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

Class RGroupDecomposition

 object --+    
          |    
??.instance --+
              |
             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)

Class RGroupDecomposition

Add(...)

GetRGroupsAsColumns(...)

GetRGroupsAsRows(...)

Process(...)

__init__(...) (Constructor)

__reduce__(...)

init(...)
(Constructor)

reduce(...)