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In reviewing #122, I was reminded that residues have a limited number of linking bonds/crosslinks:
Each residue in a PDB file can have up to two linking bonds: A “posterior bond” where the first atom is in the current residue and the second atom is in the next residue, and a “prior bond” where the first atom is in the previous residue and the second atom is in the current residue.
A crosslink can be between any two residues, but the bond must be specified by a CONECT record. The first atom is always in the current residue, and the second is in the other residue; this means that for asymmetric crosslinks, the crosslink attributes have a reversed atom order from one residue definition to the other.
I think we'd discussed the possibility of refactoring things to allow arbitrary numbers of at least one of these linkage types in the future. I'll use this issue to record discussion of this feature.
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