text: #!/usr/bin/env python
  
  import pdb_parser as parser
  import get_atom_distances as gad
  import residue_mutator as mut
  from config import *
  
  
  def mutate_to_alanines(protein_pdb):
      protein_lines = list(parser.parse_file(protein_pdb))
      res_lines = list(parser.parse_file(residue_path.format("ALA")))
      buried_residues = gad.get_buried_residues_pdb(protein_pdb)
      current_pdb = protein_lines
      for i in buried_residues:
          current_pdb = mut.mutate(current_pdb, i, res_lines)
      return current_pdb
  
  if __name__=="__main__":
      from sys import argv
      orig_protein = argv[-1]
      new_protein = mutate_to_alanines(orig_protein)
      for l in new_protein:
          print(parser.pdb_format(l))
  