Hi Paolo, Thank you very much for this! This clarified issues I hadn’t even thought about yet
Cheers Markus From: Paolo Tosco <paolo.tosco.m...@gmail.com> Sent: Tuesday, November 5, 2019 2:49 PM To: Markus Heller <mhel...@admarebio.com>; rdkit-discuss (rdkit-discuss@lists.sourceforge.net) <rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] Explicit H in substructure searches Hi Markus, I tried to put together a comprehensible explanation in his gist: https://gist.github.com/ptosco/1088937ce332bd66c999a2a5fbc855b3 Please also refer to the following threads on the mailing list: https://sourceforge.net/p/rdkit/mailman/message/29679834/ https://sourceforge.net/p/rdkit/mailman/message/36696340/ and to this blog post by Roger Sayle: https://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/ for further clarifications. Cheers, p. On 05/11/2019 19:52, Markus Heller wrote: Hi, I’m trying to understand how to properly use explicit hydrogens in substructure searches. Below is an example. I would like to find all molecules that contain my query with hydrogens at the nitrogens, and I thought I was on the right track … Why does the first query with the explicit H not match m1? Thanks Markus <code> from rdkit import Chem from rdkit.Chem.Draw import IPythonConsole from rdkit.Chem import rdDepictor rdDepictor.SetPreferCoordGen(True) IPythonConsole.ipython_useSVG = True m1 = Chem.MolFromSmiles('c1cn[nH]c1N') m2 = Chem.MolFromSmiles('CNc1ccn[nH]1') m3 = Chem.MolFromSmiles('Nc1ccnn(C)1') # do not remove explicit H params = Chem.SmilesParserParams() params.removeHs=False query = Chem.MolFromSmiles('c1cn[nH]c(N([H])([H]))1', params) # first should be True, but all are False m1.HasSubstructMatch(query) m2.HasSubstructMatch(query) m3.HasSubstructMatch(query) # rebuild query with explicit H removed, not what I want query = Chem.MolFromSmiles('c1cn[nH]c(N([H])([H]))1') m1.HasSubstructMatch(query) m2.HasSubstructMatch(query) m3.HasSubstructMatch(query) </code> -- Markus Heller, PhD Senior Scientist Direct: 604.827.1122 Main: 604.827.1147 [A027228F] 2405 Wesbrook Mall, 4th Floor, Vancouver, BC V6T 1Z3 This email and any attachments thereto may contain confidential material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto. _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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