new_contents: #!/usr/bin/env python3
  #==============================================================================
  # author          : Pavel Polishchuk
  # date            : 19-08-2018
  # version         : 
  # python_version  : 
  # copyright       : Pavel Polishchuk 2018
  # license         : 
  #==============================================================================
  
  import argparse
  import os
  from subprocess import Popen
  
  
  if __name__ == '__main__':
  
      parser = argparse.ArgumentParser(description='Generate files for fragment database.')
      parser.add_argument('-o', '--out', metavar='OUTPUT_DIR', required=True,
                          help='output dir to store files.')
      parser.add_argument('-k', '--keep_ids', required=True,
                          help='path to the file with mol ids to keep at SB generation.')
  
      args = vars(parser.parse_args())
      for o, v in args.items():
          if o == "out": output_dir = os.path.abspath(v)
          if o == "keep_ids": fname = os.path.abspath(v)
  
      if not os.path.exists(output_dir):
          os.mkdir(output_dir)
  
      job_dir = os.path.join(output_dir, 'jobs')
      if not os.path.exists(job_dir):
          os.mkdir(job_dir)
  
      for r in [1, 2, 3]:
          pbs_name = os.path.join(job_dir, '%s_r%i.pbs' % (os.path.basename(output_dir), r))
          script = """
          #!/usr/bin/env bash
          #PBS -l select=1:ncpus=32
          #PBS -k oe
          
          RADIUS=%i
          
          cd %s
          source ~/anaconda3/bin/activate rdkit-1709
          
          python3 ~/python/crem/frag_to_env_mp.py -i ~/imtm/crem/frags.txt -o r${RADIUS}.txt -k %s -r ${RADIUS} -c 32 -v
          sort r${RADIUS}.txt | uniq -c > r${RADIUS}_c.txt
          """ % (r, output_dir, fname)
          with open(pbs_name, "wt") as f:
              f.write(script)
          p = Popen(['qsub', pbs_name], encoding='utf8')
  
  
subject: Add script to run PBS jobs to create fragment database