As mentioned there, the h5_to_pdb.py incorrectly splits some GLN and ASN residues when converting to pdb format. While the script accounts for this by ignoring index 12 and 9 in GLN and ASN respectively it misses the fact that the O-N pair can be in another location within the AA. From atoms_name_map_for_pdb.pickle we can see that this can also occur at indices 14 (GLN) and 11 (ASN).
This is a simple fix but I think it would be a good idea to look into cleaning up and refactoring the format conversion code to make it easier to understand.
Fixes #8.
As mentioned there, the h5_to_pdb.py incorrectly splits some GLN and ASN residues when converting to pdb format. While the script accounts for this by ignoring index 12 and 9 in
GLNandASNrespectively it misses the fact that the O-N pair can be in another location within the AA. Fromatoms_name_map_for_pdb.picklewe can see that this can also occur at indices 14 (GLN) and 11 (ASN).This is a simple fix but I think it would be a good idea to look into cleaning up and refactoring the format conversion code to make it easier to understand.