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>
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




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