Recognize the equivalence of circularity and crosslinks which generate circular molecules. #109

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1. jonrkarr

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2. jonrkarr commented on Oct 5, 2020

   

   jonrkarr

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   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.

   • For circular polymers, there isn't necessarily a well-defined start position
   • There's nothing that prevents the community from defining monomeric forms which are themselves polymers. If such a monomeric form is semantically meaningful on its own and has a commonly accepted id or name, I don't see a problem with this.

   The main goal of BpForms is to be concrete. I don't think this requires a unique representation of each molecule.
3. paulflang commented on Oct 5, 2020

   

   paulflang

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   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.
4. jonrkarr commented on Oct 5, 2020

   

   jonrkarr

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   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

   • equality
   • it shouldn't be possible to describe a circular molecule with a crosslink between the same atoms; this should result in an error.
5. jonrkarr

   changed the title [-]The `circular` attribute is redundant to crosslinking[/-] [+]Recognize the equivalence of circularity and crosslinks which generate circular molecules.[/+] on Oct 5, 2020
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