old_contents: #!/usr/bin/env python
  
  """Evaluate SOAP score for each AllosMod model."""
  
  from __future__ import print_function, absolute_import
  import glob
  import optparse
  
  def soap_score():
      import modeller
      from modeller.scripts import complete_pdb
      from modeller import soap_protein_od
  
      env = modeller.environ()
      env.libs.topology.read(file='$(LIB)/top_heav.lib')
      env.libs.parameters.read(file='$(LIB)/par.lib')
  
      # Set up SOAP-Protein-OD scoring (we create the scorer once and keep it
      # around, since reading in the potential from disk can take a long time).
      sp = soap_protein_od.Scorer()
  
      out = open('SnapList.txt','w')
  
      cnt = 0
      files = [i for i in glob.glob('pm.pdb*.pdb')
               if 'pm.pdb.B10010002.pdb' not in i]
      for fil in files:
  
          try:
              cnt += 1
              # Read a model previously generated by Modeller's automodel class
              mdl = complete_pdb(env, fil)
              # Select all atoms
              atmsel = modeller.selection(mdl)
  
              # Assess with the above Scorer
              try:
                  score = atmsel.assess(sp)
                  out.write(fil+'\t'+str(score)+'\n')
              except modeller.ModellerError:
                  print("The SOAP-Protein-OD library file is not included "
                        "with MODELLER.")
                  print("Please get it from https://salilab.org/SOAP/.")
          # Was 'except: pass' but this will hide genuine errors. Replace with
          # a more specific list of exceptions (and test)
          except: raise
  
      out.close()
  
  def parse_args():
      usage = """%prog [opts]
  
  Evaluate SOAP-Protein score for each AllosMod model in the current directory.
  A new file SnapList.txt is created which tabluates this score for each model.
  This file is used as input by 'cryptosite am_bmi' and 'cryptosite pockets'.
  
  Note that the SOAP-Protein potential is not included with MODELLER; it can
  be downloaded separately from https://salilab.org/SOAP/.
  """
      parser = optparse.OptionParser(usage)
      opts, args = parser.parse_args()
      if len(args) != 0:
          parser.error("incorrect number of arguments")
  
  def main():
      parse_args()
      soap_score()
  
  if __name__ == '__main__':
      main()
  
new_contents: #!/usr/bin/env python
  
  """Evaluate SOAP score for each AllosMod model."""
  
  from __future__ import print_function, absolute_import
  import glob
  import optparse
  
  def soap_score():
      import modeller
      from modeller.scripts import complete_pdb
      from modeller import soap_protein_od
  
      env = modeller.environ()
      env.libs.topology.read(file='$(LIB)/top_heav.lib')
      env.libs.parameters.read(file='$(LIB)/par.lib')
  
      # Set up SOAP-Protein-OD scoring (we create the scorer once and keep it
      # around, since reading in the potential from disk can take a long time).
      sp = soap_protein_od.Scorer()
  
      out = open('SnapList.txt','w')
  
      cnt = 0
      files = [i for i in glob.glob('pm.pdb*.pdb')
               if 'pm.pdb.B10010002.pdb' not in i]
      for fil in files:
  
          try:
              cnt += 1
              # Read a model previously generated by Modeller's automodel class
              mdl = complete_pdb(env, fil)
              # Select all atoms
              atmsel = modeller.selection(mdl)
  
              # Assess with the above Scorer
              try:
                  score = atmsel.assess(sp)
                  out.write(fil+'\t'+str(score)+'\n')
              except modeller.ModellerError:
                  print("The SOAP-Protein-OD library file is not included "
                        "with MODELLER.")
                  print("Please get it from https://salilab.org/SOAP/.")
          # Was 'except: pass' but this will hide genuine errors. Replace with
          # a more specific list of exceptions (and test)
          except: raise
  
      out.close()
  
  def parse_args():
      usage = """%prog [opts]
  
  Evaluate SOAP-Protein score for each AllosMod model in the current directory.
  A new file SnapList.txt is created which tabulates this score for each model.
  This file is used as input by 'cryptosite am_bmi' and 'cryptosite pockets'.
  
  Note that the SOAP-Protein potential is not included with MODELLER; it can
  be downloaded separately from https://salilab.org/SOAP/.
  """
      parser = optparse.OptionParser(usage)
      opts, args = parser.parse_args()
      if len(args) != 0:
          parser.error("incorrect number of arguments")
  
  def main():
      parse_args()
      soap_score()
  
  if __name__ == '__main__':
      main()
  
subject: Fix typo.