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...