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From: Noel O'B. <bao...@gm...> - 2018-03-13 09:39:27
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Good points, all. Yes - the mapping to a reference molecule should work. The following blogpost should help: https://baoilleach.blogspot.co.uk/2010/11/automorphisms-isomorphisms-symmetry.html Have a look at that, and I'll talk you through the details if you have questions. OBMol.RenumberAtoms will be needed in the end - I'm not sure though how well tested this is. - Noel On 12 March 2018 at 15:12, Dénes Türei <tur...@gm...> wrote: > 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 <bao...@gm...>: > > 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 <tur...@gm...> 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 <bao...@gm...>: > >> > 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 <tur...@gm...> 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 > >> >> Ope...@li... > >> >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >> > > >> > > >> > >> > >> > >> -- > >> Denes Turei, Ph.D. > >> > >> postdoc @ Uniklinik RWTH Aachen & EMBL Heidelberg > >> +4915166299976 Germany > >> +447442970610 UK > >> de...@eb... > >> 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...@eb... > http://www.ebi.ac.uk/~denes > public key: http://pgp.mit.edu:11371/pks/lookup?op=get&search= > 0x5706A4B609DD65A6 > |