HETATM cleanup

[amelie-stein]

The current version seems to remove

• MSEs, which Rosetta can deal with just fine
• the backbone N of the next residue after a HETATM, leading to Rosetta kicking out that entire residue
  This should be fixed. One option might be to simply run
  /path/to/rosetta/source/bin/score.linuxgccrelease -s 1PGA.pdb -out::output
  either before or instead of the cleanup script. This will take care of MSE.

In the longer run it may also be relevant to look into post-translationally modified residues, such as p[STY]. If Rosetta can handle them, would we want them in ddG calculations? How would we deal with them on the single-letter level?