Re: [Open Babel] Atoms order in exported PDB

[Noel O'B. <bao...@gm...>]

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