Hi Noel, Thanks a lot for your suggestion.
For structures with different position of double bond apparently it results different orders. Here is how I tested: https://bitbucket.org/snippets/deeenes/peGEnG Do you think the mapping to a reference molecule could work? Best, Denes 2018-03-12 14:58 GMT+01:00 Noel O'Boyle <baoille...@gmail.com>: > The "--canonical" option of obabel can reorder atoms into a canonical order. > This can also be accessed through the API, e.g. through Pybel, via > _operations["canonical"]. > > An alternative approach would be to take a particular reference molecule, > find the mapping of a query molecule onto this, and then rearrange the atoms > accordingly. If this is of interest, I can look up the corresponding API > functions. > > Regards, > - Noel > > On 12 March 2018 at 13:05, Dénes Türei <turei.de...@gmail.com> wrote: >> >> Hi Noel, >> >> Thanks for your reply. >> I would like the latter, i.e. to rearrange and achieve a uniform oder. >> Is there a way to do this? >> >> Best, >> >> Denes >> >> 2018-03-12 13:43 GMT+01:00 Noel O'Boyle <baoille...@gmail.com>: >> > Hi Denes, >> > >> > It's not quite clear to me whether you are saying that Open Babel is >> > rearranging the atom order (and want us to fix that) or you are asking >> > how >> > to rearrange the atom order in two molecules such that corresponding >> > atoms >> > are in the same order? Can you clarify? >> > >> > Regards, >> > - Noel >> > >> > On 9 March 2018 at 12:14, denes <turei.de...@gmail.com> wrote: >> >> >> >> Dear All, >> >> >> >> I would like to export multiple 3D structures into PDB to use them as >> >> ensembles in docking. >> >> I get constitutions from databases in MOL format or as SMILEs and via >> >> pybel >> >> I use Open Babel's `make3D()` method to generate 3D. Then I export them >> >> one >> >> by one into PDB and subsequently I merge them. >> >> >> >> My problem is that the order of atoms, which must be fix accross models >> >> in >> >> order to use the ensembles in docking, is not always the same. See here >> >> an >> >> example: >> >> >> >> >> >> http://www.ebi.ac.uk/~denes/54b510889336eb2591d8beff/00127_0a949dbfc5df14c6619e5acf726e0d11_16.pdb.txt >> >> As you see here the only P atom is either number 25 or 45 in the >> >> sequence. >> >> >> >> Important: these molecules are constitutional isomers only different in >> >> double bond positions on their aliphatic chains. >> >> >> >> Any suggestion would be appreciated. >> >> >> >> Best, >> >> >> >> Denes >> >> >> >> >> >> >> >> >> >> -- >> >> Sent from: http://forums.openbabel.org/General-discussion-f3090658.html >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> 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 >> > >> > >> >> >> >> -- >> Denes Turei, Ph.D. >> >> postdoc @ Uniklinik RWTH Aachen & EMBL Heidelberg >> +4915166299976 Germany >> +447442970610 UK >> de...@ebi.ac.uk >> http://www.ebi.ac.uk/~denes >> public key: >> http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x5706A4B609DD65A6 > > -- Denes Turei, Ph.D. postdoc @ Uniklinik RWTH Aachen & EMBL Heidelberg +4915166299976 Germany +447442970610 UK de...@ebi.ac.uk http://www.ebi.ac.uk/~denes public key: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x5706A4B609DD65A6 ------------------------------------------------------------------------------ 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
