Marshall,
On Tue, Apr 14, 2009 at 11:35 PM, Marshall Levesque
<marsh...@emolecules.com> wrote:
>
> Here is the file and the output of a short test with the molecules, which
> match visual inspection of produced 3D structures via AddHs() and
> EmbedMolecule:
>
>>>> supp = Chem.SDMolSupplier('4aminoacids.separated.sdf')
>>>> for m in supp:
> ... Chem.FindMolChiralCenters(m)
> ...
> [(2, 'S')]
> [(1, 'S')]
> [(3, 'S')]
> [(1, 'S')]
>>>> for m in supp:
> ... mH = Chem.AddHs(m)
> ... Chem.FindMolChiralCenters(mH)
> ...
> [(2, 'R')]
> [(1, 'R')]
> [(3, 'S')]
> [(1, 'R')]
Thanks for sending the file. The problem with these structures and
AddHs() was in fact the same one leading to bug 2762917:
https://sourceforge.net/tracker/?func=detail&aid=2762917&group_id=160139&atid=814650
I just checked in a fix for the bug. Your test molecules now run
correctly, as do the 4500+ in the pubchem test suite I put together.
-greg
