Re: [Rdkit-discuss] Hydrogens not recognised as Dummy Atoms?

Tubert-Brohman Sent: 08 July 2021 19:02:10 To: Adelene LAI Cc: rdkit-discuss Subject: Re: [Rdkit-discuss] Hydrogens not recognised as Dummy Atoms? Hi Adelene, You can't match an atom that doesn't exist as a node in the molecular graph, so if you really want to match a hydrogen, you'll have to add

Re: [Rdkit-discuss] Hydrogens not recognised as Dummy Atoms?

Hi Adelene, You can't match an atom that doesn't exist as a node in the molecular graph, so if you really want to match a hydrogen, you'll have to add explicit hydrogens to your molecule: molh = Chem.AddHs(mol) molh.HasSubstructMatch(q1) > True However, if all you want to know is whether the

[Rdkit-discuss] Hydrogens not recognised as Dummy Atoms?

Hi RDKit Community, I've observed that hydrogens are not recognised as dummy atoms when trying to do substructure matching. Is there a way to make them so? Ideally without adding explicitHs. - smi = 'CCOCCOCCCO' mol = Chem.MolFromSmiles(smi) #with dummy atom q1s = 'CCOCCOCCCO*' q1m =