Polymer bond code makes (sometimes) incorrect assumption

Created by: jag1g13

The calculation of bonds between residues of a polymer makes the assumption that bead names are the same and appear in the same order in adjacent residues that are bonded. This is true of homopolymers and true of bonds along a protein backbone, but is not true of general heteropolymers.

Issue presents for DNA terminal residues with error File "/home/james/projects/pycgtool/pycgtool/bondset.py", line 177, in <listcomp> bond.atom_numbers = [index.index(atom.lstrip("+-")) for atom in bond.atoms] ValueError: 'BB1' is not in list