Hi Thomas,

On Fri, Mar 3, 2017 at 12:22 AM, Thomas Evangelidis <teva...@gmail.com>

> Just a quick question. I start from correct geometries (generated with
> ligprep) and I superpose many molecules on a reference ligand. The overlap
> is very good but sometimes the aromatic rings are not planar due to the
> restraints. How can I check automatically in batch mode that the atoms in
> the aligned molecules written in the sdf file have the same valence as in
> the original sdf file (e.g. the atoms in the non-planar rings are still
> aromatic)? Can I do that by comparing the canonical SMILES of the original
> molecule with the canonical SMILES of the aligned?

To answer the immediate question: That would be a relatively easy way to do
it. Note however that simply doing an alignment or minimization isn't going
to change the valence of any of the atoms in the molecule.

To a larger point: I may be misunderstanding what you mean by
"superposition", but unless you are generating new conformations or doing
force-field minimizations there shouldn't be anything that changes the
geometry of aromatic rings.

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