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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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Implement dihedrals for 2 independent planes #69

Open jbarnoud opened 6 years ago

jbarnoud commented 6 years ago

See conversation in #67.

I see two possible implementations. One is to have geometry.dihedral be able to recognize the two cases, the other is to have a separate function.

The 2 independent planes an be described either as 1 times 6 points or 2 times 3. I think the 2 times 3 is more explicit.

If we go for the 2 different functions, what name should take the version for 2 independent planes?

pckroon commented 6 years ago

Let's just make 2 functions. That'll make everyone happy. You could also argue that the function geometry.dihedral should take 2x3 points, and it's current signature be renamed to e.g. geometry.torsion. Note that this should also mean that geometry.angle changes to take 2x2 points.