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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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atomnames of edges in modifications limited to 1 character #410

Closed fgrunewald closed 2 years ago

fgrunewald commented 2 years ago

Does anyone know why this check is here? It seems to limit the node atomnames to one character but specifically for modifications.

https://github.com/marrink-lab/vermouth-martinize/blob/c437876bd494b7842737da48533c44d374fb0526/vermouth/ffinput.py#L968-L970

pckroon commented 2 years ago

On 962: prefixed_atoms.append([prefixed_reference, full_attributes]). So it's not limited to 1 character. The reason I added that check is because I kept typo-ing atomnames in modification edges, which gives utterly untracable errors. If you don't do this check 972 will add rubbish nodes.

fgrunewald commented 2 years ago

@pckroon thanks for the explanation. I see what's happening there. This is also what allows parsing of node attributes via the edges section.