rdkit.Avalon.pyAvalonTools

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
      - GetAvalonCountFP()      : return the Avalon fingerprint for a molecule as
                                  an RDKit SparseIntVector
      - 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 |
GetAvalonCountFP(...) GetAvalonCountFP( (Mol)mol [, (int)nBits=512 [, (bool)isQuery=False [, (int)bitFlags=15761407]]]) -> UIntSparseIntVect : returns the Avalon count fingerprint 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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > Generate2DCoords(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,bool)

### GetAvalonCountFP(...) |
    GetAvalonCountFP( (Mol)mol [, (int)nBits=512 [, (bool)isQuery=False [, (int)bitFlags=15761407]]]) -> UIntSparseIntVect :
        returns the Avalon count fingerprint for an RDKit molecule

        C++ signature :
            RDKit::SparseIntVect<unsigned int>* GetAvalonCountFP(RDKit::ROMol [,unsigned int=512 [,bool=False [,unsigned int=15761407]]])

    GetAvalonCountFP( (str)molData, (bool)isSmiles [, (int)nBits=512 [, (bool)isQuery=False [, (int)bitFlags=15761407]]]) -> UIntSparseIntVect :
        returns the Avalon count 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 :
            RDKit::SparseIntVect<unsigned int>* GetAvalonCountFP(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,bool [,unsigned int=512 [,bool=False [,unsigned int=15761407]]])

### 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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > 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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetCanonSmiles(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=''])