Migrate to new charging engine (waiting)

[davidlmobley]

The February OpenEye toolkit release introduces 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.

[jchodera]

How is this used in the "current best practices" manner?

[davidlmobley]

@jchodera - I think it's a drop-in-replacement for the old one, but it's possible @cbayly13 has built some of his conformer stuff into it so that we can remove some of the machinery we had to use with the old one. I have this on the list to bring up in my next call with him but have not yet discussed it with him.

[davidlmobley]

See choderalab/openmoltools#252 -- we need to NOT do this for now as there is no partial bond order access in the new charging engine; marking as "wontfix" for now.