search

marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
97 stars 43 forks source link

Remove resid from reference blocks in repair graph #340

Closed pckroon closed 3 years ago

pckroon commented 3 years ago

Turns out that when repairing your graph you can't use blocks from ITP files as reference. Those contain resid numbers/attributes, which will overwrite the resids from your (e.g.) PDB file, causing all sorts of chaos. This should fix it. I'll also add a test.

pckroon commented 3 years ago

Indeed all attributes of the reference nodes get used (except now resid).

I'm not completely sure what's wisdom here, can we think of a scenario where you may want to run a processor to do something based on atom type or mass, before mapping to the output resolution?

Opposite question, can we think of any other attribute that doesn't make sense? "charge_group" (not defined from PDB/GRO)? "index" ("atomid" in PDB/GRO)?