Package rdkit :: Package DataStructs

Package DataStructs

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

Submodules

[hide private]

rdkit.DataStructs.BitEnsemble: #DOC
rdkit.DataStructs.BitEnsembleDb: This functionality gets mixed into the BitEnsemble class
rdkit.DataStructs.BitUtils
rdkit.DataStructs.HierarchyVis: functionality for drawing hierarchical catalogs on sping...
rdkit.DataStructs.LazySignature
rdkit.DataStructs.TopNContainer
rdkit.DataStructs.VectCollection
rdkit.DataStructs.cDataStructs: Module containing an assortment of functionality for basic data structures.

Functions

[hide private]

FingerprintSimilarity(fp1, fp2, metric=<Boost.Python.function object at 0x55e34b5c46c0>)
returns the calculated similarity between two fingerprints,...

source code

FoldToTargetDensity(fp, density=0.3, minLength=64)

source code

Variables

[hide private]

__doc__ = cDataStructs.__doc__

similarityFunctions = [('Tanimoto', TanimotoSimilarity, ''), (...

EIGHTBITVALUE = rdkit.DataStructs.cDataStructs.DiscreteValueTy...

FOURBITVALUE = rdkit.DataStructs.cDataStructs.DiscreteValueTyp...

ONEBITVALUE = rdkit.DataStructs.cDataStructs.DiscreteValueType...

SIXTEENBITVALUE = rdkit.DataStructs.cDataStructs.DiscreteValue...

TWOBITVALUE = rdkit.DataStructs.cDataStructs.DiscreteValueType...

__package__ = 'rdkit.DataStructs'

Imports: rdBase, cDataStructs, AllBitSimilarity, AllProbeBitsMatch, AsymmetricSimilarity, BitEnsemble, BitEnsembleDb, BitUtils, BitVectToBinaryText, BitVectToFPSText, BitVectToText, BraunBlanquetSimilarity, BulkAllBitSimilarity, BulkAsymmetricSimilarity, BulkBraunBlanquetSimilarity, BulkCosineSimilarity, BulkDiceSimilarity, BulkKulczynskiSimilarity, BulkMcConnaugheySimilarity, BulkOnBitSimilarity, BulkRogotGoldbergSimilarity, BulkRusselSimilarity, BulkSokalSimilarity, BulkTanimotoSimilarity, BulkTverskySimilarity, ComputeL1Norm, ConvertToExplicit, ConvertToNumpyArray, CosineSimilarity, CreateFromBinaryText, CreateFromBitString, CreateFromFPSText, DiceSimilarity, DiscreteValueType, DiscreteValueVect, ExplicitBitVect, FPBReader, FoldFingerprint, InitFromDaylightString, IntSparseIntVect, KulczynskiSimilarity, LazySignature, LongSparseIntVect, McConnaugheySimilarity, NumBitsInCommon, OffBitProjSimilarity, OffBitsInCommon, OnBitProjSimilarity, OnBitSimilarity, OnBitsInCommon, RogotGoldbergSimilarity, RusselSimilarity, SokalSimilarity, SparseBitVect, TanimotoSimilarity, TopNContainer, TverskySimilarity, UIntSparseIntVect, ULongSparseIntVect, VectCollection

Function Details

[hide private]

FingerprintSimilarity(fp1, fp2, metric=<Boost.Python.function object at 0x55e34b5c46c0>)

source code

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

Variables Details

[hide private]

similarityFunctions

Value:

[('Tanimoto', TanimotoSimilarity, ''), ("Dice", DiceSimilarity, ''), (
"Cosine", CosineSimilarity, ''), ("Sokal", SokalSimilarity, ''), ("Rus
sel", RusselSimilarity, ''), ("RogotGoldberg", RogotGoldbergSimilarity
, ''), ("AllBit", AllBitSimilarity, ''), ("Kulczynski", KulczynskiSimi
larity, ''), ("McConnaughey", McConnaugheySimilarity, ''), ("Asymmetri
c", AsymmetricSimilarity, ''), ("BraunBlanquet", BraunBlanquetSimilari
ty, ''),]

EIGHTBITVALUE

Value:

rdkit.DataStructs.cDataStructs.DiscreteValueType.EIGHTBITVALUE

FOURBITVALUE

Value:

rdkit.DataStructs.cDataStructs.DiscreteValueType.FOURBITVALUE

ONEBITVALUE

Value:

rdkit.DataStructs.cDataStructs.DiscreteValueType.ONEBITVALUE

SIXTEENBITVALUE

Value:

rdkit.DataStructs.cDataStructs.DiscreteValueType.SIXTEENBITVALUE

TWOBITVALUE

Value:

rdkit.DataStructs.cDataStructs.DiscreteValueType.TWOBITVALUE