Good afternoon folks, I would imagine that if you remove the hydrogens, the resulting molecule would be a substructure of the original molecule. However, when I do the following to the attached MDL mol file, there is no matches.
>>> from rdkit import Chem
>>> mol = Chem.MolFromMolFile('temp.mol', removeHs=False)
>>> mhvy = Chem.RemoveHs(mol)
>>> matches = mol.GetSubstructMatches(mhvy)
matches turns out to be empty.
Is it something to do with the difference between Smarts
and Smiles? If so, how can I work around this to obtain
the atomic index relationship between the two molecules?
Thank you for your insight.
Ling
temp.mol
Description: Binary data
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