rdkit.Chem.rdRGroupDecomposition.RGroupDecomposition

Package rdkit :: Package Chem :: Module rdRGroupDecomposition :: Class RGroupDecomposition |
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# Class RGroupDecomposition

     object --+
              |
    ??.instance --+
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                 RGroupDecomposition

    RGroupDecompositionParameters controls how the RGroupDecomposition sets labelling and matches structures
    OPTIONS:
      - RGroupCoreAlignment: can be one of RGroupCoreAlignment.None or RGroupCoreAlignment.MCS
                             If set to MCS, cores labels are mapped to each other using their
                             Maximum common substructure overlap.
      - RGroupLabels: optionally set where the rgroup labels to use are encoded.
                       RroupLabels.IsotopeLabels - labels are stored on isotopes
                       RroupLabels.AtomMapLabels - labels are stored on atommaps
                       RroupLabels.AtomIndexLabels - use the atom index as the label
                       RGroupLabels.RelabelDuplicateLabels - fix any duplicate labels
                       RGroupLabels.AutoDetect - auto detect the label [default]
         Note: in all cases, any rgroups found on unlabelled atoms will be automatically
                labelled.
      - RGroupLabelling: choose where the rlabels are stored on the decomposition
                          RGroupLabels.AtomMap - store rgroups as atom maps (for smiles)
                          RGroupLabels.Isotope - stroe rgroups on the isotope
                          RGroupLabels.MDLRGroup - store rgroups as mdl rgroups (for molblocks)
                         default: AtomMap | MDLRGroup
      - matchOnlyAtRGroups: only allow rgroup decomposition at the specified rgroups
      - setRemoveRGroupsThatAreAllHydrogen: remove all rgroups that only have hydrogens
      - removeHydrogensPostMatch: remove all hydrogens from the output molecules

Instance Methods | [hide private]
Add(...) Add( (RGroupDecomposition)arg1, (Mol)arg2) -> int : |
GetRGroupsAsColumns(...) GetRGroupsAsColumns( (RGroupDecomposition)arg1 [, (bool)asSmiles=False]) -> dict : Return the rgroups as columns (note: can be fed directrly into a pandas datatable) ARGUMENTS: - asSmiles: if True return smiles strings, otherwise return molecules [default: False] Column structure: columns[rgroup_label] = [ mols_or_smiles ] |
GetRGroupsAsRows(...) GetRGroupsAsRows( (RGroupDecomposition)arg1 [, (bool)asSmiles=False]) -> list : Return the rgroups as rows (note: can be fed directrly into a pandas datatable) ARGUMENTS: - asSmiles: if True return smiles strings, otherwise return molecules [default: False] Row structure: rows[idx] = {rgroup_label: molecule_or_smiles} |
Process(...) Process( (RGroupDecomposition)arg1) -> bool : Process the rgroups (must be done prior to GetRGroupsAsRows/Columns) |
__init__(...) __init__( (object)arg1, (AtomPairsParameters)arg2) -> None : Construct from a molecule or sequence of molecules |
__reduce__(...) helper for pickle |
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__ = `24`

Properties | [hide private]
Inherited from `object`: `__class__`

Method Details | [hide private]

### Add(...) |
    Add( (RGroupDecomposition)arg1, (Mol)arg2) -> int :

        C++ signature :
            int Add(RDKit::RGroupDecompositionHelper {lvalue},RDKit::ROMol)

### GetRGroupsAsColumns(...) |
    GetRGroupsAsColumns( (RGroupDecomposition)arg1 [, (bool)asSmiles=False]) -> dict :
        Return the rgroups as columns (note: can be fed directrly into a pandas datatable)
          ARGUMENTS:
           - asSmiles: if True return smiles strings, otherwise return molecules [default: False]
            Column structure:
               columns[rgroup_label] = [ mols_or_smiles ]

        C++ signature :
            boost::python::dict GetRGroupsAsColumns(RDKit::RGroupDecompositionHelper {lvalue} [,bool=False])

### GetRGroupsAsRows(...) |
    GetRGroupsAsRows( (RGroupDecomposition)arg1 [, (bool)asSmiles=False]) -> list :
        Return the rgroups as rows (note: can be fed directrly into a pandas datatable)
          ARGUMENTS:
           - asSmiles: if True return smiles strings, otherwise return molecules [default: False]
            Row structure:
               rows[idx] = {rgroup_label: molecule_or_smiles}

        C++ signature :
            boost::python::list GetRGroupsAsRows(RDKit::RGroupDecompositionHelper {lvalue} [,bool=False])

### Process(...) |
    Process( (RGroupDecomposition)arg1) -> bool :
        Process the rgroups (must be done prior to GetRGroupsAsRows/Columns)

        C++ signature :
            bool Process(RDKit::RGroupDecompositionHelper {lvalue})

### __init__(...) (Constructor) |
    __init__( (object)arg1, (AtomPairsParameters)arg2) -> None :
        Construct from a molecule or sequence of molecules

        C++ signature :
            void __init__(_object*,boost::python::api::object)

    __init__( (object)arg1, (AtomPairsParameters)arg2, (RGroupDecompositionParameters)arg3) -> None :
        Construct from a molecule or sequence of molecules and a parameters object

        C++ signature :
            void __init__(_object*,boost::python::api::object,RDKit::RGroupDecompositionParameters)
Overrides: object.__init__

### __reduce__(...) |
    helper for pickle
Overrides: object.__reduce__ (inherited documentation)