Hi Gustavo,
Doesn't the substructure match only works for the whole substructure, as an all-or-nothing? Is it possible to get a partial match with substructure search? >> I think it would depend on how you specify your query SMARTS. There's >> probably a way to do partial SS using SMARTS, but really depends on your >> goal and what you want to 'allow' as a match. MCSS might be the better way to go but at this point, more example molecules and 'allowed matches' would help :) A 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 [github.png] adelenelai ________________________________ From: Rajarshi Guha <rajarshi.g...@gmail.com> Sent: Friday, November 20, 2020 4:16:11 PM To: Gustavo Seabra Cc: Dan Nealschneider; Adelene LAI; RDKit Discuss Subject: Re: [Rdkit-discuss] Partial substructure match? One approach could be to assign scoring functions for bond and atom matches (such as what OE supports<https://docs.eyesopen.com/toolkits/python/oechemtk/patternmatch.html#mcs-scoring-functions>) On Fri, Nov 20, 2020 at 9:58 AM Gustavo Seabra <gustavo.sea...@gmail.com<mailto:gustavo.sea...@gmail.com>> wrote: Hi Adelene, Doesn't the substructure match only works for the whole substructure, as an all-or-nothing? I suppose I could use the MCSS and count the number of matching atoms, then calculate the percentage match myself. Is it possible to get a partial match with substructure search? Gustavo. -- Gustavo Seabra ________________________________ From: Adelene LAI <adelene....@uni.lu<mailto:adelene....@uni.lu>> Sent: Friday, November 20, 2020 9:13:15 AM To: Dan Nealschneider <dan.nealschnei...@schrodinger.com<mailto:dan.nealschnei...@schrodinger.com>>; Gustavo Seabra <gustavo.sea...@gmail.com<mailto:gustavo.sea...@gmail.com>> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>> Subject: Re: [Rdkit-discuss] Partial substructure match? Hi Dan and Gustavo, MCSS sounds good, but depends on the goal. >From the way Gustavo wrote, it sounds like a Query-Target substructure search >- he has a list of targets and one specific query, and he wants to compare >matching rate amongst the members of the list. If so, I would try query SMARTS. https://www.rdkit.org/docs/GettingStartedInPython.html#substructure-searching Regarding the % substructure match, interesting question. How would you quantify that? Not sure such a thing exists in RDKit right now. Adelene 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 [github.png] adelenelai ________________________________ From: Dan Nealschneider <dan.nealschnei...@schrodinger.com<mailto:dan.nealschnei...@schrodinger.com>> Sent: Thursday, November 19, 2020 6:01:37 PM To: Gustavo Seabra Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Partial substructure match? Gustavo - That sounds like the "maximum common substructure" problem. Here's the relevant section in RDKit's "Getting started in Python" https://www.rdkit.org/docs/GettingStartedInPython.html#maximum-common-substructure dan nealschneider | lead developer [Schrodinger Logo]<https://www.schrodinger.com/> On Thu, Nov 19, 2020 at 8:50 AM Gustavo Seabra <gustavo.sea...@gmail.com<mailto:gustavo.sea...@gmail.com>> wrote: Hi all, Is it possible to search for *partial* substructure matches using RDKit? I'm aware of "HasSubstructMatch/ GetSubstructMatch", but my impression is that it only returns full matches (100%) of the required pattern in a structure. However, what I'd like to do is a bit different: Imagine I have one specific substructure (scaffold), and I'd like to search for molecules that have the full substructure *or part of it*, and maybe get the percentage of the substructure match? (100% = the full substructure is contained in the molecule). For example, if the pattern is a naphthalene and the molecule to search has a benzene, that would count as a 60% match. Is there a way to do that in RDKit? Thanks a lot! -- Gustavo Seabra _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Rajarshi Guha | http://blog.rguha.net | @rguha<https://twitter.com/rguha>
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