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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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Coords after #391

Closed fgrunewald closed 2 years ago

fgrunewald commented 2 years ago

This is essentially an updated version of the coordinate builder but after the fact. This fixes mutations and everything where at the CG level coordinates are missing. This could also fix modifications like phosphorylation that are not actually present in the mapped pdb. Currently missing is a good routine for rebuilding VS. Luckily there is a very well tested routine in polyply. For now it only rebuilds VSN but that's good enough for proteins in Martini3 our main target.

@pckroon Should we move the vs_builder from polyply to here eventually?

@Tsjerk As we discussed can you update the doc-strings with a little more information regarding how the coordinates are built and what quality checks are done. Also we'll need some tests here. Perhaps @pckroon can help with those as well a little.

@paulocts You can use this branch for checking some examples, if you like.

fgrunewald commented 2 years ago

will take a second look at this in a clean PR that's not based on some other branches.