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

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

__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__

Class Variables

[hide private]

__instance_size__ = 240

Inherited from Mol: __safe_for_unpickling__

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*)

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, (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: Mol.__init__

class RWMol

AddAtom(...)

AddBond(...)

GetMol(...)

RemoveAtom(...)

RemoveBond(...)

ReplaceAtom(...)

__copy__(...)

__deepcopy__(...)

__init__(...) (Constructor)

copy(...)

deepcopy(...)

init(...)
(Constructor)