Package rdkit :: Package Chem :: Module rdchem :: Class RWMol
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Class RWMol

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

The RW molecule class (read/write)

This class is a more-performant version of the EditableMolecule class in that
it is a 'live' molecule and shares the interface from the Mol class.
All changes are performed without the need to create a copy of the
molecule using GetMol() (this is still available, however).

n.b. Eventually this class may become a direct replacement for EditableMol

Instance Methods [hide private]
 
AddAtom(...)
AddAtom( (RWMol)mol, (Atom)atom) -> int : add an atom, returns the index of the newly added atom
 
AddBond(...)
AddBond( (RWMol)mol, (int)beginAtomIdx, (int)endAtomIdx [, (BondType)order=rdkit.Chem.rdchem.BondType.UNSPECIFIED]) -> int : add a bond, returns the new number of bonds
 
GetMol(...)
GetMol( (RWMol)arg1) -> Mol : Returns a Mol (a normal molecule)
 
RemoveAtom(...)
RemoveAtom( (RWMol)arg1, (int)arg2) -> None : Remove the specified atom from the molecule
 
RemoveBond(...)
RemoveBond( (RWMol)arg1, (int)arg2, (int)arg3) -> None : Remove the specified bond from the molecule
 
ReplaceAtom(...)
ReplaceAtom( (RWMol)mol, (int)index, (Atom)newAtom) -> None : replaces the specified atom with the provided one
 
ReplaceBond(...)
ReplaceBond( (RWMol)mol, (int)index, (Bond)newBond) -> None : replaces the specified bond with the provided one
 
__copy__(...)
__copy__( (AtomPairsParameters)arg1) -> object :
 
__deepcopy__(...)
__deepcopy__( (AtomPairsParameters)arg1, (dict)arg2) -> object :
 
__init__(...)
__init__( (object)arg1, (Mol)arg2) -> None : Construct from a Mol

Inherited from Mol: AddConformer, ClearComputedProps, ClearProp, Compute2DCoords, ComputeGasteigerCharges, Debug, GetAromaticAtoms, GetAtomWithIdx, GetAtoms, GetAtomsMatchingQuery, GetBondBetweenAtoms, GetBondWithIdx, GetBonds, GetBoolProp, GetConformer, GetConformers, GetDoubleProp, GetIntProp, GetNumAtoms, GetNumBonds, GetNumConformers, GetNumHeavyAtoms, GetProp, GetPropNames, GetPropsAsDict, GetRingInfo, GetSubstructMatch, GetSubstructMatches, GetUnsignedProp, HasProp, HasSubstructMatch, NeedsUpdatePropertyCache, RemoveAllConformers, RemoveConformer, SetBoolProp, SetDoubleProp, SetIntProp, SetProp, SetUnsignedProp, ToBinary, UpdatePropertyCache, __ge__, __getinitargs__, __reduce__, __str__

Inherited from unreachable.instance: __new__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Variables [hide private]
  __instance_size__ = 256

Inherited from Mol: __safe_for_unpickling__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

AddAtom(...)

 

AddAtom( (RWMol)mol, (Atom)atom) -> int :
    add an atom, returns the index of the newly added atom

    C++ signature :
        int AddAtom(RDKit::ReadWriteMol {lvalue},RDKit::Atom*)

AddBond(...)

 

AddBond( (RWMol)mol, (int)beginAtomIdx, (int)endAtomIdx [, (BondType)order=rdkit.Chem.rdchem.BondType.UNSPECIFIED]) -> int :
    add a bond, returns the new number of bonds

    C++ signature :
        int AddBond(RDKit::ReadWriteMol {lvalue},unsigned int,unsigned int [,RDKit::Bond::BondType=rdkit.Chem.rdchem.BondType.UNSPECIFIED])

GetMol(...)

 

GetMol( (RWMol)arg1) -> Mol :
    Returns a Mol (a normal molecule)

    C++ signature :
        RDKit::ROMol* GetMol(RDKit::ReadWriteMol {lvalue})

RemoveAtom(...)

 

RemoveAtom( (RWMol)arg1, (int)arg2) -> None :
    Remove the specified atom from the molecule

    C++ signature :
        void RemoveAtom(RDKit::ReadWriteMol {lvalue},unsigned int)

RemoveBond(...)

 

RemoveBond( (RWMol)arg1, (int)arg2, (int)arg3) -> None :
    Remove the specified bond from the molecule

    C++ signature :
        void RemoveBond(RDKit::ReadWriteMol {lvalue},unsigned int,unsigned int)

ReplaceAtom(...)

 

ReplaceAtom( (RWMol)mol, (int)index, (Atom)newAtom) -> None :
    replaces the specified atom with the provided one

    C++ signature :
        void ReplaceAtom(RDKit::ReadWriteMol {lvalue},unsigned int,RDKit::Atom*)

ReplaceBond(...)

 

ReplaceBond( (RWMol)mol, (int)index, (Bond)newBond) -> None :
    replaces the specified bond with the provided one

    C++ signature :
        void ReplaceBond(RDKit::ReadWriteMol {lvalue},unsigned int,RDKit::Bond*)

__copy__(...)

 

__copy__( (AtomPairsParameters)arg1) -> object :

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

Overrides: Mol.__copy__

__deepcopy__(...)

 

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

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

Overrides: Mol.__deepcopy__

__init__(...)
(Constructor)

 

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

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

__init__( (object)arg1) -> None :

    C++ signature :
        void __init__(_object*)

__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__