From owner-chemistry@ccl.net Tue Sep 20 07:58:00 2016
From: "Yury Minenkov yury.minenkov ~~ gmail.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: substructure search
Message-Id: <-52380-160920052644-12950-WFClny3615vpaWI5NX71kg|,|server.ccl.net>
X-Original-From: "Yury  Minenkov" <yury.minenkov- -gmail.com>
Date: Tue, 20 Sep 2016 05:26:43 -0400


Sent to CCL by: "Yury  Minenkov" [yury.minenkov=-=gmail.com]
Dear colleagues,

I would like to ask a (basic) question which is perhaps on the border between the fields of Computational chemistry, chemoinformatics and drug design, in particular I am interested in the sub-stricture search algorithms.

At the beginning I have the two things:

a) The small XYZ molecular fragment for which I know the connectivity (I know in which way the atoms are connected, but I do not know the bond orders  this is not that important for me at the beginning)

b) Many XYZ coordinates of different molecules for which I also know the connectives (again, not the bond orders)

I want to search for the given fragment in each of the XYZ molecular file I have. Something similar is organized in the CSD Cambridge structural database.

I am quite certain that this is a general problem and there are should be many ready solutions available. Do we have any available libraries (preferably open-source & free with C API) in which such substructure search is implemented? Perhaps any codes? Or easy to implement algorithms?

I tried once few Python-based implementations based on SMARTS/SMILES  but these are failed for the Transition metal complexes. That is why I believe 3d search would be better.

Thank you in advance! Sorry if this too general question.  

With kind regards,
Yury