Filtering PDBs

#!/usr/bin/env python

from Bio.PDB import PDBParser, PDBIO,

class PREFilter(Select):
  def accept_atom(self, atom):
      forbidden_atoms = set(['N', 'C', '...'])
      if atom.parent.resname == 'CYS' and atom.name in  forbidden_atoms:
          if atom - atom.parent['CA'] > 3.0:
              continue
          
parser = PDBParser(QUIET=1)
structure = parser.get_structure('example', 'example.pdb')

io = PDBIO()
io.set_structure(structure)
io.save('exmaple_filtered.pdb', PREFilter())