Side chain clashes in docks.

[primaryodors]

Sometimes, the docker produces output in which residue side chains have been flexed into impossible positions clashing with other side chains of the protein.

TODO: Find an example.

[primaryodors]

http://primaryodors.net/viewer.php?view=dock&prot=OR51E2&odor=capric_acid&mode=active

Arg262 is clashing with Val195.

[primaryodors]

This seems to be happening in the FYG-motif active model, not in the dock. It may be wise to add a final step in all the active model predictors to flex any clashing side chains just enough to bring their clash energy below some set threshold.

[primaryodors]

This was addressed in #491 .

If the problem persists, this issue may be reopened.

[primaryodors]

Seems to happen pretty consistently between H104~Q158 with Z-3-hexenol (non-agonist) in OR10G7. There is no excuse for this.

If hexenol is a non agonist due to being energetically unfavorable in OR10G7, then the docker shouldn't output any poses. It should never produce any pose with such a serious clash between side chains.