filter molecule for templates

[fgrunewald]

This PR sets the stage for some important changes:

• instead of matching templates by resnames each residue now requires a template_name attribute. This allows matching of non-identical residues that has the same resname
• extract blocks now takes a template graph as input to extract the interactions, which is also used in PR #327

To Do

• [x] move ExtractBlock to separate file something like manipulate_molecules.py
• [x] speed up equivalence check or at least enable a bypass

@pckroon do you have any idea how to do the code below in faster? https://github.com/marrink-lab/polyply_1.0/blob/b97ba7126cfb972bd33f2a1315059f5cbf16a2b8/polyply/src/generate_templates.py#L295-L314

[fgrunewald]

note to self vf2pp from networkx 3 might speed up matching process also proper line by line benchmark is needed

[pckroon]

Not fundamentally, no. I'm also not sure what the goal you're trying to achieve is.

[fgrunewald]

Currently polyply assumes all residues are unique. That is mostly true but not quite at least at the all-atom level. For example, there might be a hydrogen extra or less depending on if a residue is located in the center or at the terminal. This functionality checks each residue against a collection of unique residues in order to find those that have the same resname but deviate as graphs. It makes generating the templates more robust for complicated AA structures

[pckroon]

Alright. I don't think there's really a faster way then. Unless you are willing to accept approximation, e.g. only check atom names.

[fgrunewald]

@csbrasnett this PR should fix the issue with the residue names; I think it is about time that we added this functionality