rdkit.Chem.rdchem.RWMol

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)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__