Package rdkit :: Package Avalon :: Module pyAvalonTools
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Module pyAvalonTools

Module containing functionality from the Avalon toolkit.

The functions currently exposed are:
  - GetCanonSmiles()   : return the canonical smiles for a molecule
  - GetAvalonFP()      : return the Avalon fingerprint for a molecule as
                         an RDKit ExplicitBitVector
  - Generate2DCoords() : use the Avalon coordinate generator to create
                         a set of 2D coordinates for a molecule
Each function can be called with either an RDKit molecule or some
molecule data as text (e.g. a SMILES or an MDL mol block).

See the individual docstrings for more information.

Classes [hide private]
  StruChkFlag
  StruChkResult
Functions [hide private]
 
CheckMolecule(...)
CheckMolecule( (str)molstring, (bool)isSmiles) -> tuple : check a molecule passed in as a string.
 
CheckMoleculeString(...)
CheckMoleculeString( (str)molstring, (bool)isSmiles) -> tuple : check a molecule passed in as a string and returns the result as a string.
None :

CloseCheckMolFiles()
close open files used by molecule-checking functions.
 
Generate2DCoords(...)
Generate2DCoords( (Mol)mol [, (bool)clearConfs=True]) -> int : Generates 2d coordinates for an RDKit molecule
 
GetAvalonFP(...)
GetAvalonFP( (Mol)mol [, (int)nBits=512 [, (bool)isQuery=False [, (bool)resetVect=False [, (int)bitFlags=15761407]]]]) -> ExplicitBitVect : returns the Avalon fingerprint for an RDKit molecule
 
GetAvalonFPAsWords(...)
GetAvalonFPAsWords( (Mol)mol [, (int)nBits=512 [, (bool)isQuery=False [, (bool)resetVect=False [, (int)bitFlags=15761407]]]]) -> list : returns the Avalon fingerprint for an RDKit molecule as a list of ints
 
GetCanonSmiles(...)
GetCanonSmiles( (Mol)mol [, (int)flags=-1]) -> str : returns canonical smiles for an RDKit molecule
 
InitializeCheckMol(...)
InitializeCheckMol([ (str)options='']) -> int : initializes the structure checker.
Variables [hide private]
  __package__ = None
hash(x)
  avalonSSSBits = 32767
  avalonSimilarityBits = 15761407
Function Details [hide private]

CheckMolecule(...)

 

CheckMolecule( (str)molstring, (bool)isSmiles) -> tuple :
    check a molecule passed in as a string.
    If the isSmiles argument is true, the string should represent the SMILES encoding
    of the molecule, otherwise it should be encoded as an MDL molfile.
    The first member of the return tuple contains the bit-encoded corrections made to the molecule.
    If possible, the molecule (corrected when appropriate) is returned as the second member of 
    the return tuple. Otherwise, None is returned.

    C++ signature :
        boost::python::tuple CheckMolecule(std::string,bool)

CheckMolecule( (Mol)mol) -> tuple :
    check a molecule passed in as an RDKit molecule.
    The first member of the return tuple contains the bit-encoded corrections made to the molecule.
    If possible, the molecule (corrected when appropriate) is returned as the second member of 
    the return tuple. Otherwise, None is returned.

    C++ signature :
        boost::python::tuple CheckMolecule(RDKit::ROMol {lvalue})

CheckMoleculeString(...)

 

CheckMoleculeString( (str)molstring, (bool)isSmiles) -> tuple :
    check a molecule passed in as a string and returns the result as a string.
    If the isSmiles argument is true, the string should represent the SMILES encoding
    of the molecule, otherwise it should be encoded as an MDL molfile.
    The first member of the return tuple contains the bit-encoded corrections made to the molecule.
    If possible, a corrected CTAB for the molecule is returned as the second member of 
    the return tuple.

    C++ signature :
        boost::python::tuple CheckMoleculeString(std::string,bool)

CloseCheckMolFiles()

 
    close open files used by molecule-checking functions.

    C++ signature :
        void CloseCheckMolFiles()

Returns:
None :

Generate2DCoords(...)

 

Generate2DCoords( (Mol)mol [, (bool)clearConfs=True]) -> int :
    Generates 2d coordinates for an RDKit molecule

    C++ signature :
        unsigned int Generate2DCoords(RDKit::ROMol {lvalue} [,bool=True])

Generate2DCoords( (str)molData, (bool)isSmiles) -> str :
    returns an MDL mol block with 2D coordinates for some molecule data.
    If the isSmiles argument is true, the data is assumed to be SMILES, otherwise
    MDL mol data is assumed.

    C++ signature :
        std::string Generate2DCoords(std::string,bool)

GetAvalonFP(...)

 

GetAvalonFP( (Mol)mol [, (int)nBits=512 [, (bool)isQuery=False [, (bool)resetVect=False [, (int)bitFlags=15761407]]]]) -> ExplicitBitVect :
    returns the Avalon fingerprint for an RDKit molecule

    C++ signature :
        ExplicitBitVect* GetAvalonFP(RDKit::ROMol [,unsigned int=512 [,bool=False [,bool=False [,unsigned int=15761407]]]])

GetAvalonFP( (str)molData, (bool)isSmiles [, (int)nBits=512 [, (bool)isQuery=False [, (bool)resetVect=False [, (int)bitFlags=15761407]]]]) -> ExplicitBitVect :
    returns the Avalon fingerprint for some molecule data.
    If the isSmiles argument is true, the data is assumed to be SMILES, otherwise
    MDL mol data is assumed.

    C++ signature :
        ExplicitBitVect* GetAvalonFP(std::string,bool [,unsigned int=512 [,bool=False [,bool=False [,unsigned int=15761407]]]])

GetAvalonFPAsWords(...)

 

GetAvalonFPAsWords( (Mol)mol [, (int)nBits=512 [, (bool)isQuery=False [, (bool)resetVect=False [, (int)bitFlags=15761407]]]]) -> list :
    returns the Avalon fingerprint for an RDKit molecule as a list of ints

    C++ signature :
        boost::python::list GetAvalonFPAsWords(RDKit::ROMol [,unsigned int=512 [,bool=False [,bool=False [,unsigned int=15761407]]]])

GetAvalonFPAsWords( (str)molData, (bool)isSmiles [, (int)nBits=512 [, (bool)isQuery=False [, (bool)resetVect=False [, (int)bitFlags=15761407]]]]) -> list :
    returns the Avalon fingerprint for some molecule data as a list of ints.
    If the isSmiles argument is true, the data is assumed to be SMILES, otherwise
    MDL mol data is assumed.

    C++ signature :
        boost::python::list GetAvalonFPAsWords(std::string,bool [,unsigned int=512 [,bool=False [,bool=False [,unsigned int=15761407]]]])

GetCanonSmiles(...)

 

GetCanonSmiles( (Mol)mol [, (int)flags=-1]) -> str :
    returns canonical smiles for an RDKit molecule

    C++ signature :
        std::string GetCanonSmiles(RDKit::ROMol {lvalue} [,int=-1])

GetCanonSmiles( (str)molData, (bool)isSmiles [, (int)flags=-1]) -> str :
    Returns canonical smiles for some molecule data.
    If the isSmiles argument is true, the data is assumed to be SMILES, otherwise
    MDL mol data is assumed.

    C++ signature :
        std::string GetCanonSmiles(std::string,bool [,int=-1])

InitializeCheckMol(...)

 

InitializeCheckMol([  (str)options='']) -> int :
    initializes the structure checker.
    The argument should contain option lines separated by embedded newlines.An empty string will be used if the argument is omitted.An non-zero error code is returned in case of failure.

    C++ signature :
        int InitializeCheckMol([ std::string=''])