Class Mol

AddConformer( (Mol)self, (Conformer)conf [, (bool)assignId=False]) -> int :
    Add a conformer to the molecule and return the conformer ID

    C++ signature :
        unsigned int AddConformer(RDKit::ROMol {lvalue},RDKit::Conformer* [,bool=False])

ClearComputedProps( (Mol)arg1) -> None :
    Removes all computed properties from the molecule.
    
    

    C++ signature :
        void ClearComputedProps(RDKit::ROMol)

ClearProp( (Mol)arg1, (str)arg2) -> None :
    Removes a property from the molecule.
    
      ARGUMENTS:
        - key: the name of the property to clear (a string).
    

    C++ signature :
        void ClearProp(RDKit::ROMol,char const*)

Debug( (Mol)mol [, (bool)useStdout=True]) -> None :
    Prints debugging information about the molecule.
    

    C++ signature :
        void Debug(RDKit::ROMol [,bool=True])

GetAromaticAtoms( (Mol)arg1) -> _ROQAtomSeq :
    Returns a read-only sequence containing all of the molecule's aromatic Atoms.
    

    C++ signature :
        RDKit::ReadOnlySeq<RDKit::QueryAtomIterator_<RDKit::Atom, RDKit::ROMol>, RDKit::Atom*>* GetAromaticAtoms(RDKit::ROMol*)

GetAtomWithIdx( (Mol)arg1, (int)arg2) -> Atom :
    Returns a particular Atom.
    
      ARGUMENTS:
        - idx: which Atom to return
    
      NOTE: atom indices start at 0
    

    C++ signature :
        RDKit::Atom* GetAtomWithIdx(RDKit::ROMol {lvalue},unsigned int)

GetAtoms( (Mol)arg1) -> _ROAtomSeq :
    Returns a read-only sequence containing all of the molecule's Atoms.
    

    C++ signature :
        RDKit::ReadOnlySeq<RDKit::AtomIterator_<RDKit::Atom, RDKit::ROMol>, RDKit::Atom*>* GetAtoms(RDKit::ROMol*)

GetAtomsMatchingQuery( (Mol)arg1, (QueryAtom)arg2) -> _ROQAtomSeq :
    Returns a read-only sequence containing all of the atoms in a molecule that match the query atom.
    

    C++ signature :
        RDKit::ReadOnlySeq<RDKit::QueryAtomIterator_<RDKit::Atom, RDKit::ROMol>, RDKit::Atom*>* GetAtomsMatchingQuery(RDKit::ROMol*,RDKit::QueryAtom*)

GetBondBetweenAtoms( (Mol)arg1, (int)arg2, (int)arg3) -> Bond :
    Returns the bond between two atoms, if there is one.
    
      ARGUMENTS:
        - idx1,idx2: the Atom indices
    
      Returns:
        The Bond between the two atoms, if such a bond exists.
        If there is no Bond between the atoms, None is returned instead.
    
      NOTE: bond indices start at 0
    

    C++ signature :
        RDKit::Bond* GetBondBetweenAtoms(RDKit::ROMol {lvalue},unsigned int,unsigned int)

GetBondWithIdx( (Mol)arg1, (int)arg2) -> Bond :
    Returns a particular Bond.
    
      ARGUMENTS:
        - idx: which Bond to return
    
      NOTE: bond indices start at 0
    

    C++ signature :
        RDKit::Bond* GetBondWithIdx(RDKit::ROMol {lvalue},unsigned int)

GetBonds( (Mol)arg1) -> _ROBondSeq :
    Returns a read-only sequence containing all of the molecule's Bonds.
    

    C++ signature :
        RDKit::ReadOnlySeq<RDKit::BondIterator_, RDKit::Bond*>* GetBonds(RDKit::ROMol*)

GetBoolProp( (Mol)arg1, (str)arg2) -> bool :
    Returns the double value of the property if possible.
    
      ARGUMENTS:
        - key: the name of the property to return (a string).
    
      RETURNS: a bool
    
      NOTE:
        - If the property has not been set, a KeyError exception will be raised.
    

    C++ signature :
        bool GetBoolProp(RDKit::ROMol*,char const*)

GetConformer( (Mol)self [, (int)id=-1]) -> Conformer :
    Get the conformer with a specified ID

    C++ signature :
        RDKit::Conformer* GetConformer(RDKit::ROMol {lvalue} [,int=-1])

GetConformers( (Mol)arg1) -> object :
    Get all the conformers as a tuple

    C++ signature :
        _object* GetConformers(RDKit::ROMol {lvalue})

GetDoubleProp( (Mol)arg1, (str)arg2) -> float :
    Returns the double value of the property if possible.
    
      ARGUMENTS:
        - key: the name of the property to return (a string).
    
      RETURNS: a double
    
      NOTE:
        - If the property has not been set, a KeyError exception will be raised.
    

    C++ signature :
        double GetDoubleProp(RDKit::ROMol*,char const*)

GetIntProp( (Mol)arg1, (str)arg2) -> int :
    Returns the integer value of the property if possible.
    
      ARGUMENTS:
        - key: the name of the property to return (a string).
    
      RETURNS: an integer
    
      NOTE:
        - If the property has not been set, a KeyError exception will be raised.
    

    C++ signature :
        int GetIntProp(RDKit::ROMol*,char const*)

GetNumAtoms( (Mol)arg1 [, (int)onlyHeavy=-1 [, (bool)onlyExplicit=True]]) -> int :
    Returns the number of atoms in the molecule.
    
      ARGUMENTS:
        - onlyExplicit: (optional) include only explicit atoms (atoms in the molecular graph)
                        defaults to 1.
      NOTE: the onlyHeavy argument is deprecated
    

    C++ signature :
        int GetNumAtoms(RDKit::ROMol [,int=-1 [,bool=True]])

GetNumBonds( (Mol)arg1 [, (bool)onlyHeavy=True]) -> int :
    Returns the number of Bonds in the molecule.
    
      ARGUMENTS:
        - onlyHeavy: (optional) include only bonds to heavy atoms (not Hs)
                      defaults to 1.
    

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

GetNumConformers( (Mol)arg1) -> int :
    Return the number of conformations on the molecule

    C++ signature :
        unsigned int GetNumConformers(RDKit::ROMol {lvalue})

GetNumHeavyAtoms( (Mol)arg1) -> int :
    Returns the number of heavy atoms (atomic number >1) in the molecule.
    
    

    C++ signature :
        unsigned int GetNumHeavyAtoms(RDKit::ROMol {lvalue})

GetProp( (Mol)arg1, (str)arg2) -> str :
    Returns the value of the property.
    
      ARGUMENTS:
        - key: the name of the property to return (a string).
    
      RETURNS: a string
    
      NOTE:
        - If the property has not been set, a KeyError exception will be raised.
    

    C++ signature :
        std::string GetProp(RDKit::ROMol*,char const*)

GetPropNames( (Mol)self [, (bool)includePrivate=False [, (bool)includeComputed=False]]) -> _vectSs :
    Returns a tuple with all property names for this molecule.
    
      ARGUMENTS:
        - includePrivate: (optional) toggles inclusion of private properties in the result set.
                          Defaults to 0.
        - includeComputed: (optional) toggles inclusion of computed properties in the result set.
                          Defaults to 0.
    
      RETURNS: a tuple of strings
    

    C++ signature :
        std::vector<std::string, std::allocator<std::string> > GetPropNames(RDKit::ROMol {lvalue} [,bool=False [,bool=False]])

GetPropsAsDict( (Mol)self [, (bool)includePrivate=False [, (bool)includeComputed=False]]) -> dict :
    Returns a dictionary populated with the molecules properties.
     n.b. Some properties are not able to be converted to python types.
    
      ARGUMENTS:
        - includePrivate: (optional) toggles inclusion of private properties in the result set.
                          Defaults to False.
        - includeComputed: (optional) toggles inclusion of computed properties in the result set.
                          Defaults to False.
    
      RETURNS: a dictionary
    

    C++ signature :
        boost::python::dict GetPropsAsDict(RDKit::ROMol [,bool=False [,bool=False]])

GetRingInfo( (Mol)arg1) -> RingInfo :
    Returns the number of molecule's RingInfo object.
    
    

    C++ signature :
        RDKit::RingInfo* GetRingInfo(RDKit::ROMol {lvalue})

GetSubstructMatch( (Mol)self, (Mol)query [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]) -> object :
    Returns the indices of the molecule's atoms that match a substructure query.
    
      ARGUMENTS:
        - query: a Molecule
    
        - useChirality: enables the use of stereochemistry in the matching
    
        - useQueryQueryMatches: use query-query matching logic
    
      RETURNS: a tuple of integers
    
      NOTES:
         - only a single match is returned
         - the ordering of the indices corresponds to the atom ordering
             in the query. For example, the first index is for the atom in
             this molecule that matches the first atom in the query.
    

    C++ signature :
        _object* GetSubstructMatch(RDKit::ROMol,RDKit::ROMol [,bool=False [,bool=False]])

GetSubstructMatches( (Mol)self, (Mol)query [, (bool)uniquify=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False [, (int)maxMatches=1000]]]]) -> object :
    Returns tuples of the indices of the molecule's atoms that match a substructure query.
    
      ARGUMENTS:
        - query: a Molecule.
        - uniquify: (optional) determines whether or not the matches are uniquified.
                    Defaults to 1.
    
        - useChirality: enables the use of stereochemistry in the matching
    
        - useQueryQueryMatches: use query-query matching logic
    
        - maxMatches: The maximum number of matches that will be returned.
                      In high-symmetry cases with medium-sized molecules, it is
                      very easy to end up with a combinatorial explosion in the
                      number of possible matches. This argument prevents that from
                      having unintended consequences
    
      RETURNS: a tuple of tuples of integers
    
      NOTE:
         - the ordering of the indices corresponds to the atom ordering
             in the query. For example, the first index is for the atom in
             this molecule that matches the first atom in the query.
    

    C++ signature :
        _object* GetSubstructMatches(RDKit::ROMol,RDKit::ROMol [,bool=True [,bool=False [,bool=False [,unsigned int=1000]]]])

GetUnsignedProp( (Mol)arg1, (str)arg2) -> int :
    Returns the unsigned int value of the property if possible.
    
      ARGUMENTS:
        - key: the name of the property to return (a string).
    
      RETURNS: an unsigned integer
    
      NOTE:
        - If the property has not been set, a KeyError exception will be raised.
    

    C++ signature :
        unsigned int GetUnsignedProp(RDKit::ROMol*,char const*)

HasProp( (Mol)arg1, (str)arg2) -> int :
    Queries a molecule to see if a particular property has been assigned.
    
      ARGUMENTS:
        - key: the name of the property to check for (a string).
    

    C++ signature :
        int HasProp(RDKit::ROMol,char const*)

HasSubstructMatch( (Mol)self, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool :
    Queries whether or not the molecule contains a particular substructure.
    
      ARGUMENTS:
        - query: a Molecule
    
        - recursionPossible: (optional)
    
        - useChirality: enables the use of stereochemistry in the matching
    
        - useQueryQueryMatches: use query-query matching logic
    
      RETURNS: True or False
    

    C++ signature :
        bool HasSubstructMatch(RDKit::ROMol,RDKit::ROMol [,bool=True [,bool=False [,bool=False]]])

NeedsUpdatePropertyCache( (Mol)self) -> bool :
    Returns true or false depending on whether implicit and explicit valence of the molecule have already been calculated.
    
    

    C++ signature :
        bool NeedsUpdatePropertyCache(RDKit::ROMol {lvalue})

RemoveAllConformers( (Mol)arg1) -> None :
    Remove all the conformations on the molecule

    C++ signature :
        void RemoveAllConformers(RDKit::ROMol {lvalue})

RemoveConformer( (Mol)arg1, (int)arg2) -> None :
    Remove the conformer with the specified ID

    C++ signature :
        void RemoveConformer(RDKit::ROMol {lvalue},unsigned int)

SetBoolProp( (Mol)self, (str)key, (bool)val [, (bool)computed=False]) -> None :
    Sets a boolean valued molecular property
    
      ARGUMENTS:
        - key: the name of the property to be set (a string).
        - value: the property value as a bool.
        - computed: (optional) marks the property as being computed.
                    Defaults to False.
    
    

    C++ signature :
        void SetBoolProp(RDKit::ROMol,char const*,bool [,bool=False])

SetDoubleProp( (Mol)self, (str)key, (float)val [, (bool)computed=False]) -> None :
    Sets a double valued molecular property
    
      ARGUMENTS:
        - key: the name of the property to be set (a string).
        - value: the property value as a double.
        - computed: (optional) marks the property as being computed.
                    Defaults to 0.
    
    

    C++ signature :
        void SetDoubleProp(RDKit::ROMol,char const*,double [,bool=False])

SetIntProp( (Mol)self, (str)key, (int)val [, (bool)computed=False]) -> None :
    Sets an integer valued molecular property
    
      ARGUMENTS:
        - key: the name of the property to be set (an unsigned number).
        - value: the property value as an integer.
        - computed: (optional) marks the property as being computed.
                    Defaults to False.
    
    

    C++ signature :
        void SetIntProp(RDKit::ROMol,char const*,int [,bool=False])

SetProp( (Mol)self, (str)key, (str)val [, (bool)computed=False]) -> None :
    Sets a molecular property
    
      ARGUMENTS:
        - key: the name of the property to be set (a string).
        - value: the property value (a string).
        - computed: (optional) marks the property as being computed.
                    Defaults to False.
    
    

    C++ signature :
        void SetProp(RDKit::ROMol,char const*,std::string [,bool=False])

SetUnsignedProp( (Mol)self, (str)key, (int)val [, (bool)computed=False]) -> None :
    Sets an unsigned integer valued molecular property
    
      ARGUMENTS:
        - key: the name of the property to be set (a string).
        - value: the property value as an unsigned integer.
        - computed: (optional) marks the property as being computed.
                    Defaults to False.
    
    

    C++ signature :
        void SetUnsignedProp(RDKit::ROMol,char const*,unsigned int [,bool=False])

ToBinary( (Mol)arg1) -> object :
    Returns a binary string representation of the molecule.
    

    C++ signature :
        boost::python::api::object ToBinary(RDKit::ROMol)

UpdatePropertyCache( (Mol)self [, (bool)strict=True]) -> None :
    Regenerates computed properties like implicit valence and ring information.
    
    

    C++ signature :
        void UpdatePropertyCache(RDKit::ROMol {lvalue} [,bool=True])

__copy__( (object)arg1) -> object :

    C++ signature :
        boost::python::api::object __copy__(boost::python::api::object)

__deepcopy__( (object)arg1, (dict)arg2) -> object :

    C++ signature :
        boost::python::api::object __deepcopy__(boost::python::api::object,boost::python::dict)

__getinitargs__( (Mol)arg1) -> tuple :

    C++ signature :
        boost::python::tuple __getinitargs__(RDKit::ROMol)

__init__( (object)arg1) -> None :
    Constructor, takes no arguments

    C++ signature :
        void __init__(_object*)

__init__( (object)arg1, (str)arg2) -> None :

    C++ signature :
        void __init__(_object*,std::string)

__init__( (object)arg1, (Mol)arg2) -> None :

    C++ signature :
        void __init__(_object*,RDKit::ROMol)

__init__( (object)arg1, (Mol)arg2, (bool)arg3) -> None :

    C++ signature :
        void __init__(_object*,RDKit::ROMol,bool)

__init__( (object)arg1, (Mol)arg2, (bool)arg3, (int)arg4) -> None :

    C++ signature :
        void __init__(_object*,RDKit::ROMol,bool,int)

Overrides: object.__init__

helper for pickle

Overrides: object.__reduce__

(inherited documentation)