CCL:G: substructure search

Hi Yury,
 as far as I understood your question you are just looking for a
 substructure search based on pure connectivity (2D). I think this paper is
 an excellent starting point with a lot of references:
 https://jcheminf.springeropen.com/articles/10.1186/1758-2946-4-13
 As you can see from the references it is a long time since on a solution of
 this problem has been worked on (and yet it is a problem of interest -
 everybody would be happy to have better performance).
 I think what Igor mentioned (MCS) is special case of substructure searching
 (in short, for MCS you have only molecules which you compare without using
 a specific "query" structure and the point is to find the
 "query" or "most
 common substructure" in a given set of molecules).
 If you really looking for actual "3D substructure searching" where the
 conformation of atoms matter, that is a complete different beast (but I
 don't understand your question like that).
 If you are looking for "open" implementations you should look for
 openbabel, RDKit or CDK (the latter however is Java). There are also plenty
 commercial implementations.
 Markus
 On Tue, Sep 20, 2016 at 3:08 PM, Filippov, Igor (NIH/NLM/NCBI) C filippov..
 ncbi.nlm.nih.gov <owner-chemistry]-[ccl.net> wrote:
 >
 > Sent to CCL by: "Filippov, Igor (NIH/NLM/NCBI) [C]" [filippov#
 > ncbi.nlm.nih.gov]
 > It is indeed a common task. Take a look at the following thread from a
 > couple of years ago:
 > https://www.mail-archive.com/openbabel-discuss[-]lists.
 > sourceforge.net/msg03911.html
 >
 > The gist of that exchange - here is an openbabel-based tool, not
 > particularly fast but easy to study and modify:
 > https://github.com/openbabel/contributed/tree/master/c%2B%2B/mcs-cliquer
 >
 > And here is a very advanced tool for fast MCS based on RDKit:
 > https://bitbucket.org/dalke/fmcs
 >
 > Hope this helps,
 > Igor
 >
 >
 > -----Original Message-----
 > > From: owner-chemistry+igorf==helix.nih.gov[-]ccl.net [mailto:
 > owner-chemistry+igorf==helix.nih.gov[-]ccl.net] On Behalf Of Yury
 > Minenkov yury.minenkov ~~ gmail.com
 > Sent: Tuesday, September 20, 2016 5:27 AM
 > To: Filippov, Igor (NIH/NCI/Helix) <igorf[-]helix.nih.gov>
 > Subject: CCL: substructure search
 >
 >
 > 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,
 > Yuryhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp:/
 > /www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt>;
 >
 >