Converting optimized structures back to the constraint-encoded PDB format

Keeping structures in the RINRUS constraint-encoded PDB format makes it easier to manage the frozen atoms.

Use gopt_to_pdb.py or xyz_to_pdb.py to convert coordinates from QM outputs into pdb format.

# Example usage of gopt_to_pdb
python3 $HOME/git/RINRUS/bin/gopt_to_pdb.py -gout 1.out -pdb model_N_template.pdb -name model_N_opt

# Example usage of xyz_to_pdb
python3 $HOME/git/RINRUS/bin/xyz_to_pdb.py -xyz orca.xyz -pdb model_N_template.pdb -name model_N_opt

# Arguments for gopt_to_pdb/xyz_to_pdb
-gout OUTFILE   Gaussian output file (gopt_to_pdb only)
-xyz XYZFILE    XYZ file (xyz_to_pdb only)
-frame FRAME    geometry to use: -1 for final (default), integer or "all". NOTE: COUNT STARTS AT 0.
-name SAVENAME  name for new pdb file (defaults: "gopt" or base name of specified XYZ file)

If making only final frame, structures are saved as [name].pdb. If option for -frame is “all” or an integer, file(s) will be called [name].f[num].pdb.