CCL: substructure search

 Sent to CCL by: Francois BERENGER [francois.berenger===inria.fr]
 Maybe the fmcsR package for R allows to do what you need.
 Cf. http://bioinformatics.oxfordjournals.org/content/29/21/2792.long
 On 09/20/2016 11:26 AM, Yury Minenkov yury.minenkov ~~ gmail.com wrote:
 > 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 don't think those algorithms are easy (maximum common substructure
 search).
 They might be terribly inefficient also.
 > 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>
 >
 --
 Regards,
 Francois.
 "When in doubt, use more types"