Hi JP:
On Tue, Apr 12, 2011 at 5:35 AM, JP <jeanpaul.ebe...@inhibox.com> wrote:
>
> Copying the example verbatim from the documentation (section 3.5 working
> with 3d molecules) doesn't work:
>
>>>> from rdkit import Chem
>>>> from rdkit.Chem import AllChem
>>>> m = Chem.MolFromSmiles('C1CCC1OC')
>>>> m2 = Chem.AddHs(m)
>>>> m
> <rdkit.Chem.rdchem.Mol object at 0x1f02bb0>
>>>> m2
> <rdkit.Chem.rdchem.Mol object at 0x1f021a0>
>>>> AllChem.UFFOptimizeMolecule(m2)
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ValueError: Bad Conformer Id
>
> Any ideas why?
You forgot one step, before optimizing the molecule you need to add 3D
coordinates:
>>> AllChem.EmbedMolecule(m2)
0
-greg
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