rdkit.Chem.rdchem.Mol

Package rdkit :: Package Chem :: Module rdchem :: Class Mol |
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# Class Mol

     object --+
              |
    ??.instance --+
                  |
                 Mol

    The Molecule class.

    In addition to the expected Atoms and Bonds, molecules contain:
      - a collection of Atom and Bond bookmarks indexed with integers
          that can be used to flag and retrieve particular Atoms or Bonds
          using the {get|set}{Atom|Bond}Bookmark() methods.

      - a set of string-valued properties. These can have arbitrary string
          labels and can be set and retrieved using the {set|get}Prop() methods
          Molecular properties can be tagged as being *computed*, in which case
            they will be automatically cleared under certain circumstances (when the
            molecule itself is modified, for example).
          Molecules also have the concept of *private* properties, which are tagged
            by beginning the property name with an underscore (_).

Instance Methods | [hide private]
AddConformer(...) AddConformer( (Mol)self, (Conformer)conf [, (bool)assignId=False]) -> int : Add a conformer to the molecule and return the conformer ID |
ClearComputedProps(...) ClearComputedProps( (Mol)arg1) -> None : Removes all computed properties from the molecule. |
ClearProp(...) ClearProp( (Mol)arg1, (str)arg2) -> None : Removes a property from the molecule. |
Debug(...) Debug( (Mol)arg1) -> None : Prints debugging information about the molecule. |
GetAtomWithIdx(...) GetAtomWithIdx( (Mol)arg1, (int)arg2) -> Atom : Returns a particular Atom. |
GetAtoms(...) GetAtoms( (Mol)arg1) -> _ROAtomSeq : Returns a read-only sequence containing all of the molecule's Atoms. |
GetBondBetweenAtoms(...) GetBondBetweenAtoms( (Mol)arg1, (int)arg2, (int)arg3) -> Bond : Returns the bond between two atoms, if there is one. |
GetBondWithIdx(...) GetBondWithIdx( (Mol)arg1, (int)arg2) -> Bond : Returns a particular Bond. |
GetBonds(...) GetBonds( (Mol)arg1) -> _ROBondSeq : Returns a read-only sequence containing all of the molecule's Bonds. |
GetConformer(...) GetConformer( (Mol)self [, (int)id=-1]) -> Conformer : Get the conformer with a specified ID |
GetConformers(...) GetConformers( (Mol)arg1) -> object : Get all the conformers as a tuple |
GetNumAtoms(...) GetNumAtoms( (Mol)arg1 [, (bool)onlyHeavy=True]) -> int : Returns the number of Atoms in the molecule. |
GetNumBonds(...) GetNumBonds( (Mol)arg1 [, (bool)onlyHeavy=True]) -> int : Returns the number of Bonds in the molecule. |
GetNumConformers(...) GetNumConformers( (Mol)arg1) -> int : Return the number of conformations on the molecule |
GetProp(...) GetProp( (Mol)arg1, (str)arg2) -> str : Returns the value of the property. |
GetPropNames(...) GetPropNames( (Mol)self [, (bool)includePrivate=False [, (bool)includeComputed=False]]) -> _vectSs : Returns a tuple with all property names for this molecule. |
GetRingInfo(...) GetRingInfo( (Mol)arg1) -> RingInfo : Returns the number of molecule's RingInfo object. |
GetSubstructMatch(...) GetSubstructMatch( (Mol)self, (Mol)query [, (bool)useChirality=False]) -> object : Returns the indices of the molecule's atoms that match a substructure query. |
GetSubstructMatches(...) GetSubstructMatches( (Mol)self, (Mol)query [, (bool)uniquify=True [, (bool)useChirality=False]]) -> object : Returns tuples of the indices of the molecule's atoms that match a substructure query. |
HasProp(...) HasProp( (Mol)arg1, (str)arg2) -> int : Queries a molecule to see if a particular property has been assigned. |
HasSubstructMatch(...) HasSubstructMatch( (Mol)self, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False]]) -> bool : Queries whether or not the molecule contains a particular substructure. |
RemoveAllConformers(...) RemoveAllConformers( (Mol)arg1) -> None : Remove all the conformations on the molecule |
RemoveConformer(...) RemoveConformer( (Mol)arg1, (int)arg2) -> None : Remove the conformer with the specified ID |
SetProp(...) SetProp( (Mol)self, (str)key, (str)val [, (bool)computed=False]) -> None : Sets a molecular property |
ToBinary(...) ToBinary( (Mol)arg1) -> str : Returns a binary string representation of the molecule. |
UpdatePropertyCache(...) UpdatePropertyCache( (Mol)self [, (bool)strict=True]) -> None : Regenerates computed properties like implicit valence and ring information. |
__getinitargs__(...) __getinitargs__( (Mol)arg1) -> tuple : |
__init__(...) __init__( (object)arg1) -> None : Constructor, takes no arguments |
__reduce__(...) helper for pickle |
Inherited from `unreachable.instance`: `__new__` Inherited from `object`: `__delattr__`, `__getattribute__`, `__hash__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__str__`

Class Variables | [hide private]
| __instance_size__ = `16`
| __safe_for_unpickling__ = `True`

Properties | [hide private]
Inherited from `object`: `__class__`

Method Details | [hide private]

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

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

### ClearProp(...) |
    ClearProp( (Mol)arg1, (str)arg2) -> None :
        Removes a property from the molecule.

          ARGUMENTS:
            - key: the name of the property to clear (a string).

          NOTE:
            - If the property has not been set, a KeyError exception will be raised.

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

### Debug(...) |
    Debug( (Mol)arg1) -> None :
        Prints debugging information about the molecule.

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

### GetAtomWithIdx(...) |
    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(...) |
    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*)

### GetBondBetweenAtoms(...) |
    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(...) |
    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(...) |
    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*)

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

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

### GetNumAtoms(...) |
    GetNumAtoms( (Mol)arg1 [, (bool)onlyHeavy=True]) -> int :
        Returns the number of Atoms in the molecule.

          ARGUMENTS:
            - onlyHeavy: (optional) include only heavy atoms (not Hs)
                         defaults to 1.

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

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

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

### GetProp(...) |
    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(...) |
    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]])

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

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

### GetSubstructMatch(...) |
    GetSubstructMatch( (Mol)self, (Mol)query [, (bool)useChirality=False]) -> object :
        Returns the indices of the molecule's atoms that match a substructure query.

          ARGUMENTS:
            - query: a Molecule

            - useChirality: (optional)

          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])

### GetSubstructMatches(...) |
    GetSubstructMatches( (Mol)self, (Mol)query [, (bool)uniquify=True [, (bool)useChirality=False]]) -> 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: (optional)

          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]])

### HasProp(...) |
    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(...) |
    HasSubstructMatch( (Mol)self, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False]]) -> bool :
        Queries whether or not the molecule contains a particular substructure.

          ARGUMENTS:
            - query: a Molecule

            - recursionPossible: (optional)

            - useChirality: (optional)

          RETURNS: 1 or 0

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

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

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

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

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

### SetProp(...) |
    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 0.

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

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

        C++ signature :
            std::string ToBinary(RDKit::ROMol)

### UpdatePropertyCache(...) |
    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])

### __getinitargs__(...) |
    __getinitargs__( (Mol)arg1) -> tuple :

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

### __init__(...) (Constructor) |
    __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)
Overrides: object.__init__

### __reduce__(...) |
    helper for pickle
Overrides: object.__reduce__ (inherited documentation)