rdkit.DataStructs

Package rdkit :: Package DataStructs |
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# Package DataStructs

source code

    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 0x1b8f3b0>) 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, 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, LongSparseIntVect, McConnaugheySimilarity, NumBitsInCommon, OffBitProjSimilarity, OffBitsInCommon, OnBitProjSimilarity, OnBitSimilarity, OnBitsInCommon, RogotGoldbergSimilarity, RusselSimilarity, SokalSimilarity, SparseBitVect, TanimotoSimilarity, TopNContainer, TverskySimilarity, UIntSparseIntVect, ULongSparseIntVect

Function Details | [hide private]

### FingerprintSimilarity(fp1, fp2, metric=<Boost.Python.function object at 0x1b8f3b0>) | 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