Open paulflang opened 4 years ago
Semantically, I think its useful to have a special syntactic sugar for circularity. Semantically, this connotes different meaning than a crosslink.
More generally, BpForms is not founded on the principle that there should only be 1 unique way to describe a polymer.
The main goal of BpForms is to be concrete. I don't think this requires a unique representation of each molecule.
OK, thanks. This all makes sense.
For circular polymers, there isn't necessarily a well-defined start position
I noticed that this a problem where the bpforms equality check fails. I had a brief look at the code, but the way it is structured I couldn't find a trivial fix.
Yes, that a good point. We should change the code to recognize the equivalence of this special case. This comes up in a couple places
The
circular
attribute seems redundant to crosslinking (at least for proteins). Not sure if we are OK with providing two ways to do the same thing.