pbuslaev

I think that solution proposed in this PR is not consistent with `mdtraj` writing functionality of pdb files. This can lead to a situation, when a structure read and then...

Graph conversion is fast. The problem is at `GraphMatcher` stage.

If I see it correctly, the solution that I propose won't change much for the code. Inside `are_isomorphic`, we can add something like this: ```python mol1.perceive_residues() mol2.perceive_residues() if len(mol1.residues) >...

Actually, fast testing with `Networkx`, [`igraph`](https://python.igraph.org/en/stable/), and [`graph_tools`](https://graph-tool.skewed.de/static/doc/index.html) gave the following results: ```python k = 3 print(f"Test for a system with {p1[k].n_atoms} atoms and {p1[k].n_bonds}") s = time.time() # networkx...

A slightly different approach can be to 1. Match residues first (do graph matching on the residue basis). This should be fast 2. If residues can be mapped, we run...

Following the discussion in #606 the behaviour suggested in #962 can be made optional, by adding a flag to `Interchange.to_gromacs(combine_atomtypes: bool = False)`. This will keep the possibility to write...

Thanks @IAlibay! Please let me know if you would need any help with that. I would be happy to contribute some code/test. I also have a similar, but slightly different...

Ah, ok. Thanks for the explanation. A couple of other questions: 1. Do I understand correctly, that lipids (and actually waters and ions) can actually be considered as `SmallMoleculeComponent` as...

OpenFF does not use atom types, it uses direct chemical perception to assign atom parameters. It means that residue has to be supported as a whole by OpenFF and to...

This is exactly what I am talking about. Maestro caps C atom of terminal histidine with HT hydrogen, but the amino acid (if built completely) should get OH or O$`^-`$....