search

marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
89 stars 40 forks source link

Deduplicate symmetric links #170

Open pckroon opened 5 years ago

pckroon commented 5 years ago

The problem is that some interactions (bonds, angles) are symmetric, others are sometimes (dihedrals) and others are not. And note that for angles the order of nodes matters anyway.

Although, after some discussion, this might actually be solved by using ISMAGS. To restore the transitivity of node equality however, the 'order' operation has to go. And it can, since it's designed to solve the same problem. If interaction asymmetry becomes an issue the link is underdefined anyway.

pckroon commented 5 years ago

Referencing #161, since that needs to be done in the same fell swoop.