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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]

Functions [hide private]
 
FingerprintSimilarity(fp1, fp2, metric=<Boost.Python.function object at 0x858f3a8>)
returns the calculated similarity between two fingerprints,...		 source code
 
FoldToTargetDensity(fp, density=0.3, minLength=64) source code
 
AllBitSimilarity(...)
AllBitSimilarity( (SparseBitVect)v1, (SparseBitVect)v2) -> float :...		 source code
 
AllProbeBitsMatch(...)
AllProbeBitsMatch( (SparseBitVect)arg1, (str)arg2) -> bool : C++ signature : bool AllProbeBitsMatch(SparseBitVect,std::string) AllProbeBitsMatch( (ExplicitBitVect)arg1, (str)arg2) -> bool : Returns True if all bits in the first argument match all bits in the vector defined by the pickle in the second argument.		 source code
 
AsymmetricSimilarity(...)
AsymmetricSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
BitVectToText(...)
BitVectToText( (SparseBitVect)arg1) -> str : C++ signature : std::string BitVectToText(SparseBitVect) BitVectToText( (ExplicitBitVect)arg1) -> str : Returns a string of zeros and ones representing the bit vector.		 source code
 
BraunBlanquetSimilarity(...)
BraunBlanquetSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
BulkAllBitSimilarity(...)
BulkAllBitSimilarity( (ExplicitBitVect)v1, (list)v2 [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkAsymmetricSimilarity(...)
BulkAsymmetricSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkBraunBlanquetSimilarity(...)
BulkBraunBlanquetSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkCosineSimilarity(...)
BulkCosineSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkDiceSimilarity(...)
BulkDiceSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkKulczynskiSimilarity(...)
BulkKulczynskiSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkMcConnaugheySimilarity(...)
BulkMcConnaugheySimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkOnBitSimilarity(...)
BulkOnBitSimilarity( (ExplicitBitVect)v1, (list)v2 [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkRusselSimilarity(...)
BulkRusselSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkSokalSimilarity(...)
BulkSokalSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkTanimotoSimilarity(...)
BulkTanimotoSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :...		 source code
 
BulkTverskySimilarity(...)
BulkTverskySimilarity( (SparseBitVect)bv1, (list)bvList, (float)a, (float)b [, (bool)returnDistance=0]) -> list :...		 source code
 
ComputeL1Norm(...)
ComputeL1Norm( (DiscreteValueVect)arg1, (DiscreteValueVect)arg2) -> int :...		 source code
 
ConvertToExplicit(...)
ConvertToExplicit( (SparseBitVect)arg1) -> ExplicitBitVect :...		 source code
 
CosineSimilarity(...)
CosineSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
CreateFromBitString(...)
CreateFromBitString( (str)arg1) -> ExplicitBitVect : Creates an ExplicitBitVect from a bit string (string of 0s and 1s).		 source code
 
DiceSimilarity(...)
DiceSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
FoldFingerprint(...)
FoldFingerprint( (SparseBitVect)bv [, (int)foldFactor=2]) -> SparseBitVect : C++ signature : SparseBitVect* FoldFingerprint(SparseBitVect [,unsigned int=2]) FoldFingerprint( (ExplicitBitVect)bv [, (int)foldFactor=2]) -> ExplicitBitVect : Folds the fingerprint by the provided amount.		 source code
 
InitFromDaylightString(...)
InitFromDaylightString( (SparseBitVect)arg1, (str)arg2) -> None : C++ signature : void InitFromDaylightString(SparseBitVect {lvalue},std::string) InitFromDaylightString( (ExplicitBitVect)arg1, (str)arg2) -> None : Fill a BitVect using an ASCII (Daylight) encoding of a fingerprint.		 source code
 
KulczynskiSimilarity(...)
KulczynskiSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
McConnaugheySimilarity(...)
McConnaugheySimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
NumBitsInCommon(...)
NumBitsInCommon( (SparseBitVect)arg1, (SparseBitVect)arg2) -> int :...		 source code
 
OffBitProjSimilarity(...)
OffBitProjSimilarity( (SparseBitVect)arg1, (SparseBitVect)arg2) -> _vectd :...		 source code
 
OffBitsInCommon(...)
OffBitsInCommon( (SparseBitVect)arg1, (SparseBitVect)arg2) -> _vecti :...		 source code
 
OnBitProjSimilarity(...)
OnBitProjSimilarity( (SparseBitVect)arg1, (SparseBitVect)arg2) -> _vectd :...		 source code
 
OnBitSimilarity(...)
OnBitSimilarity( (SparseBitVect)v1, (SparseBitVect)v2) -> float :...		 source code
 
OnBitsInCommon(...)
OnBitsInCommon( (SparseBitVect)arg1, (SparseBitVect)arg2) -> _vecti :...		 source code
 
RusselSimilarity(...)
RusselSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
SokalSimilarity(...)
SokalSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
TanimotoSimilarity(...)
TanimotoSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :...		 source code
 
TverskySimilarity(...)
TverskySimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2, (float)a, (float)b [, (bool)returnDistance=0]) -> float :...		 source code
Variables [hide private]
  __doc__ = cDataStructs.__doc__
  similarityFunctions = [('Tanimoto', <Boost.Python.function obj...
Function Details [hide private]

FingerprintSimilarity(fp1, fp2, metric=<Boost.Python.function object at 0x858f3a8>)

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

AllBitSimilarity(...)

source code  

AllBitSimilarity( (SparseBitVect)v1, (SparseBitVect)v2) -> float :

    C++ signature :
        double AllBitSimilarity(SparseBitVect,SparseBitVect)

AllBitSimilarity( (ExplicitBitVect)v1, (ExplicitBitVect)v2) -> float :
    (B(bv1) - B(bv1^bv2)) / B(bv1)

    C++ signature :
        double AllBitSimilarity(ExplicitBitVect,ExplicitBitVect)

AllProbeBitsMatch(...)

source code  

AllProbeBitsMatch( (SparseBitVect)arg1, (str)arg2) -> bool :

    C++ signature :
        bool AllProbeBitsMatch(SparseBitVect,std::string)

AllProbeBitsMatch( (ExplicitBitVect)arg1, (str)arg2) -> bool :
    Returns True if all bits in the first argument match all bits in the 
      vector defined by the pickle in the second argument.
    

    C++ signature :
        bool AllProbeBitsMatch(ExplicitBitVect,std::string)

AsymmetricSimilarity(...)

source code  

AsymmetricSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double AsymmetricSimilarity(SparseBitVect,SparseBitVect [,bool=0])

AsymmetricSimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / min(B(bv1),B(bv2))

    C++ signature :
        double AsymmetricSimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

AsymmetricSimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double AsymmetricSimilarity(SparseBitVect,std::string [,bool=0])

AsymmetricSimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / min(B(bv1),B(bv2))

    C++ signature :
        double AsymmetricSimilarity(ExplicitBitVect,std::string [,bool=0])

BitVectToText(...)

source code  

BitVectToText( (SparseBitVect)arg1) -> str :

    C++ signature :
        std::string BitVectToText(SparseBitVect)

BitVectToText( (ExplicitBitVect)arg1) -> str :
    Returns a string of zeros and ones representing the bit vector.

    C++ signature :
        std::string BitVectToText(ExplicitBitVect)

BraunBlanquetSimilarity(...)

source code  

BraunBlanquetSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double BraunBlanquetSimilarity(SparseBitVect,SparseBitVect [,bool=0])

BraunBlanquetSimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / max(B(bv1),B(bv2))

    C++ signature :
        double BraunBlanquetSimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

BraunBlanquetSimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double BraunBlanquetSimilarity(SparseBitVect,std::string [,bool=0])

BraunBlanquetSimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / max(B(bv1),B(bv2))

    C++ signature :
        double BraunBlanquetSimilarity(ExplicitBitVect,std::string [,bool=0])

BulkAllBitSimilarity(...)

source code  

BulkAllBitSimilarity( (ExplicitBitVect)v1, (list)v2 [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkAllBitSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkAllBitSimilarity( (ExplicitBitVect)v1, (list)v2 [, (bool)returnDistance=0]) -> list :
    (B(bv1) - B(bv1^bv2)) / B(bv1)

    C++ signature :
        boost::python::list BulkAllBitSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkAsymmetricSimilarity(...)

source code  

BulkAsymmetricSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkAsymmetricSimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkAsymmetricSimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2) / min(B(bv1),B(bv2))

    C++ signature :
        boost::python::list BulkAsymmetricSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkBraunBlanquetSimilarity(...)

source code  

BulkBraunBlanquetSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkBraunBlanquetSimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkBraunBlanquetSimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2) / max(B(bv1),B(bv2))

    C++ signature :
        boost::python::list BulkBraunBlanquetSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkCosineSimilarity(...)

source code  

BulkCosineSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkCosineSimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkCosineSimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2) / sqrt(B(bv1) * B(bv2))

    C++ signature :
        boost::python::list BulkCosineSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkDiceSimilarity(...)

source code  

BulkDiceSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkDiceSimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkDiceSimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    2*B(bv1&bv2) / (B(bv1) + B(bv2))

    C++ signature :
        boost::python::list BulkDiceSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkDiceSimilarity( (IntSparseIntVect)v1, (list)v2 [, (bool)returnDistance=False]) -> list :
    return the Dice similarities between one vector and a sequence of others

    C++ signature :
        boost::python::list BulkDiceSimilarity(RDKit::SparseIntVect<int>,boost::python::list [,bool=False])

BulkDiceSimilarity( (LongSparseIntVect)v1, (list)v2 [, (bool)returnDistance=False]) -> list :
    return the Dice similarities between one vector and a sequence of others

    C++ signature :
        boost::python::list BulkDiceSimilarity(RDKit::SparseIntVect<long long>,boost::python::list [,bool=False])

BulkDiceSimilarity( (UIntSparseIntVect)v1, (list)v2 [, (bool)returnDistance=False]) -> list :
    return the Dice similarities between one vector and a sequence of others

    C++ signature :
        boost::python::list BulkDiceSimilarity(RDKit::SparseIntVect<unsigned int>,boost::python::list [,bool=False])

BulkDiceSimilarity( (ULongSparseIntVect)v1, (list)v2 [, (bool)returnDistance=False]) -> list :
    return the Dice similarities between one vector and a sequence of others

    C++ signature :
        boost::python::list BulkDiceSimilarity(RDKit::SparseIntVect<unsigned long long>,boost::python::list [,bool=False])

BulkKulczynskiSimilarity(...)

source code  

BulkKulczynskiSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkKulczynskiSimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkKulczynskiSimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2)*(B(bv1) + B(bv2)) / (2 * B(bv1) * B(bv2))

    C++ signature :
        boost::python::list BulkKulczynskiSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkMcConnaugheySimilarity(...)

source code  

BulkMcConnaugheySimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkMcConnaugheySimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkMcConnaugheySimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    (B(bv1&bv2) * (B(bv1)+B(bv2)) - B(bv1)*B(bv2)) / (B(bv1) * B(bv2))

    C++ signature :
        boost::python::list BulkMcConnaugheySimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkOnBitSimilarity(...)

source code  

BulkOnBitSimilarity( (ExplicitBitVect)v1, (list)v2 [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkOnBitSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkOnBitSimilarity( (ExplicitBitVect)v1, (list)v2 [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2) / B(bv1|bv2)

    C++ signature :
        boost::python::list BulkOnBitSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkRusselSimilarity(...)

source code  

BulkRusselSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkRusselSimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkRusselSimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2) / B(bv1)

    C++ signature :
        boost::python::list BulkRusselSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkSokalSimilarity(...)

source code  

BulkSokalSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkSokalSimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkSokalSimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2) / (2*B(bv1) + 2*B(bv2) - 3*B(bv1&bv2))

    C++ signature :
        boost::python::list BulkSokalSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkTanimotoSimilarity(...)

source code  

BulkTanimotoSimilarity( (SparseBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkTanimotoSimilarity(SparseBitVect,boost::python::list [,bool=0])

BulkTanimotoSimilarity( (ExplicitBitVect)bv1, (list)bvList [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2) / (B(bv1) + B(bv2) - B(bv1&bv2))

    C++ signature :
        boost::python::list BulkTanimotoSimilarity(ExplicitBitVect,boost::python::list [,bool=0])

BulkTverskySimilarity(...)

source code  

BulkTverskySimilarity( (SparseBitVect)bv1, (list)bvList, (float)a, (float)b [, (bool)returnDistance=0]) -> list :

    C++ signature :
        boost::python::list BulkTverskySimilarity(SparseBitVect,boost::python::list,double,double [,bool=0])

BulkTverskySimilarity( (ExplicitBitVect)bv1, (list)bvList, (float)a, (float)b [, (bool)returnDistance=0]) -> list :
    B(bv1&bv2) / (a*B(bv1)+b*B(bv2)+(1-a-b)*B(bv1&bv2)

    C++ signature :
        boost::python::list BulkTverskySimilarity(ExplicitBitVect,boost::python::list,double,double [,bool=0])

ComputeL1Norm(...)

source code  

ComputeL1Norm( (DiscreteValueVect)arg1, (DiscreteValueVect)arg2) -> int :
    Compute the distance between two discrete vector values
    

    C++ signature :
        unsigned int ComputeL1Norm(RDKit::DiscreteValueVect,RDKit::DiscreteValueVect)

ConvertToExplicit(...)

source code  

ConvertToExplicit( (SparseBitVect)arg1) -> ExplicitBitVect :
    Converts a SparseBitVector to an ExplicitBitVector and returns the ExplicitBitVector

    C++ signature :
        ExplicitBitVect* ConvertToExplicit(SparseBitVect const*)

CosineSimilarity(...)

source code  

CosineSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double CosineSimilarity(SparseBitVect,SparseBitVect [,bool=0])

CosineSimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / sqrt(B(bv1) * B(bv2))

    C++ signature :
        double CosineSimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

CosineSimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double CosineSimilarity(SparseBitVect,std::string [,bool=0])

CosineSimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / sqrt(B(bv1) * B(bv2))

    C++ signature :
        double CosineSimilarity(ExplicitBitVect,std::string [,bool=0])

CreateFromBitString(...)

source code  

CreateFromBitString( (str)arg1) -> ExplicitBitVect :
    Creates an ExplicitBitVect from a bit string (string of 0s and 1s).

    C++ signature :
        ExplicitBitVect* CreateFromBitString(std::string)

DiceSimilarity(...)

source code  

DiceSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double DiceSimilarity(SparseBitVect,SparseBitVect [,bool=0])

DiceSimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    2*B(bv1&bv2) / (B(bv1) + B(bv2))

    C++ signature :
        double DiceSimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

DiceSimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double DiceSimilarity(SparseBitVect,std::string [,bool=0])

DiceSimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    2*B(bv1&bv2) / (B(bv1) + B(bv2))

    C++ signature :
        double DiceSimilarity(ExplicitBitVect,std::string [,bool=0])

DiceSimilarity( (IntSparseIntVect)siv1, (IntSparseIntVect)siv2 [, (bool)returnDistance=False [, (float)bounds=0.0]]) -> float :
    return the Dice similarity between two vectors

    C++ signature :
        double DiceSimilarity(RDKit::SparseIntVect<int>,RDKit::SparseIntVect<int> [,bool=False [,double=0.0]])

DiceSimilarity( (LongSparseIntVect)siv1, (LongSparseIntVect)siv2 [, (bool)returnDistance=False [, (float)bounds=0.0]]) -> float :
    return the Dice similarity between two vectors

    C++ signature :
        double DiceSimilarity(RDKit::SparseIntVect<long long>,RDKit::SparseIntVect<long long> [,bool=False [,double=0.0]])

DiceSimilarity( (UIntSparseIntVect)siv1, (UIntSparseIntVect)siv2 [, (bool)returnDistance=False [, (float)bounds=0.0]]) -> float :
    return the Dice similarity between two vectors

    C++ signature :
        double DiceSimilarity(RDKit::SparseIntVect<unsigned int>,RDKit::SparseIntVect<unsigned int> [,bool=False [,double=0.0]])

DiceSimilarity( (ULongSparseIntVect)siv1, (ULongSparseIntVect)siv2 [, (bool)returnDistance=False [, (float)bounds=0.0]]) -> float :
    return the Dice similarity between two vectors

    C++ signature :
        double DiceSimilarity(RDKit::SparseIntVect<unsigned long long>,RDKit::SparseIntVect<unsigned long long> [,bool=False [,double=0.0]])

FoldFingerprint(...)

source code  

FoldFingerprint( (SparseBitVect)bv [, (int)foldFactor=2]) -> SparseBitVect :

    C++ signature :
        SparseBitVect* FoldFingerprint(SparseBitVect [,unsigned int=2])

FoldFingerprint( (ExplicitBitVect)bv [, (int)foldFactor=2]) -> ExplicitBitVect :
    Folds the fingerprint by the provided amount. The default, foldFactor=2, returns a fingerprint that is half the size of the original.

    C++ signature :
        ExplicitBitVect* FoldFingerprint(ExplicitBitVect [,unsigned int=2])

InitFromDaylightString(...)

source code  

InitFromDaylightString( (SparseBitVect)arg1, (str)arg2) -> None :

    C++ signature :
        void InitFromDaylightString(SparseBitVect {lvalue},std::string)

InitFromDaylightString( (ExplicitBitVect)arg1, (str)arg2) -> None :
    Fill a BitVect using an ASCII (Daylight) encoding of a fingerprint.
    
       **Arguments**
         - bv: either a _SparseBitVect_ or an _ExplicitBitVect_
         - txt: a string with the Daylight encoding (this is the text that
                the Daylight tools put in the FP field of a TDT)
    
    

    C++ signature :
        void InitFromDaylightString(ExplicitBitVect {lvalue},std::string)

KulczynskiSimilarity(...)

source code  

KulczynskiSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double KulczynskiSimilarity(SparseBitVect,SparseBitVect [,bool=0])

KulczynskiSimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2)*(B(bv1) + B(bv2)) / (2 * B(bv1) * B(bv2))

    C++ signature :
        double KulczynskiSimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

KulczynskiSimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double KulczynskiSimilarity(SparseBitVect,std::string [,bool=0])

KulczynskiSimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2)*(B(bv1) + B(bv2)) / (2 * B(bv1) * B(bv2))

    C++ signature :
        double KulczynskiSimilarity(ExplicitBitVect,std::string [,bool=0])

McConnaugheySimilarity(...)

source code  

McConnaugheySimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double McConnaugheySimilarity(SparseBitVect,SparseBitVect [,bool=0])

McConnaugheySimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    (B(bv1&bv2) * (B(bv1)+B(bv2)) - B(bv1)*B(bv2)) / (B(bv1) * B(bv2))

    C++ signature :
        double McConnaugheySimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

McConnaugheySimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double McConnaugheySimilarity(SparseBitVect,std::string [,bool=0])

McConnaugheySimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    (B(bv1&bv2) * (B(bv1)+B(bv2)) - B(bv1)*B(bv2)) / (B(bv1) * B(bv2))

    C++ signature :
        double McConnaugheySimilarity(ExplicitBitVect,std::string [,bool=0])

NumBitsInCommon(...)

source code  

NumBitsInCommon( (SparseBitVect)arg1, (SparseBitVect)arg2) -> int :

    C++ signature :
        int NumBitsInCommon(SparseBitVect,SparseBitVect)

NumBitsInCommon( (ExplicitBitVect)arg1, (ExplicitBitVect)arg2) -> int :
    Returns the total number of bits in common between the two bit vectors

    C++ signature :
        int NumBitsInCommon(ExplicitBitVect,ExplicitBitVect)

OffBitProjSimilarity(...)

source code  

OffBitProjSimilarity( (SparseBitVect)arg1, (SparseBitVect)arg2) -> _vectd :

    C++ signature :
        std::vector<double, std::allocator<double> > OffBitProjSimilarity(SparseBitVect,SparseBitVect)

OffBitProjSimilarity( (ExplicitBitVect)arg1, (ExplicitBitVect)arg2) -> _vectd :

    C++ signature :
        std::vector<double, std::allocator<double> > OffBitProjSimilarity(ExplicitBitVect,ExplicitBitVect)

OffBitsInCommon(...)

source code  

OffBitsInCommon( (SparseBitVect)arg1, (SparseBitVect)arg2) -> _vecti :

    C++ signature :
        std::vector<int, std::allocator<int> > OffBitsInCommon(SparseBitVect,SparseBitVect)

OffBitsInCommon( (ExplicitBitVect)arg1, (ExplicitBitVect)arg2) -> _vecti :
    Returns the number of off bits in common between the two bit vectors

    C++ signature :
        std::vector<int, std::allocator<int> > OffBitsInCommon(ExplicitBitVect,ExplicitBitVect)

OnBitProjSimilarity(...)

source code  

OnBitProjSimilarity( (SparseBitVect)arg1, (SparseBitVect)arg2) -> _vectd :

    C++ signature :
        std::vector<double, std::allocator<double> > OnBitProjSimilarity(SparseBitVect,SparseBitVect)

OnBitProjSimilarity( (ExplicitBitVect)arg1, (ExplicitBitVect)arg2) -> _vectd :
    Returns a 2-tuple: (B(bv1&bv2) / B(bv1), B(bv1&bv2) / B(bv2))

    C++ signature :
        std::vector<double, std::allocator<double> > OnBitProjSimilarity(ExplicitBitVect,ExplicitBitVect)

OnBitSimilarity(...)

source code  

OnBitSimilarity( (SparseBitVect)v1, (SparseBitVect)v2) -> float :

    C++ signature :
        double OnBitSimilarity(SparseBitVect,SparseBitVect)

OnBitSimilarity( (ExplicitBitVect)v1, (ExplicitBitVect)v2) -> float :
    B(bv1&bv2) / B(bv1|bv2)

    C++ signature :
        double OnBitSimilarity(ExplicitBitVect,ExplicitBitVect)

OnBitsInCommon(...)

source code  

OnBitsInCommon( (SparseBitVect)arg1, (SparseBitVect)arg2) -> _vecti :

    C++ signature :
        std::vector<int, std::allocator<int> > OnBitsInCommon(SparseBitVect,SparseBitVect)

OnBitsInCommon( (ExplicitBitVect)arg1, (ExplicitBitVect)arg2) -> _vecti :
    Returns the number of on bits in common between the two bit vectors

    C++ signature :
        std::vector<int, std::allocator<int> > OnBitsInCommon(ExplicitBitVect,ExplicitBitVect)

RusselSimilarity(...)

source code  

RusselSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double RusselSimilarity(SparseBitVect,SparseBitVect [,bool=0])

RusselSimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / B(bv1)

    C++ signature :
        double RusselSimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

RusselSimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double RusselSimilarity(SparseBitVect,std::string [,bool=0])

RusselSimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / B(bv1)

    C++ signature :
        double RusselSimilarity(ExplicitBitVect,std::string [,bool=0])

SokalSimilarity(...)

source code  

SokalSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double SokalSimilarity(SparseBitVect,SparseBitVect [,bool=0])

SokalSimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / (2*B(bv1) + 2*B(bv2) - 3*B(bv1&bv2))

    C++ signature :
        double SokalSimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

SokalSimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double SokalSimilarity(SparseBitVect,std::string [,bool=0])

SokalSimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / (2*B(bv1) + 2*B(bv2) - 3*B(bv1&bv2))

    C++ signature :
        double SokalSimilarity(ExplicitBitVect,std::string [,bool=0])

TanimotoSimilarity(...)

source code  

TanimotoSimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2 [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double TanimotoSimilarity(SparseBitVect,SparseBitVect [,bool=0])

TanimotoSimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2 [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / (B(bv1) + B(bv2) - B(bv1&bv2))

    C++ signature :
        double TanimotoSimilarity(ExplicitBitVect,ExplicitBitVect [,bool=0])

TanimotoSimilarity( (SparseBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double TanimotoSimilarity(SparseBitVect,std::string [,bool=0])

TanimotoSimilarity( (ExplicitBitVect)bv1, (str)pkl [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / (B(bv1) + B(bv2) - B(bv1&bv2))

    C++ signature :
        double TanimotoSimilarity(ExplicitBitVect,std::string [,bool=0])

TverskySimilarity(...)

source code  

TverskySimilarity( (SparseBitVect)bv1, (SparseBitVect)bv2, (float)a, (float)b [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double TverskySimilarity(SparseBitVect,SparseBitVect,double,double [,bool=0])

TverskySimilarity( (ExplicitBitVect)bv1, (ExplicitBitVect)bv2, (float)a, (float)b [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / (a*B(bv1)+b*B(bv2)+(1-a-b)*B(bv1&bv2)

    C++ signature :
        double TverskySimilarity(ExplicitBitVect,ExplicitBitVect,double,double [,bool=0])

TverskySimilarity( (SparseBitVect)bv1, (str)pkl, (float)a, (float)b [, (bool)returnDistance=0]) -> float :

    C++ signature :
        double TverskySimilarity(SparseBitVect,std::string,double,double [,bool=0])

TverskySimilarity( (ExplicitBitVect)bv1, (str)pkl, (float)a, (float)b [, (bool)returnDistance=0]) -> float :
    B(bv1&bv2) / (a*B(bv1)+b*B(bv2)+(1-a-b)*B(bv1&bv2)

    C++ signature :
        double TverskySimilarity(ExplicitBitVect,std::string,double,double [,bool=0])

Variables Details [hide private]

similarityFunctions

Value:
[('Tanimoto', TanimotoSimilarity, ''), ("Dice", DiceSimilarity, ''), (\
"Cosine", CosineSimilarity, ''), ("Sokal", SokalSimilarity, ''), ("Rus\
sel", RusselSimilarity, ''), ("Kulczynski", KulczynskiSimilarity, ''),\
 ("McConnaughey", McConnaugheySimilarity, ''), ("Asymmetric", Asymmetr\
icSimilarity, ''), ("BraunBlanquet", BraunBlanquetSimilarity, ''),]

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