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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
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add box attribute to molecule and propagate from pdb parser #537

Closed fgrunewald closed 10 months ago

fgrunewald commented 10 months ago

small fix to reading boxes. The PDB reader did not propagate the box attribute

fgrunewald commented 10 months ago

@pckroon jup will do

pckroon commented 10 months ago

Alright, stupid question. We probably already covered this with the original implementation, but is there any reason why this is a molecule attribute and not a system? Looks fine otherwise

fgrunewald commented 10 months ago

@pckroon indeed we discussed a little. In essence, adding it to the molecule keeps the API a little more consistent. For example, the read_gro function only returns a molecule. So there is no way to propagate the box except for restructuring this parser. Personally, I also prefer molecules because polyply works with molecules but not with vermouth systems. In the long run, could be smart to refactor read_gro and expose the attribute to both molecule and system. For now I think the current implementation is fine.