old_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  """rna_simrna_lowest.py
  
  Select lowest energy frames out of a SimRNA trajectory file.
  This code uses heavily the SimRNATrajectory class. Be default 100 lowest energy frames is exported.
  """
  
  from __future__ import print_function
  from rna_tools.tools.simrna_trajectory.simrna_trajectory import SimRNATrajectory
  import argparse
  
  
  def get_parser():
      parser = argparse.ArgumentParser(
          description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
      parser.add_argument('-n', '--nstruc', help="SimRNA trafl file", type=int, default=100)
      parser.add_argument('trafl', help="SimRNA trafl file")
      return parser
  
  
  if __name__ == '__main__':
      parser = get_parser()
      args = parser.parse_args()
  
      s = SimRNATrajectory()
      fn = args.trafl
  
      s.load_from_file(fn, top_level=True)
  
      # for f in s.frames:
      #    print f
  
      sorted_frames = s.sort()
  
      for c, f in enumerate(sorted_frames[:args.nstruc]):
          print(c + 1, f)
          # print f.header
          # print f.coords
  
      s2 = SimRNATrajectory()
      s2.load_from_list(sorted_frames[:args.nstruc])
      s2.plot_energy(fn.replace('.trafl', '.png'))
      s2.save(fn.replace('.trafl', '') + '_top' + str(args.nstruc) + '.trafl')
  
new_contents: #!/usr/bin/env python
  # -*- coding: utf-8 -*-
  """rna_simrna_lowest.py
  
  Select lowest energy frames out of a SimRNA trajectory file.
  This code uses heavily the SimRNATrajectory class. Be default 100 lowest energy frames is exported.
  """
  
  from __future__ import print_function
  from rna_tools.tools.simrna_trajectory.simrna_trajectory import SimRNATrajectory
  import argparse
  
  
  def get_parser():
      parser = argparse.ArgumentParser(
          description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
      parser.add_argument('-n', '--nstruc', help="SimRNA trafl file", type=int, default=100)
      parser.add_argument('trafl', help="SimRNA trafl file")
      return parser
  
  
  if __name__ == '__main__':
      parser = get_parser()
      args = parser.parse_args()
  
      s = SimRNATrajectory()
      fn = args.trafl
  
      s.load_from_file(fn, top_level=True)
  
      # for f in s.frames:
      #    print f
  
      sorted_frames = s.sort(inplace=False)
  
      for c, f in enumerate(sorted_frames[:args.nstruc]):
          print(c + 1, f)
          # print f.header
          # print f.coords
  
      s2 = SimRNATrajectory()
      s2.load_from_list(sorted_frames[:args.nstruc])
      s2.plot_energy(fn.replace('.trafl', '.png'))
      s2.save(fn.replace('.trafl', '') + '_top' + str(args.nstruc) + '.trafl')
  
subject: fix sort inplace