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)