Package rdkit :: Package Chem :: Module rdchem :: Class ResonanceMolSupplier
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Class ResonanceMolSupplier

 object --+    
          |    
??.instance --+
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             ResonanceMolSupplier

A class which supplies resonance structures (as mols) from a mol.

Usage examples:

  1) Lazy evaluation: the resonance structures are not constructed
     until we ask for them:
     >>> suppl = ResonanceMolSupplier(mol)
     >>> for resMol in suppl:
     ...    resMol.GetNumAtoms()

  2) Lazy evaluation 2:
     >>> suppl = ResonanceMolSupplier(mol)
     >>> resMol1 = suppl.next()
     >>> resMol2 = suppl.next()
     >>> suppl.reset()
     >>> resMol3 = suppl.next()
     # resMol3 and resMol1 are the same: 
     >>> MolToSmiles(resMol3)==MolToSmiles(resMol1)

  3) Random Access:
     >>> suppl = ResonanceMolSupplier(mol)
     >>> resMol1 = suppl[0] 
     >>> resMol2 = suppl[1] 
     NOTE: this will generate an IndexError if the supplier doesn't have that many
     molecules.

  4) Random Access 2: looping over all resonance structures
     >>> suppl = ResonanceMolSupplier(mol)
     >>> nResMols = len(suppl)
     >>> for i in range(nResMols):
     ...   suppl[i].GetNumAtoms()

Instance Methods [hide private]
 
Enumerate(...)
Enumerate( (ResonanceMolSupplier)arg1) -> None : Ask ResonanceMolSupplier to enumerate resonance structures(automatically done as soon as any attempt to access them is made)
 
GetAtomConjGrpIdx(...)
GetAtomConjGrpIdx( (ResonanceMolSupplier)arg1, (int)arg2) -> int : Given an atom index, it returns the index of the conjugated groupthe atom belongs to, or -1 if it is not conjugated
 
GetBondConjGrpIdx(...)
GetBondConjGrpIdx( (ResonanceMolSupplier)arg1, (int)arg2) -> int : Given a bond index, it returns the index of the conjugated groupthe bond belongs to, or -1 if it is not conjugated
 
GetIsEnumerated(...)
GetIsEnumerated( (ResonanceMolSupplier)arg1) -> bool : Returns true if resonance structure enumeration has already happened
 
GetNumConjGrps(...)
GetNumConjGrps( (ResonanceMolSupplier)arg1) -> int : Returns the number of individual conjugated groups in the molecule
 
GetSubstructMatch(...)
GetSubstructMatch( (ResonanceMolSupplier)self, (Mol)query [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]) -> object : Returns the indices of the molecule's atoms that match a substructure query, taking into account all resonance structures in ResonanceMolSupplier.
 
GetSubstructMatches(...)
GetSubstructMatches( (ResonanceMolSupplier)self, (Mol)query [, (bool)uniquify=False [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False [, (int)maxMatches=1000 [, (int)numThreads=1]]]]]) -> object : Returns tuples of the indices of the molecule's atoms that match a substructure query, taking into account all resonance structures in ResonanceMolSupplier.
 
SetNumThreads(...)
SetNumThreads( (ResonanceMolSupplier)arg1, (int)arg2) -> None : Sets the number of threads to be used to enumerate resonance structures (defaults to 1; 0 selects the number of concurrent threads supported by the hardware; negative values are added to the number of concurrent threads supported by the hardware)
 
__getitem__(...)
__getitem__( (ResonanceMolSupplier)arg1, (int)arg2) -> Mol :
 
__init__(...)
__init__( (object)arg1, (Mol)mol [, (int)flags=0 [, (int)maxStructs=1000]]) -> None :
 
__iter__(...)
__iter__( (ResonanceMolSupplier)arg1) -> ResonanceMolSupplier :
 
__len__(...)
__len__( (ResonanceMolSupplier)arg1) -> int :
 
__reduce__(...)
helper for pickle
 
atEnd(...)
atEnd( (ResonanceMolSupplier)arg1) -> bool : Returns whether or not we have hit the end of the resonance structure supplier.
 
next(...)
next( (ResonanceMolSupplier)arg1) -> Mol : Returns the next resonance structure in the supplier.
 
reset(...)
reset( (ResonanceMolSupplier)arg1) -> None : Resets our position in the resonance structure supplier to the beginning.

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__ = 152
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

Enumerate(...)

 

Enumerate( (ResonanceMolSupplier)arg1) -> None :
    Ask ResonanceMolSupplier to enumerate resonance structures(automatically done as soon as any attempt to access them is made)
    

    C++ signature :
        void Enumerate(RDKit::ResonanceMolSupplier {lvalue})

GetAtomConjGrpIdx(...)

 

GetAtomConjGrpIdx( (ResonanceMolSupplier)arg1, (int)arg2) -> int :
    Given an atom index, it returns the index of the conjugated groupthe atom belongs to, or -1 if it is not conjugated
    

    C++ signature :
        unsigned int GetAtomConjGrpIdx(RDKit::ResonanceMolSupplier {lvalue},unsigned int)

GetBondConjGrpIdx(...)

 

GetBondConjGrpIdx( (ResonanceMolSupplier)arg1, (int)arg2) -> int :
    Given a bond index, it returns the index of the conjugated groupthe bond belongs to, or -1 if it is not conjugated
    

    C++ signature :
        unsigned int GetBondConjGrpIdx(RDKit::ResonanceMolSupplier {lvalue},unsigned int)

GetIsEnumerated(...)

 

GetIsEnumerated( (ResonanceMolSupplier)arg1) -> bool :
    Returns true if resonance structure enumeration has already happened
    

    C++ signature :
        bool GetIsEnumerated(RDKit::ResonanceMolSupplier {lvalue})

GetNumConjGrps(...)

 

GetNumConjGrps( (ResonanceMolSupplier)arg1) -> int :
    Returns the number of individual conjugated groups in the molecule
    

    C++ signature :
        unsigned int GetNumConjGrps(RDKit::ResonanceMolSupplier {lvalue})

GetSubstructMatch(...)

 

GetSubstructMatch( (ResonanceMolSupplier)self, (Mol)query [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False]]) -> object :
    Returns the indices of the molecule's atoms that match a substructure query,
    taking into account all resonance structures in ResonanceMolSupplier.
    
      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::ResonanceMolSupplier {lvalue},RDKit::ROMol [,bool=False [,bool=False]])

GetSubstructMatches(...)

 

GetSubstructMatches( (ResonanceMolSupplier)self, (Mol)query [, (bool)uniquify=False [, (bool)useChirality=False [, (bool)useQueryQueryMatches=False [, (int)maxMatches=1000 [, (int)numThreads=1]]]]]) -> object :
    Returns tuples of the indices of the molecule's atoms that match a substructure query,
    taking into account all resonance structures in ResonanceMolSupplier.
    
      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
    
        - numThreads: The number of threads to be used (defaults to 1; 0 selects the
                      number of concurrent threads supported by the hardware; negative
                      values are added to the number of concurrent threads supported
                      by the hardware).
    
      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::ResonanceMolSupplier {lvalue},RDKit::ROMol [,bool=False [,bool=False [,bool=False [,unsigned int=1000 [,int=1]]]]])

SetNumThreads(...)

 

SetNumThreads( (ResonanceMolSupplier)arg1, (int)arg2) -> None :
    Sets the number of threads to be used to enumerate resonance
    structures (defaults to 1; 0 selects the number of concurrent
    threads supported by the hardware; negative values are added
    to the number of concurrent threads supported by the hardware)
    

    C++ signature :
        void SetNumThreads(RDKit::ResonanceMolSupplier {lvalue},unsigned int)

__getitem__(...)
(Indexing operator)

 

__getitem__( (ResonanceMolSupplier)arg1, (int)arg2) -> Mol :

    C++ signature :
        RDKit::ROMol* __getitem__(RDKit::ResonanceMolSupplier*,int)

__init__(...)
(Constructor)

 

__init__( (object)arg1, (Mol)mol [, (int)flags=0 [, (int)maxStructs=1000]]) -> None :

    C++ signature :
        void __init__(_object*,RDKit::ROMol {lvalue} [,unsigned int=0 [,unsigned int=1000]])

Overrides: object.__init__

__iter__(...)

 

__iter__( (ResonanceMolSupplier)arg1) -> ResonanceMolSupplier :

    C++ signature :
        RDKit::ResonanceMolSupplier* __iter__(RDKit::ResonanceMolSupplier*)

__len__(...)
(Length operator)

 

__len__( (ResonanceMolSupplier)arg1) -> int :

    C++ signature :
        unsigned int __len__(RDKit::ResonanceMolSupplier {lvalue})

__reduce__(...)

 
helper for pickle

Overrides: object.__reduce__
(inherited documentation)

atEnd(...)

 

atEnd( (ResonanceMolSupplier)arg1) -> bool :
    Returns whether or not we have hit the end of the resonance structure supplier.
    

    C++ signature :
        bool atEnd(RDKit::ResonanceMolSupplier {lvalue})

next(...)

 

next( (ResonanceMolSupplier)arg1) -> Mol :
    Returns the next resonance structure in the supplier. Raises _StopIteration_ on end.
    

    C++ signature :
        RDKit::ROMol* next(RDKit::ResonanceMolSupplier*)

reset(...)

 

reset( (ResonanceMolSupplier)arg1) -> None :
    Resets our position in the resonance structure supplier to the beginning.
    

    C++ signature :
        void reset(RDKit::ResonanceMolSupplier {lvalue})