Everything

All Classes

Chem.rdchem._ROAtomSeq

Chem.rdchem._ROBondSeq

Chem.rdchem._listPN5RDKit4AtomE

Chem.rdchem._listPN5RDKit4BondE

Chem.rdfragcatalog.FragCatGenerator
Chem.rdfragcatalog.FragCatParams
Chem.rdfragcatalog.FragCatalog
Chem.rdfragcatalog.FragFPGenerator
Chem.rdmolfiles.SDMolSupplier
Chem.rdmolfiles.SDWriter
Chem.rdmolfiles.SmilesMolSupplier
Chem.rdmolfiles.SmilesWriter
Chem.rdmolfiles.TDTMolSupplier
Chem.rdmolfiles.TDTWriter
DataStructs.BitEnsemble.BitEnsemble
DataStructs.BitVect.BitVect
DataStructs.BitVect.SparseBitVect
DataStructs.HierarchyVis.VisOpts
DataStructs.LazySignature.LazySig
DataStructs.SparseIntVect.pySparseIntVect
DataStructs.TopNContainer.TopNContainer
DataStructs.VectCollection.VectCollection
DataStructs.cDataStructs.DiscreteValueType
DataStructs.cDataStructs.DiscreteValueVect
DataStructs.cDataStructs.ExplicitBitVect
DataStructs.cDataStructs.IntSparseIntVect
DataStructs.cDataStructs.LongSparseIntVect
DataStructs.cDataStructs.SparseBitVect
DataStructs.cDataStructs.UIntSparseIntVect
DataStructs.cDataStructs.ULongSparseIntVect
Dbase.DbConnection.DbConnect
Dbase.DbConnection.DbError
Dbase.DbReport.CDXImageTransformer
Dbase.DbReport.CactvsImageTransformer
Dbase.DbReport.RDImageTransformer
Dbase.DbReport.ReportLabImageTransformer
Dbase.DbResultSet.DbResultBase
Dbase.DbResultSet.DbResultSet
Dbase.DbResultSet.RandomAccessDbResultSet
Dbase.Pubmed.Records.JournalArticleRecord
Dbase.Pubmed.Records.LinkRecord
Dbase.Pubmed.Records.Record
Dbase.Pubmed.Records.SummaryRecord
ForceField.rdForceField.ForceField
Geometry.rdGeometry.Point2D
Geometry.rdGeometry.Point3D
Geometry.rdGeometry.PointND
Geometry.rdGeometry.UniformGrid3D_
Logger.Logger.Callable
Logger.Logger.Logger
Logger.demo.Foo
ML.Cluster.ClusterVis.ClusterRenderer
ML.Cluster.ClusterVis.VisOpts
ML.Cluster.Clusters.Cluster
ML.Composite.BayesComposite.BayesComposite
ML.Composite.Composite.Composite
ML.Composite.CompositeCOM.CompositeServer
ML.CompositeRun.CompositeRun
ML.Data.MLData.MLDataSet
ML.Data.MLData.MLQuantDataSet
ML.DecTree.DecTree.DecTreeNode
ML.DecTree.Forest.Forest
ML.DecTree.QuantTree.QuantTreeNode
ML.DecTree.SigTree.SigTreeNode
ML.DecTree.Tree.TreeNode
ML.DecTree.TreeVis.VisOpts
ML.Descriptors.CompoundDescriptors.CompoundDescriptorCalculator
ML.Descriptors.Descriptors.DescriptorCalculator
ML.Descriptors.DescriptorsCOM.DescriptorServer
ML.Descriptors.MoleculeDescriptors.MolecularDescriptorCalculator
ML.InfoTheory.BitClusterer.BitClusterer
ML.InfoTheory.rdInfoTheory.BitCorrMatGenerator
ML.InfoTheory.rdInfoTheory.InfoBitRanker
ML.InfoTheory.rdInfoTheory.InfoType
ML.KNN.KNNClassificationModel.KNNClassificationModel
ML.KNN.KNNModel.KNNModel
ML.KNN.KNNRegressionModel.KNNRegressionModel
ML.ModelPackage.Packager.ClassificationError
ML.ModelPackage.Packager.DescriptorCalculationError
ML.ModelPackage.Packager.ModelPackage
ML.NaiveBayes.ClassificationModel.NaiveBayesClassifier
ML.Neural.ActFuncs.ActFunc
ML.Neural.ActFuncs.Sigmoid
ML.Neural.ActFuncs.TanH
ML.Neural.NetNode.NetNode
ML.Neural.Network.Network
ML.Neural.Trainers.BackProp
ML.Neural.Trainers.Trainer
ML.files.ReFile
PySVD.SVDSimilarity.SimilarityCalculator
RDConfig.ObsoleteCodeError
RDConfig.UnimplementedCodeError
RDLogger.logger
SimDivFilters.SimilarityPickers.GenericPicker
SimDivFilters.SimilarityPickers.SpreadPicker
SimDivFilters.SimilarityPickers.TopNOverallPicker
SimDivFilters.rdSimDivPickers.ClusterMethod
SimDivFilters.rdSimDivPickers.HierarchicalClusterPicker
SimDivFilters.rdSimDivPickers.MaxMinPicker
VLib.Filter.FilterNode

VLib.Node.VLibNode

VLib.NodeLib.DbMolSupply.DbMolSupplyNode

VLib.NodeLib.DbPickleSupplier.DbPickleSupplyNode

VLib.NodeLib.DbPickleSupplier._lazyDataSeq

VLib.NodeLib.SDSupply.SDSupplyNode

VLib.NodeLib.SmartsMolFilter.SmartsFilter

VLib.NodeLib.SmartsRemover.SmartsRemover

VLib.NodeLib.SmilesDupeFilter.DupeFilter

VLib.NodeLib.SmilesOutput.OutputNode

VLib.NodeLib.SmilesSupply.SmilesSupplyNode

VLib.Output.OutputNode

VLib.Supply.SupplyNode

VLib.Transform.TransformNode
exceptions.AssertionError

rdBase._listSt6vectorIiSaIiEE

rdBase._listi

rdBase._vectSs

rdBase._vectSt6vectorIdSaIdEE

rdBase._vectSt6vectorIiSaIiEE

rdBase._vectSt6vectorIjSaIjEE

rdBase._vectd

rdBase._vecti

rdBase._vectj

re.Scanner
sre_constants.error

All Functions

Chem.AllChem.AlignMol
Chem.AllChem.AlignMolConformers
Chem.AllChem.CanonicalizeConformer
Chem.AllChem.CanonicalizeMol
Chem.AllChem.Compute2DCoords
Chem.AllChem.Compute2DCoordsMimicDistmat
Chem.AllChem.ComputeCanonicalTransform
Chem.AllChem.ComputeCentroid
Chem.AllChem.ComputeMolShape
Chem.AllChem.ComputeMolVolume
Chem.AllChem.ConstrainedEmbed
Chem.AllChem.EnumerateLibraryFromReaction
Chem.AllChem.GenerateDepictionMatching3DStructure
Chem.AllChem.GetAlignmentTransform
Chem.AllChem.GetBestRMS
Chem.AllChem.TransformConformer
Chem.AllChem.TransformMol

Chem.AllChem._test

Chem.AssignAtomChiralTagsFromStructure
Chem.AtomPairs.Pairs.ExplainPairScore
Chem.AtomPairs.Pairs.GetAtomPairFingerprintAsBitVect

Chem.AtomPairs.Pairs._test

Chem.AtomPairs.Pairs.pyScorePair
Chem.AtomPairs.Torsions.ExplainPathScore
Chem.AtomPairs.Torsions.GetTopologicalTorsionFingerprintAsIds

Chem.AtomPairs.Torsions._test

Chem.AtomPairs.Torsions.pyScorePath
Chem.AtomPairs.Utils.BitsInCommon
Chem.AtomPairs.Utils.CosineSimilarity
Chem.AtomPairs.Utils.DiceSimilarity
Chem.AtomPairs.Utils.Dot
Chem.AtomPairs.Utils.ExplainAtomCode
Chem.AtomPairs.Utils.NumPiElectrons

Chem.AtomPairs.Utils._test

Chem.ChemUtils.TemplateExpand._exploder

Chem.ChemicalFeatures.MCFF_GetFeaturesForMol
Chem.ChemicalForceFields.UFFGetMoleculeForceField
Chem.ChemicalForceFields.UFFOptimizeMolecule
Chem.Crippen.MolLogP
Chem.Crippen.MolMR

Chem.Crippen._Init

Chem.Crippen._ReadPatts

Chem.Crippen._pyGetAtomContribs

Chem.Crippen.pyMolLogP
Chem.Crippen.pyMolMR
Chem.DaylightFingerprint
Chem.Descriptors.HeavyAtomMolWt
Chem.Descriptors.MolWt
Chem.Descriptors.NumValenceElectrons

Chem.Descriptors._test

Chem.Descriptors.pyMolWt
Chem.DisplaySmartsMatch
Chem.Draw.DrawUtils.Init
Chem.Draw.DrawUtils.MolsToJpeg
Chem.Draw.DrawUtils.SmilesToJpeg
Chem.Draw.MolDrawing.registerCanvas
Chem.Draw.MolToImage
Chem.Draw.MolToImageFile
Chem.Draw.ShowMol

Chem.Draw.aggCanvas._doLine

Chem.Draw.aggCanvas._getLinePoints

Chem.Draw.aggCanvas.addCanvasDashedWedge
Chem.Draw.aggCanvas.addCanvasLine
Chem.Draw.aggCanvas.addCanvasPolygon
Chem.Draw.aggCanvas.addCanvasText
Chem.Draw.aggCanvas.convertColor
Chem.Draw.mplCanvas.addCanvasLine
Chem.Draw.mplCanvas.addCanvasPolygon
Chem.Draw.mplCanvas.addCanvasText

Chem.Draw.spingCanvas._getLinePoints

Chem.EState.EState_VSA._InstallDescriptors

Chem.EState.Fingerprinter.FingerprintMol
Chem.FeatFinderCLI.GetAtomFeatInfo

Chem.FeatMaps.FeatMapParser._test

Chem.FeatMaps.FeatMapPoint._test

Chem.FeatMaps.FeatMapUtils.CombineFeatMaps
Chem.FeatMaps.FeatMapUtils.GetFeatFeatDistMatrix
Chem.FeatMaps.FeatMapUtils.MergeFeatPoints

Chem.FeatMaps.FeatMapUtils.__copyAll

Chem.FeatMaps.FeatMapUtils._test

Chem.FeatMaps.FeatMapUtils.familiesMatch
Chem.FeatMaps.FeatMapUtils.feq

Chem.FeatMaps.FeatMaps._test

Chem.Features.FeatDirUtils.ArbAxisRotation
Chem.Features.FeatDirUtils.GetAcceptor1FeatVects
Chem.Features.FeatDirUtils.GetAcceptor2FeatVects
Chem.Features.FeatDirUtils.GetAromaticFeatVects
Chem.Features.FeatDirUtils.GetDonor1FeatVects
Chem.Features.FeatDirUtils.GetDonor2FeatVects
Chem.Features.FeatDirUtils.GetDonor3FeatVects

Chem.Features.FeatDirUtils._checkPlanarity

Chem.Features.FeatDirUtils._findAvgVec

Chem.Features.FeatDirUtils._findHydAtoms

Chem.Features.FeatDirUtils.cross
Chem.Features.FeatDirUtils.findNeighbors
Chem.Features.FeatDirUtilsRD.ArbAxisRotation
Chem.Features.FeatDirUtilsRD.GetAcceptor1FeatVects
Chem.Features.FeatDirUtilsRD.GetAcceptor2FeatVects
Chem.Features.FeatDirUtilsRD.GetAcceptor3FeatVects
Chem.Features.FeatDirUtilsRD.GetAromaticFeatVects
Chem.Features.FeatDirUtilsRD.GetDonor1FeatVects
Chem.Features.FeatDirUtilsRD.GetDonor2FeatVects
Chem.Features.FeatDirUtilsRD.GetDonor3FeatVects

Chem.Features.FeatDirUtilsRD._GetTetrahedralFeatVect

Chem.Features.FeatDirUtilsRD._checkPlanarity

Chem.Features.FeatDirUtilsRD._findAvgVec

Chem.Features.FeatDirUtilsRD._findHydAtoms

Chem.Features.FeatDirUtilsRD.cross
Chem.Features.FeatDirUtilsRD.findNeighbors
Chem.Features.ShowFeats.ShowArrow
Chem.Features.ShowFeats.ShowMolFeats

Chem.Features.ShowFeats._buildCanonArrowhead

Chem.Features.ShowFeats._cgoArrowhead

Chem.Features.ShowFeats._getVectNormal

Chem.FindMolChiralCenters
Chem.Fingerprints.ClusterMols.ClusterFromDetails
Chem.Fingerprints.ClusterMols.ClusterPoints
Chem.Fingerprints.ClusterMols.GetDistanceMatrix

Chem.Fingerprints.DbFpSupplier._test

Chem.Fingerprints.MolSimilarity._ConstructSQL

Chem.FragmentCatalog.BuildAdjacencyList
Chem.FragmentCatalog.GetMolsMatchingBit
Chem.FragmentCatalog.ProcessGainsFile
Chem.FragmentCatalog.ShowMolsMatchingBit
Chem.FragmentCatalog.message

Chem.FragmentMatcher._test

Chem.Fragments._CountMatches

Chem.Fragments._LoadPatterns

Chem.GraphDescriptors._AssignSymmetryClasses

Chem.GraphDescriptors._CalculateEntropies

Chem.GraphDescriptors._CreateBondDictEtc

Chem.GraphDescriptors._GetCountDict

Chem.GraphDescriptors._LookUpBondOrder

Chem.GraphDescriptors._NumAdjacencies

Chem.GraphDescriptors._VertexDegrees

Chem.GraphDescriptors._hkDeltas

Chem.GraphDescriptors._log2

Chem.GraphDescriptors._nVal

Chem.Graphs.CharacteristicPolynomial
Chem.Lipinski.HeavyAtomCount
Chem.Lipinski.NHOHCount
Chem.Lipinski.NOCount
Chem.Lipinski.NumHAcceptors
Chem.Lipinski.NumHDonors
Chem.Lipinski.NumHeteroatoms
Chem.Lipinski.NumRotatableBonds
Chem.Lipinski.RingCount

Chem.Lipinski._HAcceptors

Chem.Lipinski._HDonors

Chem.Lipinski._Heteroatoms

Chem.Lipinski._NumMatches

Chem.Lipinski._RotatableBonds

Chem.MACCSkeys.GenMACCSKeys

Chem.MACCSkeys._InitKeys

Chem.MACCSkeys._test

Chem.MolSurf._InstallDescriptors

Chem.MolSurf._LabuteHelper

Chem.MolSurf._TPSAContribs

Chem.MolSurf._pyLabuteHelper

Chem.MolSurf.pyLabuteASA
Chem.MolToMolBlock
Chem.MolToSmarts
Chem.MolToTPLFile
Chem.Pharm2D.Generate.Gen2DFingerprint

Chem.Pharm2D.Generate._ShortestPathsMatch

Chem.Pharm2D.Gobbi_Pharm2D._init

Chem.Pharm2D.Matcher.GetAtomsMatchingBit
Chem.Pharm2D.Utils.BinsTriangleInequality
Chem.Pharm2D.Utils.CountUpTo
Chem.Pharm2D.Utils.GetAllCombinations
Chem.Pharm2D.Utils.GetIndexCombinations
Chem.Pharm2D.Utils.GetPossibleScaffolds
Chem.Pharm2D.Utils.GetTriangles
Chem.Pharm2D.Utils.NumCombinations
Chem.Pharm2D.Utils.ScaffoldPasses
Chem.Pharm2D.Utils.UniquifyCombinations

Chem.Pharm2D.Utils._fact

Chem.Pharm3D.EmbedLib._checkMatch

Chem.Pharm3D.EmbedLib._getFeatDict

Chem.Pharm3D.EmbedLib._test

Chem.Subshape.SubshapeAligner._getAllTriangles

Chem.Subshape.SubshapeObjects.DisplaySubshape
Chem.Subshape.SubshapeObjects.DisplaySubshapeSkeleton

Chem.Subshape.SubshapeObjects._displaySubshapeSkelPt

Chem.SupplierFromFilename
Chem.Suppliers.DbMolSupplier.warning
Chem.TemplateAlign.AlignMolToTemplate2D

Chem.TemplateAlign._test

Chem.WedgeMolBonds
Chem.rdChemReactions.ReactionFromRxnBlock
Chem.rdChemReactions.ReactionFromRxnFile
Chem.rdChemReactions.ReactionFromSmarts
Chem.rdDistGeom.EmbedMolecule
Chem.rdDistGeom.EmbedMultipleConfs
Chem.rdDistGeom.GetMoleculeBoundsMatrix
Chem.rdMolCatalog.CreateMolCatalog
Chem.rdMolChemicalFeatures.BuildFeatureFactory
Chem.rdMolChemicalFeatures.BuildFeatureFactoryFromString
Chem.rdMolChemicalFeatures.GetAtomMatch
Chem.rdMolDescriptors.CalcCrippenDescriptors
Chem.rdMolDescriptors.CalcLabuteASA
Chem.rdMolDescriptors.GetAtomPairAtomCode
Chem.rdMolDescriptors.GetAtomPairFingerprint
Chem.rdMolDescriptors.GetTopologicalTorsionFingerprint

Chem.rdMolDescriptors._CalcCrippenContribs

Chem.rdMolDescriptors._CalcLabuteASAContribs

Chem.rdMolDescriptors._CalcMolWt

Chem.rdPartialCharges.ComputeGasteigerCharges
Chem.rdShapeHelpers.ComputeConfBox
Chem.rdShapeHelpers.ComputeConfDimsAndOffset
Chem.rdShapeHelpers.ComputeUnionBox
Chem.rdShapeHelpers.EncodeShape
Chem.rdShapeHelpers.ShapeProtrudeDist
Chem.rdShapeHelpers.ShapeTanimotoDist

Chem.rdchem._HasSubstructMatchStr

Chem.rdmolfiles.MolFromMolBlock
Chem.rdmolfiles.MolFromTPLFile
Chem.rdmolfiles.MolToSmiles
Chem.rdmolfiles.MolToTPLBlock
Chem.rdmolfiles.SmilesMolSupplierFromText
Chem.rdmolops.AddHs
Chem.rdmolops.AssignAtomChiralCodes
Chem.rdmolops.AssignBondStereoCodes
Chem.rdmolops.DeleteSubstructs
Chem.rdmolops.FindAllPathsOfLengthN
Chem.rdmolops.FindAllSubgraphsOfLengthN
Chem.rdmolops.FindUniqueSubgraphsOfLengthN
Chem.rdmolops.GetAdjacencyMatrix
Chem.rdmolops.GetDistanceMatrix
Chem.rdmolops.GetFormalCharge
Chem.rdmolops.GetMolFrags
Chem.rdmolops.GetSymmSSSR
Chem.rdmolops.Kekulize
Chem.rdmolops.RDKFingerprint
Chem.rdmolops.RemoveHs
Chem.rdmolops.ReplaceCore
Chem.rdmolops.ReplaceSidechains
Chem.tossit
DataManip.Metric.rdMetricMatrixCalc.GetEuclideanDistMat
DataManip.Metric.rdMetricMatrixCalc.GetTanimotoDistMat
DataManip.Metric.rdMetricMatrixCalc.GetTanimotoSimMat
DataStructs.AllBitSimilarity

DataStructs.BitEnsembleDb._InitScoreTable

DataStructs.BitEnsembleDb._ScoreToDb

DataStructs.BitUtils.ConstructEnsembleBV

DataStructs.BitUtils._test

DataStructs.BulkAsymmetricSimilarity
DataStructs.BulkCosineSimilarity
DataStructs.BulkSokalSimilarity
DataStructs.ComputeL1Norm
DataStructs.ConvertToExplicit
DataStructs.CosineSimilarity
DataStructs.CreateFromBitString
DataStructs.FingerprintSimilarity
DataStructs.FoldToTargetDensity
DataStructs.HierarchyVis.DrawHierarchy
DataStructs.HierarchyVis.GetMinCanvasSize
DataStructs.InitFromDaylightString
DataStructs.KulczynskiSimilarity

DataStructs.LazySignature._test

DataStructs.SparseIntVect.DotProduct

DataStructs.SparseIntVect._test

DataStructs.SparseIntVect.pyDiceSimilarity
DataStructs.TanimotoSimilarity
DataStructs.TverskySimilarity

DataStructs.VectCollection._test

Dbase.DbUtils._AddDataToDb

Dbase.DbUtils._AdjustColHeadings

Dbase.DbUtils._insertBlock

Dbase.DbUtils._take

Dbase.Pubmed.PubmedUtils.FillParagraph
Dbase.Pubmed.PubmedUtils.GetSearchURL
Dbase.Pubmed.PubmedUtils.RecordsToPubmedText

Dbase.Pubmed.PubmedUtils._test

Dbase.Pubmed.QueryParams.details
Dbase.Pubmed.Searches.CheckForLinks
Dbase.Pubmed.Searches.GetLinks
Dbase.Pubmed.Searches.GetNumHits
Dbase.Pubmed.Searches.GetRecords
Dbase.Pubmed.Searches.GetSearchIds
Dbase.Pubmed.Searches.GetSummaries

Dbase.Pubmed.Searches._test

Dbase.Pubmed.Searches.openURL
Dbase.StorageUtils.GetNextId
Dbase.StorageUtils.GetNextRDId
Dbase.StorageUtils.IndexToRDId
Dbase.StorageUtils.RDIdToInt
Dbase.StorageUtils.RegisterItem
Dbase.StorageUtils.RegisterItems
Dbase.StorageUtils.ValidateRDId

Dbase.StorageUtils._test

DistanceGeometry.DistGeom.DoTriangleSmoothing
DistanceGeometry.DistGeom.EmbedBoundsMatrix
Geometry.rdGeometry.ComputeGridCentroid
Geometry.rdGeometry.FindGridTerminalPoints
Geometry.rdGeometry.ProtrudeDistance
Geometry.rdGeometry.TanimotoDistance
Geometry.rdGeometry.UniformGrid3D
Geometry.rdGeometry.WriteGridToFile
Logger.Logger.isPresent
Logger.Logger.replay
Logger.demo.demo1
Logger.demo.demo2
ML.AnalyzeComposite.ErrorStats
ML.AnalyzeComposite.ProcessIt
ML.AnalyzeComposite.ShowStats
ML.AnalyzeComposite.Usage
ML.BuildComposite.GetCommandLine
ML.BuildComposite.ParseArgs
ML.BuildComposite.RunIt
ML.BuildComposite.RunOnData
ML.BuildComposite.SetDefaults
ML.BuildComposite.ShowVersion
ML.BuildComposite.Usage
ML.BuildComposite.message
ML.BuildComposite.testall
ML.Cluster.Butina.ClusterData
ML.Cluster.ClusterUtils.FindClusterCentroidFromDists
ML.Cluster.ClusterUtils.GetNodeList
ML.Cluster.ClusterUtils.GetNodesDownToCentroids
ML.Cluster.ClusterUtils.SplitIntoNClusters

ML.Cluster.ClusterUtils._BreadthFirstSplit

ML.Cluster.ClusterUtils._HeightFirstSplit

ML.Cluster.ClusterUtils._sortHelper

ML.Cluster.ClusterVis.ClusterToImg
ML.Cluster.ClusterVis.ClusterToPDF
ML.Cluster.ClusterVis.ClusterToSVG
ML.Cluster.ClusterVis.DrawClusterTree

ML.Cluster.ClusterVis._DrawClusterTree

ML.Cluster.ClusterVis._scaleMetric

ML.Cluster.Clustering.MurtaghCluster
ML.Cluster.Clustering.MurtaghDistCluster
ML.Cluster.Murtagh.ClusterData

ML.Cluster.Murtagh._LookupDist

ML.Cluster.Murtagh._ToClusters

ML.Cluster.Resemblance.CalcMetricMatrix
ML.Cluster.Resemblance.EuclideanDistance
ML.Cluster.Resemblance.FindMinValInList
ML.Cluster.Resemblance.ShowMetricMat
ML.Cluster.Standardize.StdDev
ML.Composite.AdjustComposite.BalanceComposite
ML.Composite.BayesComposite.BayesCompositeToComposite
ML.Composite.BayesComposite.CompositeToBayesComposite
ML.CompositeRun.SetDefaults
ML.Data.DataUtils.BuildDataSet
ML.Data.DataUtils.BuildQuantDataSet
ML.Data.DataUtils.CalcNPossibleUsingMap
ML.Data.DataUtils.CountResults
ML.Data.DataUtils.DBToData
ML.Data.DataUtils.DBToQuantData
ML.Data.DataUtils.FilterData
ML.Data.DataUtils.InitRandomNumbers
ML.Data.DataUtils.QuantDataToDB
ML.Data.DataUtils.RandomizeActivities
ML.Data.DataUtils.ReadGeneralExamples
ML.Data.DataUtils.ReadQuantExamples
ML.Data.DataUtils.ReadVars
ML.Data.DataUtils.TakeEnsemble
ML.Data.DataUtils.TextFileToData
ML.Data.DataUtils.TextToData
ML.Data.DataUtils.WriteData
ML.Data.DataUtils.WritePickledData

ML.Data.DataUtils._test

ML.Data.DataUtils.permutation
ML.Data.FindQuantBounds.Usage
ML.Data.FindQuantBounds.runIt
ML.Data.Quantize.FindVarMultQuantBounds
ML.Data.Quantize.FindVarQuantBound

ML.Data.Quantize._GenVarTable

ML.Data.Quantize._NewPyFindStartPoints

ML.Data.Quantize._NewPyRecurseOnBounds

ML.Data.Quantize._PyRecurseOnBounds

ML.Data.Quantize.feq
ML.Data.SplitData.SplitDataSet
ML.Data.SplitData.SplitDbData
ML.Data.SplitData.SplitIndices

ML.Data.SplitData._test

ML.Data.Stats.FormCorrelationMatrix
ML.Data.Stats.FormCovarianceMatrix
ML.Data.Stats.GetConfidenceInterval
ML.Data.Stats.MeanAndDev
ML.Data.Stats.PrincipalComponents
ML.Data.Stats.R2
ML.Data.Stats.StandardizeMatrix
ML.Data.Stats.TransformPoints
ML.Data.Transforms.GetAvailTransforms

ML.Data.Transforms._CenterTForm

ML.Data.Transforms._NormalizeTForm

ML.Data.Transforms._StandardTForm

ML.DecTree.BuildQuantTree.BuildQuantTree
ML.DecTree.BuildQuantTree.FindBest
ML.DecTree.BuildQuantTree.QuantTreeBoot
ML.DecTree.BuildQuantTree.TestQuantTree
ML.DecTree.BuildQuantTree.TestQuantTree2
ML.DecTree.BuildQuantTree.TestTree
ML.DecTree.BuildSigTree.BuildSigTree
ML.DecTree.BuildSigTree.SigTreeBuilder

ML.DecTree.BuildSigTree._GenerateRandomEnsemble

ML.DecTree.CrossValidate.ChooseOptimalRoot
ML.DecTree.CrossValidate.CrossValidate
ML.DecTree.CrossValidate.CrossValidationDriver
ML.DecTree.CrossValidate.TestRun
ML.DecTree.ID3.CalcTotalEntropy
ML.DecTree.ID3.GenVarTable
ML.DecTree.ID3.ID3
ML.DecTree.ID3.ID3Boot
ML.DecTree.PruneTree.MaxCount
ML.DecTree.PruneTree.PruneTree

ML.DecTree.PruneTree._GetLocalError

ML.DecTree.PruneTree._Pruner

ML.DecTree.PruneTree._testChain

ML.DecTree.PruneTree._testRandom

ML.DecTree.PruneTree._testSpecific

ML.DecTree.TreeUtils.CollectDescriptorNames
ML.DecTree.TreeUtils.CollectLabelLevels

ML.DecTree.TreeUtils._test

ML.DecTree.TreeVis.CalcTreeNodeSizes
ML.DecTree.TreeVis.CalcTreeWidth
ML.DecTree.TreeVis.DrawTree
ML.DecTree.TreeVis.DrawTreeNode
ML.DecTree.TreeVis.ResetTree
ML.DecTree.TreeVis.SetNodeScales

ML.DecTree.TreeVis._ApplyNodeScales

ML.DecTree.TreeVis._ExampleCounter

ML.DecTree.TreeVis._simpleTest

ML.Descriptors.CompoundDescriptors.GetAllDescriptorNames
ML.Descriptors.Parser.CalcMultipleCompoundsDescriptor
ML.Descriptors.Parser.CalcSingleCompoundDescriptor
ML.Descriptors.Parser.DEV
ML.Descriptors.Parser.HAS
ML.Descriptors.Parser.MAX
ML.Descriptors.Parser.MEAN
ML.Descriptors.Parser.MIN
ML.Descriptors.Parser.SUM

ML.Descriptors.Parser._SubForAtomicVars

ML.Descriptors.Parser._SubForCompoundDescriptors

ML.Descriptors.Parser._SubMethodArgs

ML.EnrichPlot.AccumulateCounts
ML.EnrichPlot.MakePlot
ML.EnrichPlot.ScreenModel
ML.EnrichPlot.Usage
ML.EnrichPlot.error
ML.EnrichPlot.message
ML.FeatureSelect.CMIM.SelectFeatures

ML.FeatureSelect.CMIM._SelectFeatures

ML.FeatureSelect.rdFeatSelect.selectCMIM
ML.GrowComposite.BalanceComposite
ML.GrowComposite.GetComposites
ML.GrowComposite.GrowIt
ML.GrowComposite.ParseArgs
ML.GrowComposite.SetDefaults
ML.GrowComposite.ShowVersion
ML.GrowComposite.Usage
ML.GrowComposite.message
ML.InfoTheory.BitRank.AnalyzeSparseVects
ML.InfoTheory.BitRank.CalcInfoGains
ML.InfoTheory.BitRank.FormCounts
ML.InfoTheory.BitRank.RankBits
ML.InfoTheory.BitRank.SparseRankBits
ML.InfoTheory.entropy.PyInfoEntropy
ML.InfoTheory.entropy.PyInfoEntropy
ML.InfoTheory.entropy.PyInfoGain
ML.InfoTheory.rdInfoTheory.ChiSquare
ML.InfoTheory.rdInfoTheory.InfoGain
ML.KNN.CrossValidate.CrossValidate
ML.KNN.CrossValidate.CrossValidationDriver
ML.KNN.CrossValidate.makeClassificationModel
ML.KNN.CrossValidate.makeRegressionModel
ML.KNN.DistFunctions.EuclideanDist
ML.KNN.DistFunctions.TanimotoDist

ML.KNN.DistFunctions._test

ML.MLUtils.VoteImg.BuildVoteImage
ML.MLUtils.VoteImg.CollectVotes
ML.MLUtils.VoteImg.Usage
ML.MLUtils.VoteImg.VoteAndBuildImage
ML.ModelPackage.PackageUtils.PackageToXml

ML.ModelPackage.PackageUtils._ConvertModelPerformance

ML.NaiveBayes.ClassificationModel._getBinId

ML.ScreenComposite._processVoteList

ML.ScreenComposite.error
ML.ScreenComposite.message
ML.files.ReadDataFile
Numerics.rdAlignment.GetAlignmentTransform
PySVD.SVDPack.DoSVD
PySVD.SVDPack.HBFOut
PySVD.SVDPack.ReadSVDPackArrays
PySVD.SVDPack.ReadSVDPackOutputFile

PySVD.SVDSimilarity._test

PySVD.SVDSimilarity.showMat
RDRandom.seed

SimDivFilters.SimilarityPickers._test

VLib.Filter._test

VLib.Node._test

VLib.NodeLib.DbMolSupply.GetNode

VLib.NodeLib.DbMolSupply._test

VLib.NodeLib.DbPickleSupplier.GetNode

VLib.NodeLib.DbPickleSupplier._test

VLib.NodeLib.SDSupply._test

VLib.NodeLib.SmartsMolFilter._test

VLib.NodeLib.SmartsRemover._test

VLib.NodeLib.SmilesDupeFilter._test

VLib.NodeLib.SmilesOutput._test

VLib.NodeLib.SmilesSupply._test

VLib.Output._test

VLib.Supply._test

VLib.Transform._test

rdBase.AttachFileToLog
rdBase.DisableLog
rdBase.EnableLog
rdBase.LogMessage

rdBase._version

All Variables

Chem.AtomPairs.Pairs._maxPathLen

Chem.AtomPairs.Pairs.fpLen
Chem.AtomPairs.Pairs.numFpBits
Chem.AtomPairs.Pairs.numPathBits
Chem.AvailDescriptors.descDict
Chem.AvailDescriptors.descList
Chem.AvailDescriptors.mods
Chem.AvailDescriptors.name
Chem.AvailDescriptors.otherMods
Chem.AvailDescriptors.others
Chem.AvailDescriptors.tmp

Chem.BuildFragmentCatalog.__VERSION_STRING

Chem.BuildFragmentCatalog._cvsVersion

Chem.BuildFragmentCatalog.idx1
Chem.BuildFragmentCatalog.idx2

Chem.CDXMLWriter._fontsStartId

Chem.CDXMLWriter.header

Chem.ChemUtils.TemplateExpand._greet

Chem.ChemUtils.TemplateExpand._usage

Chem.ChemUtils.TemplateExpand._version

Chem.ChemUtils.TemplateExpand.logger
Chem.ChemUtils.TemplateExpand.nDumped

Chem.Crippen._patternOrder

Chem.Crippen._smartsPatterns

Chem.Crippen.defaultPatternFileName

Chem.DSViewer._nextDisplayId

Chem.Draw.DrawUtils._batikJar

Chem.Draw.DrawUtils._batikLoc

Chem.Draw.DrawUtils._javaExe

Chem.Draw.MolDrawing.elemDict
Chem.Draw.aggCanvas.faceMap
Chem.Draw.spingCanvas.faceMap
Chem.Draw.tkLabel
Chem.Draw.tkPI
Chem.Draw.tkRoot

Chem.EState.AtomTypes._rawD

Chem.EState.AtomTypes.esPatterns
Chem.EState.EState_VSA.estateBins
Chem.EState.EState_VSA.vsaBins

Chem.FeatFinderCLI._splashMessage

Chem.FeatFinderCLI._version

Chem.FeatFinderCLI.logger
Chem.FeatFinderCLI.splitExpr
Chem.Features.ShowFeats.ALPHA
Chem.Features.ShowFeats.BEGIN
Chem.Features.ShowFeats.COLOR
Chem.Features.ShowFeats.CYLINDER
Chem.Features.ShowFeats.END
Chem.Features.ShowFeats.NORMAL
Chem.Features.ShowFeats.SPHERE
Chem.Features.ShowFeats.TRIANGLE_FAN
Chem.Features.ShowFeats.VERTEX

Chem.Features.ShowFeats._canonArrowhead

Chem.Features.ShowFeats._featColors

Chem.Features.ShowFeats._globalArrowCGO

Chem.Features.ShowFeats._globalSphereCGO

Chem.Features.ShowFeats._usage

Chem.Features.ShowFeats._version

Chem.Features.ShowFeats._welcomeMessage

Chem.Features.ShowFeats.logger
Chem.Features.ShowFeats.parser

Chem.Fingerprints.ClusterMols.__VERSION_STRING

Chem.Fingerprints.ClusterMols._cvsVersion

Chem.Fingerprints.ClusterMols._usageDoc

Chem.Fingerprints.ClusterMols.idx1
Chem.Fingerprints.ClusterMols.idx2

Chem.Fingerprints.FingerprintMols.__VERSION_STRING

Chem.Fingerprints.FingerprintMols._cvsVersion

Chem.Fingerprints.FingerprintMols._usageDoc

Chem.Fingerprints.FingerprintMols.idx1
Chem.Fingerprints.FingerprintMols.idx2

Chem.Fingerprints.MolSimilarity.__VERSION_STRING

Chem.Fingerprints.MolSimilarity._cvsVersion

Chem.Fingerprints.MolSimilarity._dataSeq

Chem.Fingerprints.MolSimilarity._usageDoc

Chem.Fingerprints.MolSimilarity.idx1
Chem.Fingerprints.MolSimilarity.idx2
Chem.FragmentCatalog.xl
Chem.Fragments.defaultPatternFileName
Chem.Fragments.fn
Chem.Fragments.fns
Chem.Fragments.name

Chem.GraphDescriptors._log2val

Chem.Pharm2D.Generate._verbose

Chem.Pharm2D.Gobbi_Pharm2D.defaultBins
Chem.Pharm2D.Gobbi_Pharm2D.factory
Chem.Pharm2D.Gobbi_Pharm2D.labels
Chem.Pharm2D.Gobbi_Pharm2D.patts

Chem.Pharm2D.Matcher._verbose

Chem.Pharm2D.Signature._sigVersion

Chem.Pharm2D.Signature._verbose

Chem.Pharm2D.Utils._countCache

Chem.Pharm2D.Utils._indexCombinations

Chem.Pharm2D.Utils._numCombDict

Chem.Pharm2D.Utils._trianglesInPharmacophore

Chem.Pharm2D.Utils._verbose

Chem.Pharm2D.Utils.nDistPointDict
Chem.Pharm2D.Utils.nPointDistDict

Chem.Pharm3D.EmbedLib._times

Chem.Pharm3D.EmbedLib.defaultFeatLength
Chem.Pharm3D.EmbedLib.logger

Chem.PyMol._server

Chem.Recap.reactionDefs
Chem.Recap.reactions
Chem.Recap.x

Chem.SATIS._debug

Chem.SATIS.aldehydePatt
Chem.SATIS.amidePatt
Chem.SATIS.carboxylPatt
Chem.SATIS.carboxylatePatt
Chem.SATIS.esterPatt
Chem.SATIS.ketonePatt
Chem.SATIS.specialCases
Chem.Subshape.SubshapeAligner.logger
Chem.rdMolDescriptors.__CalcCrippenDescriptors_version__
Chem.rdMolDescriptors.__CalcLabuteASA_version__
Chem.rdMolDescriptors.__CalcMolWt_version__
DataStructs.HierarchyVis.visOpts
DataStructs.__doc__
DataStructs.similarityFunctions
Dbase.DbInfo.sqlBinTypes
Dbase.DbInfo.sqlFloatTypes
Dbase.DbInfo.sqlIntTypes
Dbase.DbInfo.sqlTextTypes
Dbase.DbModule.RDTestDatabase
Dbase.DbModule.binaryTypeName
Dbase.DbModule.dbFileWildcard
Dbase.DbModule.fileWildcard
Dbase.DbModule.getDbSql
Dbase.DbModule.getTablesAndViewsSql
Dbase.DbModule.getTablesSql
Dbase.DbModule.placeHolder
Dbase.DbModule.sqlBinTypes
Dbase.DbModule.sqlFloatTypes
Dbase.DbModule.sqlIntTypes
Dbase.DbModule.sqlTextTypes
Dbase.DbModule.useGvib
Dbase.DbReport.GetReportlabTable
Dbase.DbReport.QuickReport
Dbase.DbReport.hasCDX
Dbase.DbUtils.haveExcel

Dbase.Pubmed.QueryParams._details

Dbase.Pubmed.QueryParams.fetchBase
Dbase.Pubmed.QueryParams.linkBase
Dbase.Pubmed.QueryParams.queryBase
Dbase.Pubmed.QueryParams.searchBase
Dbase.Pubmed.QueryParams.searchableFields
Dbase.Pubmed.QueryParams.searchableFieldsOrder
Dbase.Pubmed.QueryParams.summaryBase
Dbase.Pubmed.QueryParams.urlBase
Dbase.Pubmed.Records.vers
Dbase.StorageUtils.__test__

Dbase.StorageUtils._roundtripTests

Logger.Logger.stringTypes
Logger.SpingDemo.c1
Logger.SpingDemo.c2
Logger.SpingDemo.sz
Logger.SpingDemo.t
ML.AnalyzeComposite.Excel

ML.AnalyzeComposite.__VERSION_STRING

ML.BuildComposite.__VERSION_STRING

ML.BuildComposite._runDetails

ML.BuildComposite._verbose

ML.Cluster.Butina.logger
ML.Cluster.Clusters.CMPTOL
ML.Cluster.Murtagh.CENTROID
ML.Cluster.Murtagh.CLINK
ML.Cluster.Murtagh.GOWER
ML.Cluster.Murtagh.MCQUITTY
ML.Cluster.Murtagh.SLINK
ML.Cluster.Murtagh.UPGMA
ML.Cluster.Murtagh.WARDS
ML.Cluster.Murtagh.methods
ML.Cluster.Resemblance.methods
ML.Cluster.Standardize.methods
ML.Data.MLData.numericTypes

ML.Data.Quantize._float_tol

ML.Data.Quantize.hascQuantize
ML.Data.SplitData.SeqTypes
ML.Data.Stats.tConfs
ML.Data.Stats.tTable

ML.Data.Transforms._availTransforms

ML.DecTree.PruneTree._verbose

ML.DecTree.TreeUtils.__test__

ML.DecTree.TreeUtils._test1

ML.DecTree.TreeVis.visOpts
ML.Descriptors.CompoundDescriptors.countOptions
ML.Descriptors.MoleculeDescriptors.logger

ML.Descriptors.Parser.__DEBUG

ML.Descriptors.Parser.e
ML.Descriptors.Parser.knownMethods
ML.Descriptors.Parser.pi

ML.EnrichPlot.__VERSION_STRING

ML.GrowComposite.__VERSION_STRING

ML.GrowComposite._runDetails

ML.GrowComposite._verbose

ML.InfoTheory.entropy._log2

ML.InfoTheory.entropy.hascEntropy
ML.ScreenComposite.Excel

ML.ScreenComposite.__VERSION_STRING

ML.ScreenComposite._details

ML.ScreenComposite.hasPil
PySVD.SVDSimilarity.__test__
PySVD.SVDSimilarity.molTest
RDConfig.RDBaseDir
RDConfig.RDBinDir
RDConfig.RDCodeDir
RDConfig.RDDataDatabase
RDConfig.RDDataDir
RDConfig.RDDemoDir
RDConfig.RDDocsDir
RDConfig.RDFont
RDConfig.RDImageDir
RDConfig.RDProjDir
RDConfig.RDTestDatabase
RDConfig.binName
RDConfig.defaultDBPassword
RDConfig.defaultDBUser
RDConfig.dgeomLoc
RDConfig.doingDemo
RDConfig.largeFont
RDConfig.logGui
RDConfig.molViewer
RDConfig.pythonExe
RDConfig.pythonTestCommand
RDConfig.rpcTestPort
RDConfig.tinkerBin
RDConfig.tinkerParams
RDConfig.tinkerPath
RDConfig.usePgSQL
RDConfig.useSqlLite
RDLogger.CRITICAL
RDLogger.DEBUG
RDLogger.ERROR
RDLogger.INFO
RDLogger.WARNING

RDLogger._levels

RDRandom._randGen

VLib.NodeLib.DbPickleSupplier._dataSeq

VLib.NodeLib.SmartsRemover.__test__

VLib.NodeLib.SmartsRemover.biggerTest

VLib.NodeLib.demo.atsFilter

VLib.NodeLib.demo.dupeFilter

VLib.NodeLib.demo.i

VLib.NodeLib.demo.io

VLib.NodeLib.demo.metals

VLib.NodeLib.demo.mols

VLib.NodeLib.demo.output

VLib.NodeLib.demo.remover

VLib.NodeLib.demo.salts

VLib.NodeLib.demo.smaFilter

VLib.NodeLib.demo.smis

VLib.NodeLib.demo.supplier

VLib.NodeLib.demo.x

re.DEBUG
re.DOTALL
re.I
re.IGNORECASE
re.L
re.LOCALE
re.M
re.MULTILINE
re.S
re.T
re.TEMPLATE
re.U
re.UNICODE
re.VERBOSE
re.X
re._MAXCACHE
re._alphanum
re._cache
re._cache_repl

[hide private]