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
>
------------------------------------------------------------------------------
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
