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
>
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