Makes sense, thank you Ivan! Doctoral Researcher Environmental Cheminformatics UNIVERSITÉ DU LUXEMBOURG
Campus Belval | Luxembourg Centre for Systems Biomedicine 6, avenue du Swing, L-4367 Belvaux T +356 46 66 44 67 18 https://adelenel.ai ________________________________ From: Ivan Tubert-Brohman <ivan.tubert-broh...@schrodinger.com> 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 explicit hydrogens to your molecule: molh = Chem.AddHs(mol) molh.HasSubstructMatch(q1) > True However, if all you want to know is whether the oxygen is next to a hydrogen, you can make the hydrogen count a property of the oxygen atom by using SMARTS: q3s = 'CCOCCOCCC[OH]' q3 = Chem.MolFromSmarts(q3s) mol.HasSubstructMatch(q3) > True Hope this helps, Ivan
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