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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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Sort nodes to group residues #469

Closed pckroon closed 1 year ago

pckroon commented 1 year ago

Adds a processor to assign consecutive atomids to molecules, sorted by chain and resid. That way residues will be grouped together in the resulting PDB and ITP file(s).

@fgrunewald Is this more or less as you intended? If yes I'll add some tests.

pckroon commented 1 year ago

It was my plan to write proper docstrings and tests, but I wanted to make sure this is roughly the desired behaviour. I'll push the commits hopefully soon.

pckroon commented 1 year ago

E: Failed to fetch http://azure.archive.ubuntu.com/ubuntu/pool/universe/d/dssp/dssp_3.0.0-3build1_amd64.deb Could not connect to azure.archive.ubuntu.com:80 (20.106.104.242), connection timed out sigh

pckroon commented 1 year ago

Tests are working again.

fgrunewald commented 1 year ago

@pckroon feel free to merge