Hi,
I've been reading this paper by Feher, where he shows undesirable
dependence of docking score on atom order in input ligands (keeping
coordinates of the atoms in the input unchanged, just moving them around).
http://pubs.acs.org/doi/pdf/10.1021/ci200598m
I wonder if there is a way to permute atom order of a molecule in rdkit. I
looked around the docs, found nothing. Also nothing comes up on the
rdkit-discuss archives when looking for randomize/scramble/permute/shuffle
atom order.
Has anyone attempted such a hack? What would be the best strategy to
follow, and what to watch out for?
Thanks,
- Jan
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