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
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.
Modified amino acid checks to include SEC.

Selenocysteine is now considered an amino acid by the PDB and DSSP
folks, so the "amino acid" checks for HETATM lines have been changed.

In addition, a new check for ATOM lines has been added.

Refs #17223
Removed explicit reference to SEC in amino_present

The amino_present function explicitly checked for selenocysteine which
caused other proteins to not import correctly.  Leaving it out makes all
the proteins import correctly.

Refs #17223.
Merge branch 'bug/17223' into develop

Some PDB files have ATOM lines for SEC (selenocysteine).  SEC is a
relatively new addition to the amino acid family, and the PGD code
does not generally acknowledge SEC as an amino acid.  The code that
parses PDB files was modified to support SEC in ATOM lines.