On Jun 21, 2017, at 01:14, Sam Tonddast-Navaei <s.tondd...@gmail.com> wrote: > Thank you in advance for taking your time and I hope to explain the problem > well. I am trying to find the largest induced subfragment given two > molecules. For example given ATP (Adenosine Triposphate) and Guanine, I would > like the algorithm to return the Purine ring.
You might try https://github.com/openbabel/contributed/tree/master/c%2B%2B/mcs-cliquer , which is part of the code contributed to Open Babel but not part of the core project. That is, you'll need to clone or download https://github.com/openbabel/contributed then compile the code under c++/mcs-cliquer . I did that just now with your use case, and got: [openbabel-contributed/c++/mcs-cliquer] dalke% cat atp.smi O=P(O)(O)OP(=O)(O)OP(=O)(O)OC[C@H]3O[C@@H](n2cnc1c(ncnc12)N)[C@H](O)[C@@H]3O ATP [openbabel-contributed/c++/mcs-cliquer] dalke% cat guanine.smi c1[nH]c2c(n1)c(=O)[nH]c(n2)N guanine [openbabel-contributed/c++/mcs-cliquer] dalke% ./mcs atp.smi guanine.smi [nH]1cnc2cncnc12 0.243902 The "0.243902" is a similarity score based on (the number of bonds "C" in the MCS)/(the number of bonds in both input structures - "C"). > I am wondering what's the algorithm behind SMARTS match and is there an > easier way to do what I did using existing Openbabel libraries. Open Babel uses the VF2 algorithm. Andrew da...@dalkescientific.com ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
