Greg, You hit the nail on the head! I did attempt to use it for a substructure search with the intention of restricting valence states, but I screwed up and forgot the Chem.MergeQueryHs() command!
I did end up taking a different approach as described in an older RDkit blog post [1] using dummy atoms, since this seems to be an easier way to define substitutions on carbon atoms. Either way, I’ve just started to work on my Python skills and have to say that I’m beginning to appreciate what a powerful tool RDkit is, so thanks for that!! Markus [1] http://rdkit.blogspot.com/2016/07/tuning-substructure-queries-ii.html From: Greg Landrum <greg.land...@gmail.com> Sent: Tuesday, November 5, 2019 11:26 PM To: Markus Heller <mhel...@admarebio.com> Cc: rdkit-discuss (rdkit-discuss@lists.sourceforge.net) <rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] Explicit H in substructure searches Paolo's answer was completely correct, but there's an additional point that's worth mentioning here. Hs are often included in query molecules with the intent of restricting possible valence states of atoms, not because the user is actually interested in matching Hs. In this case you can use the function Chem.MergeQueryHs() to remove the H atoms in your query molecule and add/adjust H count queries on the heavy atoms they are connected to. Here's how that works in your example: In [6]: params = Chem.SmilesParserParams() ...: params.removeHs=False ...: query = Chem.MolFromSmiles('c1cn[nH]c(N([H])([H]))1', params) In [7]: m1 = Chem.MolFromSmiles('c1cn[nH]c1N') ...: m2 = Chem.MolFromSmiles('CNc1ccn[nH]1') ...: m3 = Chem.MolFromSmiles('Nc1ccnn(C)1') In [8]: m1.HasSubstructMatch(query) Out[8]: False In [15]: q2 = Chem.MergeQueryHs(query) In [16]: m1.HasSubstructMatch(q2) Out[16]: True In [17]: m2.HasSubstructMatch(q2) Out[17]: False In [18]: m3.HasSubstructMatch(q2) Out[18]: True You can see what has happened by calling MolToSmarts: In [19]: Chem.MolToSmarts(q2) Out[19]: '[#6]1:[#6]:[#7]:[#7H]:[#6]:1-[#7&!H0&!H1]' Notice that the N atom now has query features attached to it. I hope this helps, -greg On Tue, Nov 5, 2019 at 7:53 PM Markus Heller <mhel...@admarebio.com<mailto:mhel...@admarebio.com>> 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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