rdkit.ML package

Subpackages

• rdkit.ML.Cluster package
  • Submodules
    • rdkit.ML.Cluster.Butina module
      • ClusterData()
      • EuclideanDist()
      • compute_distance_matrix()
    • rdkit.ML.Cluster.ClusterUtils module
      • FindClusterCentroidFromDists()
      • GetNodeList()
      • GetNodesDownToCentroids()
      • SplitIntoNClusters()
    • rdkit.ML.Cluster.ClusterVis module
      • ClusterRenderer
        • ClusterRenderer.DrawTree()
      • ClusterToImg()
      • ClusterToPDF()
      • ClusterToSVG()
      • DrawClusterTree()
      • VisOpts
        • VisOpts.hideColor
        • VisOpts.hideWidth
        • VisOpts.highlightColor
        • VisOpts.highlightRad
        • VisOpts.lineColor
        • VisOpts.lineWidth
        • VisOpts.nodeColor
        • VisOpts.nodeRad
        • VisOpts.terminalColors
        • VisOpts.xOffset
        • VisOpts.yOffset
    • rdkit.ML.Cluster.Clusters module
      • Cluster
        • Cluster.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
      • ClusterData()
    • rdkit.ML.Cluster.Resemblance module
      • CalcMetricMatrix()
      • EuclideanDistance()
      • FindMinValInList()
      • ShowMetricMat()
    • rdkit.ML.Cluster.Standardize module
      • StdDev()
    • rdkit.ML.Cluster.Clustering module
      • MurtaghCluster()
      • MurtaghDistCluster()
  • Module contents
• rdkit.ML.Data package
  • Submodules
    • rdkit.ML.Data.DataUtils module
      • BuildDataSet()
      • BuildQuantDataSet()
      • CalcNPossibleUsingMap()
      • CountResults()
      • DBToData()
      • FilterData()
      • InitRandomNumbers()
      • RandomizeActivities()
      • ReadGeneralExamples()
      • ReadQuantExamples()
      • ReadVars()
      • TakeEnsemble()
      • TextFileToData()
      • TextToData()
      • WriteData()
      • WritePickledData()
      • permutation()
    • rdkit.ML.Data.FindQuantBounds module
      • Usage()
      • runIt()
    • rdkit.ML.Data.MLData module
      • MLDataSet
        • MLDataSet.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
        • MLQuantDataSet.GetAllData()
        • MLQuantDataSet.GetInputData()
        • MLQuantDataSet.GetNamedData()
        • MLQuantDataSet.GetResults()
    • rdkit.ML.Data.Quantize module
      • FindVarMultQuantBounds()
      • FindVarQuantBound()
      • feq()
    • rdkit.ML.Data.cQuantize module
    • rdkit.ML.Data.SplitData module
      • SplitDataSet()
      • SplitDbData()
      • SplitIndices()
    • rdkit.ML.Data.Stats module
      • FormCorrelationMatrix()
      • FormCovarianceMatrix()
      • GetConfidenceInterval()
      • MeanAndDev()
      • PrincipalComponents()
      • R2()
      • StandardizeMatrix()
      • TransformPoints()
    • rdkit.ML.Data.Transforms module
      • GetAvailTransforms()
  • Module contents
• rdkit.ML.Descriptors package
  • Submodules
    • rdkit.ML.Descriptors.CompoundDescriptors module
      • CompoundDescriptorCalculator
        • CompoundDescriptorCalculator.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
      • DescriptorCalculator
        • DescriptorCalculator.CalcDescriptors()
        • DescriptorCalculator.GetDescriptorNames()
        • DescriptorCalculator.SaveState()
        • DescriptorCalculator.ShowDescriptors()
    • rdkit.ML.Descriptors.MoleculeDescriptors module
      • MolecularDescriptorCalculator
        • MolecularDescriptorCalculator.CalcDescriptors()
        • MolecularDescriptorCalculator.GetDescriptorFuncs()
        • MolecularDescriptorCalculator.GetDescriptorNames()
        • MolecularDescriptorCalculator.GetDescriptorSummaries()
        • MolecularDescriptorCalculator.GetDescriptorVersions()
        • MolecularDescriptorCalculator.SaveState()
    • rdkit.ML.Descriptors.Parser module
      • AVG()
      • CalcMultipleCompoundsDescriptor()
      • CalcSingleCompoundDescriptor()
      • DEV()
      • HAS()
      • MAX()
      • MEAN()
      • MIN()
      • SUM()
  • Module contents
• rdkit.ML.InfoTheory package
  • Submodules
    • rdkit.ML.InfoTheory.BitClusterer module
      • BitClusterer
        • BitClusterer.ClusterBits()
        • BitClusterer.GetClusters()
        • BitClusterer.MapToClusterFP()
        • BitClusterer.MapToClusterScores()
        • BitClusterer.SetClusters()
    • rdkit.ML.InfoTheory.BitRank module
      • AnalyzeSparseVects()
      • CalcInfoGains()
      • FormCounts()
      • RankBits()
      • SparseRankBits()
    • rdkit.ML.InfoTheory.entropy module
      • PyInfoEntropy()
      • PyInfoGain()
    • rdkit.ML.InfoTheory.rdInfoTheory module
      • BitCorrMatGenerator
        • BitCorrMatGenerator.CollectVotes()
        • BitCorrMatGenerator.GetCorrMatrix()
        • BitCorrMatGenerator.SetBitList()
      • ChiSquare()
      • InfoBitRanker
        • InfoBitRanker.AccumulateVotes()
        • InfoBitRanker.GetTopN()
        • InfoBitRanker.SetBiasList()
        • InfoBitRanker.SetMaskBits()
        • InfoBitRanker.Tester()
        • InfoBitRanker.WriteTopBitsToFile()
      • InfoEntropy()
      • InfoGain()
      • InfoType
        • InfoType.BIASCHISQUARE
        • InfoType.BIASENTROPY
        • InfoType.CHISQUARE
        • InfoType.ENTROPY
        • InfoType.names
        • InfoType.values
  • Module contents
• rdkit.ML.MLUtils package
  • Submodules
    • rdkit.ML.MLUtils.VoteImg module
      • BuildVoteImage()
      • CollectVotes()
      • Usage()
      • VoteAndBuildImage()
  • Module contents
• rdkit.ML.SLT package
  • Submodules
    • rdkit.ML.SLT.Risk module
      • BurgesRiskBound()
      • CherkasskyRiskBound()
      • CristianiRiskBound()
      • log2()
  • Module contents
• rdkit.ML.Scoring package
  • Submodules
    • rdkit.ML.Scoring.Scoring module
      • CalcAUC()
      • CalcBEDROC()
      • CalcEnrichment()
      • CalcRIE()
      • CalcROC()
  • Module contents

Submodules

• rdkit.ML.MatOps module
• rdkit.ML.files module
  • ReFile
    • ReFile.readline()
    • ReFile.readlines()
    • ReFile.rewind()
  • ReadDataFile()

Module contents

module containing machine learning code