David L. Mobley

As discussed, I would just browse through it and see how ParmEd is used, then make sure we can (or eventually will be able to) do the same kinds of...

It seems like at some level you're asking about two things here: 1) Philosophically, what our terminology ought to be (is a "virtual site" a single particle/single site, or multiple...

@CompRhys - depending on whether/how much effort you want to put in to this, it's possible we could set up a call to kind of walk you through what would...

This is odd; I will have to think about this more, but it's not obvious to me that we should ever have 90/270 degree phase angles (unless we have both...

For the record, we have ongoing conversations about this. After discussion in a meeting last week, we more or less concluded that: 1) 90 or 270 phases can sometimes make...

I agree my statement may be unclear, but I doubt it's necessary for me to clarify, since the whole point here is that I don't understand what the doc string...

How about "A `SingleGraph` converts..." which I think fixes both?

Per discussion on Slack, it looks like we don't sample decorators for chirality, so this would have to be added. I think we're willing to take a pull request to...

If computing resources prevent it, one could also run calculations which are inclusive of (edges suggested by LOMAP) plus (edges suggested by HiMAP) so one can compare the full set,...

To my knowledge there is no literature yet which has studied what are the best practices here. The practice you recommend seems reasonable.