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)arg1, (Atom)atom) -> int : add an atom, returns the index of the newly added atom

AddBond(...)
AddBond( (RWMol)arg1, (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)arg1, (int)index, (Atom)newAtom [, (bool)updateLabel=False [, (bool)preserveProps=False]]) -> None : replaces the specified atom with the provided one If updateLabel is True, the new atom becomes the active atom If preserveProps is True preserve keep the existing props unless explicit set on the new atom

ReplaceBond(...)
ReplaceBond( (RWMol)arg1, (int)index, (Bond)newBond [, (bool)preserveProps=False]) -> 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)arg1, (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)arg1, (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)arg1, (int)index, (Atom)newAtom [, (bool)updateLabel=False [, (bool)preserveProps=False]]) -> None :
    replaces the specified atom with the provided one
    If updateLabel is True, the new atom becomes the active atom
    If preserveProps is True preserve keep the existing props unless explicit set on the new atom

    C++ signature :
        void ReplaceAtom(RDKit::ReadWriteMol {lvalue},unsigned int,RDKit::Atom* [,bool=False [,bool=False]])

ReplaceBond(...)


ReplaceBond( (RWMol)arg1, (int)index, (Bond)newBond [, (bool)preserveProps=False]) -> None :
    replaces the specified bond with the provided one.
    If preserveProps is True preserve keep the existing props unless explicit set on the new bond

    C++ signature :
        void ReplaceBond(RDKit::ReadWriteMol {lvalue},unsigned int,RDKit::Bond* [,bool=False])

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__

Class RWMol

AddAtom(...)

AddBond(...)

GetMol(...)

RemoveAtom(...)

RemoveBond(...)

ReplaceAtom(...)

ReplaceBond(...)

__copy__(...)

__deepcopy__(...)

__init__(...) (Constructor)

copy(...)

deepcopy(...)

init(...)
(Constructor)