Package rdkit :: Package DataStructs :: Module cDataStructs :: Class FPBReader

Class FPBReader

 object --+    
          |    
??.instance --+
              |
             FPBReader

A class for reading and searching FPB files from Andrew Dalke's chemfp.
Note that this functionality is still experimental and the API may
change in future releases.

Instance Methods

[hide private]

GetBytes(...)
GetBytes( (FPBReader)arg1, (int)arg2) -> object : returns a particular fingerprint as bytes

GetContainingNeighbors(...)
GetContainingNeighbors( (FPBReader)arg1, (str)bv) -> tuple : returns indices of neighbors that contain this fingerprint (where all bits from this fingerprint are also set)

GetFP(...)
GetFP( (FPBReader)arg1, (int)arg2) -> ExplicitBitVect : returns a particular fingerprint as an ExplicitBitVect

GetId(...)
GetId( (FPBReader)arg1, (int)arg2) -> str : returns the id of a particular fingerprint

GetNumBits(...)
GetNumBits( (FPBReader)arg1) -> int : returns the number of bits in a fingerprint

GetTanimoto(...)
GetTanimoto( (FPBReader)arg1, (int)arg2, (str)arg3) -> float : return the tanimoto similarity of a particular fingerprint to the bytes provided

GetTanimotoNeighbors(...)
GetTanimotoNeighbors( (FPBReader)arg1, (str)bv [, (float)threshold=0.7]) -> tuple : returns tanimoto similarities to and indices of all neighbors above the specified threshold

GetTversky(...)
GetTversky( (FPBReader)arg1, (int)arg2, (str)arg3, (float)arg4, (float)arg5) -> float : return the Tverksy similarity of a particular fingerprint to the bytes provided

GetTverskyNeighbors(...)
GetTverskyNeighbors( (FPBReader)arg1, (str)bv, (float)ca, (float)cb [, (float)threshold=0.7]) -> tuple : returns Tversky similarities to and indices of all neighbors above the specified threshold

Init(...)
Init( (FPBReader)arg1) -> None : Read the fingerprints from the file.

__getitem__(...)
__getitem__( (FPBReader)arg1, (int)arg2) -> tuple :

__init__(...)
__init__( (object)arg1, (str)filename [, (bool)lazy=False]) -> None : docstring

__len__(...)
__len__( (FPBReader)arg1) -> int :

__reduce__(...)
helper for pickle

Inherited from unreachable.instance: __new__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

__instance_size__ = 40

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

GetBytes(...)


GetBytes( (FPBReader)arg1, (int)arg2) -> object :
    returns a particular fingerprint as bytes

    C++ signature :
        boost::python::api::object GetBytes(RDKit::FPBReader const*,unsigned int)

GetContainingNeighbors(...)


GetContainingNeighbors( (FPBReader)arg1, (str)bv) -> tuple :
    returns indices of neighbors that contain this fingerprint (where all bits from this fingerprint are also set)

    C++ signature :
        boost::python::tuple GetContainingNeighbors(RDKit::FPBReader const*,std::string)

GetFP(...)


GetFP( (FPBReader)arg1, (int)arg2) -> ExplicitBitVect :
    returns a particular fingerprint as an ExplicitBitVect

    C++ signature :
        boost::shared_ptr<ExplicitBitVect> GetFP(RDKit::FPBReader {lvalue},unsigned int)

GetId(...)


GetId( (FPBReader)arg1, (int)arg2) -> str :
    returns the id of a particular fingerprint

    C++ signature :
        std::string GetId(RDKit::FPBReader {lvalue},unsigned int)

GetNumBits(...)


GetNumBits( (FPBReader)arg1) -> int :
    returns the number of bits in a fingerprint

    C++ signature :
        unsigned int GetNumBits(RDKit::FPBReader {lvalue})

GetTanimoto(...)


GetTanimoto( (FPBReader)arg1, (int)arg2, (str)arg3) -> float :
    return the tanimoto similarity of a particular fingerprint to the bytes provided

    C++ signature :
        double GetTanimoto(RDKit::FPBReader const*,unsigned int,std::string)

GetTanimotoNeighbors(...)


GetTanimotoNeighbors( (FPBReader)arg1, (str)bv [, (float)threshold=0.7]) -> tuple :
    returns tanimoto similarities to and indices of all neighbors above the specified threshold

    C++ signature :
        boost::python::tuple GetTanimotoNeighbors(RDKit::FPBReader const*,std::string [,double=0.7])

GetTversky(...)


GetTversky( (FPBReader)arg1, (int)arg2, (str)arg3, (float)arg4, (float)arg5) -> float :
    return the Tverksy similarity of a particular fingerprint to the bytes provided

    C++ signature :
        double GetTversky(RDKit::FPBReader const*,unsigned int,std::string,double,double)

GetTverskyNeighbors(...)


GetTverskyNeighbors( (FPBReader)arg1, (str)bv, (float)ca, (float)cb [, (float)threshold=0.7]) -> tuple :
    returns Tversky similarities to and indices of all neighbors above the specified threshold

    C++ signature :
        boost::python::tuple GetTverskyNeighbors(RDKit::FPBReader const*,std::string,double,double [,double=0.7])

Init(...)


Init( (FPBReader)arg1) -> None :
    Read the fingerprints from the file. This can take a while.
    

    C++ signature :
        void Init(RDKit::FPBReader {lvalue})

getitem(...)
(Indexing operator)


__getitem__( (FPBReader)arg1, (int)arg2) -> tuple :

    C++ signature :
        boost::python::tuple __getitem__(RDKit::FPBReader const*,unsigned int)

init(...)
(Constructor)


__init__( (object)arg1, (str)filename [, (bool)lazy=False]) -> None :
    docstring

    C++ signature :
        void __init__(_object*,std::string [,bool=False])

Overrides: object.__init__

len(...)
(Length operator)


__len__( (FPBReader)arg1) -> int :

    C++ signature :
        unsigned int __len__(RDKit::FPBReader {lvalue})

reduce(...)

helper for pickle

Overrides: object.__reduce__: (inherited documentation)

Class FPBReader

GetBytes(...)

GetContainingNeighbors(...)

GetFP(...)

GetId(...)

GetNumBits(...)

GetTanimoto(...)

GetTanimotoNeighbors(...)

GetTversky(...)

GetTverskyNeighbors(...)

Init(...)

__getitem__(...) (Indexing operator)

__init__(...) (Constructor)

__len__(...) (Length operator)

__reduce__(...)

getitem(...)
(Indexing operator)

init(...)
(Constructor)

len(...)
(Length operator)

reduce(...)