From owner-chemistry@ccl.net Tue Sep 20 09:20:00 2016 From: "Michel Petitjean petitjean.chiral(a)gmail.com" To: CCL Subject: CCL: substructure search Message-Id: <-52381-160920091850-5445-ZWjn3nWCETWbgD3NUZv58w{:}server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 20 Sep 2016 15:18:41 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral,,gmail.com] Dear Yuri, A combined 2Dand 3D substructure search is not trivial to do. In the case of xyz files, may I suggest that you do first a 3D search with the CSR freeware: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Best regards, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral:_:gmail.com (preferred), michel.petitjean:_:univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2016-09-20 11:26 GMT+02:00 Yury Minenkov yury.minenkov ~~ gmail.com : > 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