVars()MLDataSet.GetNamedData()MLDataSet.GetPtNames()MLDataSet.GetQuantBounds()MLDataSet.GetResults()MLDataSet.GetVarNames()
MLQuantDataSet
- rdkit.ML.Data.Quantize module
- rdkit.ML.Data.cQuantize module
- rdkit.ML.Data.SplitData module
- rdkit.ML.Data.Stats module
- rdkit.ML.Data.Transforms module
- Module contents
- Submodules
- rdkit.ML.DecTree package
- Submodules
- rdkit.ML.DecTree.BuildQuantTree module
- rdkit.ML.DecTree.BuildSigTree module
- rdkit.ML.DecTree.CrossValidate module
- rdkit.ML.DecTree.DecTree module
- rdkit.ML.DecTree.Forest module
- rdkit.ML.DecTree.ID3 module
- rdkit.ML.DecTree.PruneTree module
- rdkit.ML.DecTree.QuantTree module
- rdkit.ML.DecTree.SigTree module
- rdkit.ML.DecTree.Tree module
- rdkit.ML.DecTree.TreeUtils module
- rdkit.ML.DecTree.TreeVis module
- Module contents
- Submodules
- rdkit.ML.Descriptors package
- Submodules
- rdkit.ML.Descriptors.CompoundDescriptors module
CompoundDescriptorCalculatorCompoundDescriptorCalculator.BuildAtomDict()CompoundDescriptorCalculator.CalcCompoundDescriptorsForComposition()CompoundDescriptorCalculator.CalcDescriptors()CompoundDescriptorCalculator.CalcDescriptorsForComposition()CompoundDescriptorCalculator.CalcSimpleDescriptorsForComposition()CompoundDescriptorCalculator.DEV()CompoundDescriptorCalculator.GetDescriptorNames()CompoundDescriptorCalculator.MAX()CompoundDescriptorCalculator.MEAN()CompoundDescriptorCalculator.MIN()CompoundDescriptorCalculator.ProcessCompoundList()CompoundDescriptorCalculator.ProcessSimpleList()CompoundDescriptorCalculator.SUM()
GetAllDescriptorNames()
- rdkit.ML.Descriptors.Descriptors module
- rdkit.ML.Descriptors.MoleculeDescriptors module
MolecularDescriptorCalculatorMolecularDescriptorCalculator.CalcDescriptors()MolecularDescriptorCalculator.GetDescriptorFuncs()MolecularDescriptorCalculator.GetDescriptorNames()MolecularDescriptorCalculator.GetDescriptorSummaries()MolecularDescriptorCalculator.GetDescriptorVersions()MolecularDescriptorCalculator.SaveState()
- rdkit.ML.Descriptors.Parser module
- rdkit.ML.Descriptors.CompoundDescriptors module
- Module contents
- Submodules
- rdkit.ML.InfoTheory package
- rdkit.ML.KNN package
- rdkit.ML.MLUtils package
- rdkit.ML.ModelPackage package
- rdkit.ML.NaiveBayes package
- rdkit.ML.Neural package
- rdkit.ML.SLT package
- rdkit.ML.Scoring package
- rdkit.ML.Cluster package
- Submodules
- Module contents
- Subpackages
- rdkit.Numerics package
- rdkit.SimDivFilters package
- rdkit.VLib package
- Subpackages
- rdkit.VLib.NodeLib package
- Submodules
- rdkit.VLib.NodeLib.DbMolSupply module
- rdkit.VLib.NodeLib.DbPickleSupplier module
- rdkit.VLib.NodeLib.SDSupply module
- rdkit.VLib.NodeLib.SmartsMolFilter module
- rdkit.VLib.NodeLib.SmartsRemover module
- rdkit.VLib.NodeLib.SmilesDupeFilter module
- rdkit.VLib.NodeLib.SmilesOutput module
- rdkit.VLib.NodeLib.SmilesSupply module
- Module contents
- Submodules
- rdkit.VLib.NodeLib package
- Submodules
- Module contents
- Subpackages
- rdkit.utils package
Submodules¶
- rdkit.rdBase module
AttachFileToLog()BlockLogsDisableLog()EnableLog()LogDebugMsg()LogErrorMsg()LogInfoMsg()LogMessage()LogStatus()LogToCppStreams()LogToPythonLogger()LogToPythonStderr()LogWarningMsg()MatchTypeVectSeedRandomNumberGenerator()UnsignedLong_VectVectorOfStringVectorsWrapLogs()ostreamstd_ostreamstreambuf
- rdkit.RDConfig module
- rdkit.RDLogger module
- rdkit.RDPaths module
- rdkit.RDRandom module
- rdkit.TestRunner module
- rdkit.six module
Module contents¶
- class rdkit.VectIter(vect)¶
Bases:
object
