old_contents: """
      Write specified cluster representative structures to pdb
  """
  from AdaptivePELE.utilities import clusteringUtilities
  import argparse
  
  
  def parseArgs():
      """
          Parse command line arguments
  
          :returns: object -- Object containing command line options
      """
      parser = argparse.ArgumentParser(description="Write the requested cluster "
                                       "structures from a clustering object")
      parser.add_argument('clObject', type=str, help="Path to the clustering object")
      parser.add_argument('outputPath', type=str,
                          help="Path where to write the structures, including "
                          "name of the files, i.e output/path/cluster.pdb")
      parser.add_argument("structures", nargs='*', type=list, default=None,
                          help="Structures to write")
      parser.add_argument("--threshold", type=float, default=None,
                          help="Only print those structures with mathcing threshold")
      args = parser.parse_args()
      return args
  
  
  def main(clObject, structures, condition, outputPath):
      clusteringUtilities.writeStructures(clObject, structures, condition, outputPath)
  
  
  if __name__ == "__main__":
      arguments = parseArgs()
      if arguments.threshold is not None:
          condition = lambda x: abs(x.threshold-arguments.threshold) < 0.01
      else:
          condition = None
      main(arguments.clObject, arguments.structures, condition, arguments.outputPath)
  
new_contents: """
      Write specified cluster representative structures to pdb
  """
  from AdaptivePELE.utilities import clusteringUtilities
  import argparse
  
  
  def parseArgs():
      """
          Parse command line arguments
  
          :returns: object -- Object containing command line options
      """
      parser = argparse.ArgumentParser(description="Write the requested cluster "
                                       "structures from a clustering object")
      parser.add_argument('clObject', type=str, help="Path to the clustering object")
      parser.add_argument('outputPath', type=str,
                          help="Path where to write the structures, including "
                          "name of the files, i.e output/path/cluster.pdb")
      parser.add_argument("structures", nargs='*', type=int, default=None,
                          help="Structures to write")
      parser.add_argument("--threshold", type=float, default=None,
                          help="Only print those structures with mathcing threshold")
      args = parser.parse_args()
      return args
  
  
  def main(clObject, structures, condition, outputPath):
      clusteringUtilities.writeStructures(clObject, structures, condition, outputPath)
  
  
  if __name__ == "__main__":
      arguments = parseArgs()
      if arguments.threshold is not None:
          condition = lambda x: abs(x.threshold-arguments.threshold) < 0.01
      else:
          condition = None
      main(arguments.clObject, arguments.structures, condition, arguments.outputPath)
  
subject: Fix minor bug in writeClusteringStructures script