rdkit.Chem.rdchem.MolBundle

Package rdkit :: Package Chem :: Module rdchem :: Class MolBundle |
[hide private]
[frames] | no frames]

# Class MolBundle

     object --+
              |
    ??.instance --+
                  |
                 MolBundle

    A class for storing gropus of related molecules.
    Here related means that the molecules have to have the same number of atoms.

Instance Methods | [hide private]
AddMol(...) AddMol( (MolBundle)arg1, (Mol)arg2) -> int : |
GetMol(...) GetMol( (MolBundle)arg1, (int)arg2) -> Mol : |
GetSubstructMatch(...) GetSubstructMatch( (MolBundle)self, (Mol)query [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]) -> object : Returns the indices of the atoms from the first molecule in a bundle that matches a substructure query. |
GetSubstructMatches(...) GetSubstructMatches( (MolBundle)self, (Mol)query [, (bool)uniquify=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False [, (int)maxMatches=1000]]]]) -> object : Returns tuple of all indices of the atoms from the first molecule in a bundle that matches a substructure query. |
HasSubstructMatch(...) HasSubstructMatch( (MolBundle)self, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool : Queries whether or not any molecule in the bundle contains a particular substructure. |
Size(...) Size( (MolBundle)arg1) -> int : |
__getitem__(...) __getitem__( (MolBundle)arg1, (int)arg2) -> Mol : |
__init__(...) __init__( (object)arg1) -> None : |
__len__(...) __len__( (MolBundle)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__ = `80`

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

Method Details | [hide private]

### AddMol(...) |
    AddMol( (MolBundle)arg1, (Mol)arg2) -> int :

        C++ signature :
            unsigned long AddMol(RDKit::MolBundle {lvalue},boost::shared_ptr<RDKit::ROMol>)

### GetMol(...) |
    GetMol( (MolBundle)arg1, (int)arg2) -> Mol :

        C++ signature :
            boost::shared_ptr<RDKit::ROMol> GetMol(RDKit::MolBundle {lvalue},unsigned long)

### GetSubstructMatch(...) |
    GetSubstructMatch( (MolBundle)self, (Mol)query [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]) -> object :
        Returns the indices of the atoms from the first molecule in a bundle that matches 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::MolBundle,RDKit::ROMol [,bool=False [,bool=False]])

    GetSubstructMatch( (MolBundle)self, (MolBundle)query [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]) -> object :
        Returns the indices of the atoms from the first molecule in a bundle that matches a substructure query from a bundle.

          ARGUMENTS:
            - query: a MolBundle

            - 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::MolBundle,RDKit::MolBundle [,bool=False [,bool=False]])

### GetSubstructMatches(...) |
    GetSubstructMatches( (MolBundle)self, (Mol)query [, (bool)uniquify=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False [, (int)maxMatches=1000]]]]) -> object :
        Returns tuple of all indices of the atoms from the first molecule in a bundle that matches 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::MolBundle,RDKit::ROMol [,bool=True [,bool=False [,bool=False [,unsigned int=1000]]]])

    GetSubstructMatches( (MolBundle)self, (MolBundle)query [, (bool)uniquify=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False [, (int)maxMatches=1000]]]]) -> object :
        Returns tuple of all indices of the atoms from the first molecule in a bundle that matches a substructure query from the second bundle.

          ARGUMENTS:
            - query: a MolBundle.
            - 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::MolBundle,RDKit::MolBundle [,bool=True [,bool=False [,bool=False [,unsigned int=1000]]]])

### HasSubstructMatch(...) |
    HasSubstructMatch( (MolBundle)self, (Mol)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool :
        Queries whether or not any molecule in the bundle 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::MolBundle,RDKit::ROMol [,bool=True [,bool=False [,bool=False]]])

    HasSubstructMatch( (MolBundle)self, (MolBundle)query [, (bool)recursionPossible=True [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]]) -> bool :
        Queries whether or not any molecule in the first bundle matches any molecule in the second bundle.

          ARGUMENTS:
            - query: a MolBundle

            - 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::MolBundle,RDKit::MolBundle [,bool=True [,bool=False [,bool=False]]])

### Size(...) |
    Size( (MolBundle)arg1) -> int :

        C++ signature :
            unsigned long Size(RDKit::MolBundle {lvalue})

### __getitem__(...) (Indexing operator) |
    __getitem__( (MolBundle)arg1, (int)arg2) -> Mol :

        C++ signature :
            boost::shared_ptr<RDKit::ROMol> __getitem__(RDKit::MolBundle {lvalue},unsigned long)

### __init__(...) (Constructor) |
    __init__( (object)arg1) -> None :

        C++ signature :
            void __init__(_object*)
Overrides: object.__init__

### __len__(...) (Length operator) |
    __len__( (MolBundle)arg1) -> int :

        C++ signature :
            unsigned long __len__(RDKit::MolBundle {lvalue})

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