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
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
DiscreteValueVect
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
FoldFingerprint()
InitFromDaylightString()
IntSparseIntVect
KulczynskiSimilarity()
KulczynskiSimilarityNeighbors()
KulczynskiSimilarityNeighbors_sparse()
LongSparseIntVect
McConnaugheySimilarity()
McConnaugheySimilarityNeighbors()
McConnaugheySimilarityNeighbors_sparse()
MultiFPBReader
NumBitsInCommon()
OffBitProjSimilarity()
OffBitsInCommon()
OnBitProjSimilarity()
OnBitSimilarity()
OnBitsInCommon()
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
ULongSparseIntVect
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)¶