DOH!!! ****
Apologies...
On 12 April 2011 11:02, Greg Landrum <greg.land...@gmail.com> wrote:
> 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
>
--
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
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Oxford
OX1 1BP
UK
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