rdkit.DataStructs package

Submodules

• rdkit.DataStructs.BitEnsemble module
  • BitEnsemble
    • BitEnsemble.AddBit()
    • BitEnsemble.GetBits()
    • BitEnsemble.GetNumBits()
    • BitEnsemble.ScoreWithIndex()
    • BitEnsemble.ScoreWithOnBits()
    • BitEnsemble.SetBits()
• rdkit.DataStructs.BitEnsembleDb module
• rdkit.DataStructs.BitUtils module
  • ConstructEnsembleBV()
• rdkit.DataStructs.LazySignature module
  • LazySig
• rdkit.DataStructs.TopNContainer module
  • TopNContainer
    • TopNContainer.GetExtras()
    • TopNContainer.GetPts()
    • TopNContainer.Insert()
    • TopNContainer.reverse()
• rdkit.DataStructs.VectCollection module
  • VectCollection
    • VectCollection.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()
  • DiscreteValueType
    • DiscreteValueType.EIGHTBITVALUE
    • DiscreteValueType.FOURBITVALUE
    • DiscreteValueType.ONEBITVALUE
    • DiscreteValueType.SIXTEENBITVALUE
    • DiscreteValueType.TWOBITVALUE
    • DiscreteValueType.names
    • DiscreteValueType.values
  • DiscreteValueVect
    • DiscreteValueVect.GetTotalVal()
    • DiscreteValueVect.GetValueType()
  • ExplicitBitVect
    • ExplicitBitVect.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()
  • FPBReader
    • FPBReader.GetBytes()
    • FPBReader.GetContainingNeighbors()
    • FPBReader.GetFP()
    • FPBReader.GetId()
    • FPBReader.GetNumBits()
    • FPBReader.GetTanimoto()
    • FPBReader.GetTanimotoNeighbors()
    • FPBReader.GetTversky()
    • FPBReader.GetTverskyNeighbors()
    • FPBReader.Init()
  • FoldFingerprint()
  • InitFromDaylightString()
  • IntSparseIntVect
    • IntSparseIntVect.GetLength()
    • IntSparseIntVect.GetNonzeroElements()
    • IntSparseIntVect.GetTotalVal()
    • IntSparseIntVect.ToBinary()
    • IntSparseIntVect.ToList()
    • IntSparseIntVect.UpdateFromSequence()
  • KulczynskiSimilarity()
  • KulczynskiSimilarityNeighbors()
  • KulczynskiSimilarityNeighbors_sparse()
  • LongSparseIntVect
    • LongSparseIntVect.GetLength()
    • LongSparseIntVect.GetNonzeroElements()
    • LongSparseIntVect.GetTotalVal()
    • LongSparseIntVect.ToBinary()
    • LongSparseIntVect.ToList()
    • LongSparseIntVect.UpdateFromSequence()
  • McConnaugheySimilarity()
  • McConnaugheySimilarityNeighbors()
  • McConnaugheySimilarityNeighbors_sparse()
  • MultiFPBReader
    • MultiFPBReader.AddReader()
    • MultiFPBReader.GetContainingNeighbors()
    • MultiFPBReader.GetNumBits()
    • MultiFPBReader.GetReader()
    • MultiFPBReader.GetTanimotoNeighbors()
    • MultiFPBReader.GetTverskyNeighbors()
    • MultiFPBReader.Init()
  • NumBitsInCommon()
  • OffBitProjSimilarity()
  • OffBitsInCommon()
  • OnBitProjSimilarity()
  • OnBitSimilarity()
  • OnBitsInCommon()
  • RealValueVect
    • RealValueVect.GetTotalVal()
  • RogotGoldbergSimilarity()
  • RogotGoldbergSimilarityNeighbors()
  • RogotGoldbergSimilarityNeighbors_sparse()
  • RusselSimilarity()
  • RusselSimilarityNeighbors()
  • RusselSimilarityNeighbors_sparse()
  • SokalSimilarity()
  • SokalSimilarityNeighbors()
  • SokalSimilarityNeighbors_sparse()
  • SparseBitVect
    • SparseBitVect.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()
  • UIntSparseIntVect
    • UIntSparseIntVect.GetLength()
    • UIntSparseIntVect.GetNonzeroElements()
    • UIntSparseIntVect.GetTotalVal()
    • UIntSparseIntVect.ToBinary()
    • UIntSparseIntVect.ToList()
    • UIntSparseIntVect.UpdateFromSequence()
  • ULongSparseIntVect
    • ULongSparseIntVect.GetLength()
    • ULongSparseIntVect.GetNonzeroElements()
    • ULongSparseIntVect.GetTotalVal()
    • ULongSparseIntVect.ToBinary()
    • ULongSparseIntVect.ToList()
    • ULongSparseIntVect.UpdateFromSequence()

Module contents

Module containing an assortment of functionality for basic data structures.

At the moment the data structures defined are:

Bit Vector classes (for storing signatures, fingerprints and the like:

• ExplicitBitVect: class for relatively small (10s of thousands of bits) or

  dense bit vectors.

• SparseBitVect: class for large, sparse bit vectors

DiscreteValueVect: class for storing vectors of integers SparseIntVect: class for storing sparse vectors of integers

rdkit.DataStructs.FingerprintSimilarity(fp1, fp2, metric=<Boost.Python.function object>)

returns the calculated similarity between two fingerprints, handles any folding that may need to be done to ensure that they are compatible

rdkit.DataStructs.FoldToTargetDensity(fp, density=0.3, minLength=64)

rdkit.DataStructs.getElementFromFlatMatrix(matrix, i, j)

Return element (i,j); diagonal is 0; lower side mirrors upper.

rdkit.DataStructs.getNForFlatMatrix(matrix)

Get n for a strict upper- (or lower-) triangular matrix.