Lily Wang

Update: and as implied, not an issue with AmberTools (for this molecule at least). The charge difference I found when I opened the issue might be from conformer generation then....

@mattwthompson Atom ordering still affects, separately, both conformer generation and AM1 optimization. Below is OpenEye's recommendation to minimize effects on AM1 optimization, but I think that conformer generation is an...

Could you just do that under the hood -- check if a wrapper is passed in, and if so, make a single-wrapper registry?

One can override the GLOBAL_TOOLKIT_REGISTRY by switching the order of the precedence inside the object instead of creating a new GLOBAL_TOOLKIT_REGISTRY, but I recall using private attributes to do that...

> I'm concerned that what's really happening here is that a new GLOBAL_TOOLKIT_REGISTRY is being imported for each module. I just wanted to clear this up a little. Each module...

@mattwthompson Thanks for the links to earlier issues. > In this case, you wouldn't be able to pick which toolkit is used for what - is that okay? I realize...

Yeah, sounds about right. I guess if you really wanted to have fun you could make separate default registries for each method. CHEMICAL_ENVIRONMENT_MATCHES_TOOLKIT_REGISTRY, ASSIGN_PARTIAL_CHARGES_TOOLKIT_REGISTRY, ... 🎊

~Does the bug still get fixed if you just canonically reorder the atoms inside the Molecule before pushing to the toolkits?~ e.g. https://github.com/openforcefield/openff-toolkit/blob/684e25a27cade6090d53af6c97fa53485b4c3de2/openff/toolkit/topology/molecule.py#L3436-L3438 Actually looking more closely, partial charge assignment...

@ahy3nz [in 2019](https://github.com/MDAnalysis/mdanalysis/issues/2386#issuecomment-556916859) I came to the conclusion that parmed had the central atom first for harmonic impropers but third for periodic impropers. I didn't link to any part of...

I opened a PR at #3941 addressing this with a keyword argument (`use_nested_encoders`). It's a fairly simple band-aid onto the issue and probably the top flaw is that it does...