Popped keys instead of deleting them.

If a residue has chi corrections and both atoms in the dictionary are
absent, the code attempts to delete non-existent keys.  The code has
been changed to pop the keys, which will prevent the KeyError from
being thrown.

Refs #17229
Merge branch 'bug/17229' into develop

After discussion with Dale and Ken, this change can be merged into develop.

Refs #17229
Any lines with ATOM that contain SEC should be changed to HETATM.

The PDB contains files for proteins that treat selenocysteine as an
amino acid, but DSSP does not yet support this condition.  Temporary
files generated for DSSP will now be modified if they have ATOM lines
that contain SEC.

Refs #17223
Merge branch 'bug/17223' of github.com:osuosl/pgd into bug/17223

Periodic changes in develop require rebasing.