Hi,
If you really want to rely on the order of atom you can renumber them
anyhow you like with Chem.RenumberAtoms()
http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms
There is also a function which returns canonical order of atoms for
you: Chem.CanonicalRankAtoms() As I remember correctly the order may differ
from the canonical smiles, although that might have changed.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-06-15 9:03 GMT+02:00 Brian Kelley <fustiga...@gmail.com>:
> Yes, atoms are always added in file order. It would take a major change
> in rdkit to change/violate this.
>
> ----
> Brian Kelley
>
> > On Jun 15, 2017, at 7:52 AM, Francois BERENGER <
> beren...@bioreg.kyushu-u.ac.jp> wrote:
> >
> > Hello,
> >
> > If I read a molecule from a .sdf file, will the atom indexes be
> conserved/preserved?
> >
> > 1st atom in the file will have index 0,
> > 2nd index 1, etc.
> >
> > And, will this always hold in the future?
> > Is this an invariant of rdkit?
> >
> > Thanks,
> > F.
> >
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