Dear colleagues, I've been reading the documentation and a series of online
posts about RDKit and the use of the ETKDG algorithm to effictiently find
conformers for organic structures. RDKit's own page showd that:
>>> m = Chem.MolFromSmiles('C1CCC1OC')
>>> m2=Chem.AddHs(m)
>>> # run ETKDG 10 times
>>> cids = AllChem.EmbedMultipleConfs(m2, numConfs=10)
>>> print(len(cids))
10
>>> rmslist = []
>>> AllChem.AlignMolConformers(m2, RMSlist=rmslist)
>>> print(len(rmslist))
9
Can find and sort conformers by similarity. In the code above I can't figure
out any way to actually see how the conformers look in a visual representation.
I know that we have lots of 3rd party tools that can find and sort conformers
by their relative energies, but I'd like to do it using RDKit (and print each
conformational molecule at the end).
I'd be grateful if you could share your bits about how a newbie can achieve
this task and, maybe, suggest a good book or resource to learn how to use RDKit
(for dummies).
Thanks in advance.
--
Henrique C. S. Junior
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