Hi,
On Fri, Oct 8, 2010 at 6:11 PM, Jean-Paul Ebejer
<jeanpaul.ebe...@inhibox.com> wrote:
>
> Is it possible to automatically generate say - 50 conformers out of a SMILES
> string ?
> Something like -
> x = generateConformers(50, 'C1CCC1OC')
There's not anything quite that simple out-of-the-box, but it wouldn't
be hard to do on your own. The calls you need to make are:
[6]>>> from rdkit.Chem import AllChem
[7]>>> m=AllChem.AddHs(AllChem.MolFromSmiles('C1CCC1OC'))
[8]>>> cids = AllChem.EmbedMultipleConfs(m,50)
you should probably then check the list of conformation ids to make
sure you actually got 50:
[11]>>> len(cids)
Out[11] 50
The next likely question is what to do with those conformations,
Here's an example of writing them all to an SD file:
[12]>>> w = AllChem.SDWriter('mol.confs.sdf')
[13]>>> for cid in cids: w.write(m,confId=cid)
....:
[14]>>> w.close()
In the past there have been several posts to the mailing list about
generating 3D coordinates with the RDKit that include some useful
tips. I'd suggest searching the list archive
(http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/) to
find these.
Best Regards,
-greg
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