[Open Babel] Atoms order in exported PDB

[denes <tur...@gm...>]

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




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