Lily Wang

I guess the easiest way to do it would be to map it in `properties` as atom mapping is currently done.

The implementation would differ based on whether isotopes should be chemically relevant or just labels, yeah. I'm not sure which direction OpenFF wants to go -- but ignoring SMILES does...

> I need to think more on this, because I forgot all the details of how this method is used - Is this separable from the other aspects of this...

.index_of appears to only be used in one place: the VirtualSiteHandler. It looks like it calls `ImproperDict.index_of`, but not certain. @trevorgokey is it right that the ValenceDict should order dihedrals...

> Releasing the limit check makes the dictionary 1. not a valence dictionary anymore and 2. changes the behavior of the class. One should use the SortedDict if one wants...

> Are there 5-body valence terms that we need to support? Not currently; that's why this is a feature request instead of a bug report. It seems unnecessarily restrictive to...

> Also, it's much more idiomatic python to make this a classmethod instead of a staticmethod that uses `__class__`. ValenceDict and ImproperDict both have staticmethods that use `__class__`, so I...

> This seems to be a common feature of pickling; we don't have much custom code there. Here it seems to comes down to Molecule only serializing allowed attributes in...

This does not appear to be solely a result of different conformer generation. Instead, the order of the atoms even in the same conformer affects the charges, e.g. to 0.015...

Thanks for the suggestion @davidlmobley. It does seem to occur from the OpenEye side. Not sure how best to contact them about it. ```python import numpy as np from openeye...