Package rdkit :: Package Chem :: Module rdchem :: Class MolBundle
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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)