> Sorry, small error in the loop variable labels. Here is the correct version:
I think my bigger question is "how are you getting here?" That is, are you
reading a PDB file and the bonds aren't created correctly? Or are you reading
in an XYZ file and perhaps bond perception and residue perception gets confused?
I can see you have workaround code, but it's not clear what the state of the
molecule is prior to your problem. Normally bonds in residues are assigned
through data/resdata.txt which does have the CD-CG bond:
RES PRO
ATOM CA C3 3
...
BOND CD CG 1
…
Thanks,
-Geoff
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