Migrate to new OpenEye charging engine

[davidlmobley]

The February toolkit release uses OEAssignCharges and OEAssignPartialCharges is basically deprecated (see https://docs.eyesopen.com/toolkits/python/quacpactk/OEProtonFunctions/OEAssignCharges.html#OEProton::OEAssignCharges) so we should migrate at some point.

[davidlmobley]

After discussion with Christopher Bayly, we should migrate to the new charging engine, OEAssignCharges, everywhere EXCEPT in SMIRNOFF forcefields (because it does not yet expose partial bond orders). Usage will basically be the same, though it implements the latest charge ELF procedure so its performance should be more reliable.

HOWEVER, there is one extension of the charging protocol that he recommends. Specifically, the normal (small) RMSD threshold for omega is still recommended as long as the maximum number of conformers (maxconfs) is not reached. But when maxconfs is hit, what will happen is that omega will begin to prune the least favorable conformers in order to maintain only maxconfs; with a low RMSD threshold this can result in a gradual loss of diversity of the conformers and thus correspondingly worse performance for the charge calculations.

Thus, Chris's recommendation was this: Whenever maxconfs is hit, increase the RMSD threshold for conformer generation until maxconfs is no longer hit. This will ensure that conformers are diverse for very flexible molecules, while still using the recommended low RMSD threshold for relatively rigid molecules.