rdkit.VLib.NodeLib.SmartsRemover module — The RDKit 2025.09.6 documentation

# rdkit.VLib.NodeLib.SmartsRemover module

class rdkit.VLib.NodeLib.SmartsRemover.SmartsRemover(patterns=[], wholeFragments=1, **kwargs)

  Bases: `TransformNode`

  transforms molecules by removing atoms matching smarts patterns

  Assumptions:

  > - inputs are molecules

  Sample Usage:

        >>> smis = ['C1CCC1.C=O','C1CCC1C=O','CCC=O.C=O','NCC=O.C=O.CN']
        >>> mols = [Chem.MolFromSmiles(x) for x in smis]
        >>> from rdkit.VLib.Supply import SupplyNode
        >>> suppl = SupplyNode(contents=mols)
        >>> ms = [x for x in suppl]
        >>> len(ms)
        4

    We can pass in SMARTS strings: >>> smas = [‘C=O’,’CN’] >>> tform = SmartsRemover(patterns=smas) >>> tform.AddParent(suppl) >>> ms = [x for x in tform] >>> len(ms) 4 >>> Chem.MolToSmiles(ms[0]) ‘C1CCC1’ >>> Chem.MolToSmiles(ms[1]) ‘O=CC1CCC1’ >>> Chem.MolToSmiles(ms[2]) ‘CCC=O’ >>> Chem.MolToSmiles(ms[3]) ‘NCC=O’

    We can also remove pieces of the molecule that are not complete fragments: >>> tform.Destroy() >>> smas = [‘C=O’,’CN’] >>> smas = [Chem.MolFromSmarts(x) for x in smas] >>> tform = SmartsRemover(patterns=smas,wholeFragments=0) >>> tform.AddParent(suppl) >>> ms = [x for x in tform] >>> len(ms) 4 >>> Chem.MolToSmiles(ms[0]) ‘C1CCC1’ >>> Chem.MolToSmiles(ms[1]) ‘C1CCC1’ >>> Chem.MolToSmiles(ms[3]) ‘’

    Or patterns themselves: >>> tform.Destroy() >>> smas = [‘C=O’,’CN’] >>> smas = [Chem.MolFromSmarts(x) for x in smas] >>> tform = SmartsRemover(patterns=smas) >>> tform.AddParent(suppl) >>> ms = [x for x in tform] >>> len(ms) 4 >>> Chem.MolToSmiles(ms[0]) ‘C1CCC1’ >>> Chem.MolToSmiles(ms[3]) ‘NCC=O’

  transform(cmpd)