Common protein caps such as -NH3 and -O- prevents the fully assignment of bonds from known residue types as the termination groups adds extra atoms which aren't included in the template, producing missing bonds. The only solution is guessing bonds for now. Adding common TER groups such that bonds of the extra atoms can be added from the templates could solve this issue so that reading a PDB with protein residues (common case) would yield a correct structure without requiring bond guessing (which is expensive and error-prone).
Common protein caps such as -NH3 and -O- prevents the fully assignment of bonds from known residue types as the termination groups adds extra atoms which aren't included in the template, producing missing bonds. The only solution is guessing bonds for now. Adding common TER groups such that bonds of the extra atoms can be added from the templates could solve this issue so that reading a PDB with protein residues (common case) would yield a correct structure without requiring bond guessing (which is expensive and error-prone).
Depends on #101