old_contents: 
  import glob
  systemNames = [i.split('/')[-1].replace('_aligned.pdb','') for i in glob.glob('../1-trajectories/*_aligned.pdb')]
  
  
  povmeInputTemplate = '''
  PDBFileName	../1-trajectories/!!!SYSTEM NAME!!!_aligned.pdb
  GridSpacing	1.0
  #InclusionSphere	25.400 37.100 34.200 12.0
  InclusionSphere		38.2 -47.5 63.7 15
  #SeedSphere	25.400 37.100 34.200 4.0 
  #SeedBox	27.472 19.570 40.038 6.0 6.0 6.0
  #SeedBox	13.487 23.673 36.818 6.0 6.0 6.0
  ContiguousPointsCriteria 3
  DistanceCutoff	1.09
  ConvexHullExclusion	none
  OutputFilenamePrefix	./!!!SYSTEM NAME!!!/!!!SYSTEM NAME!!!_
  CompressOutput	false
  NumProcessors	5
  
  
  '''
  
  for systemName in systemNames:
      scriptText = povmeInputTemplate.replace('!!!SYSTEM NAME!!!',systemName)
      with open('povme_%s_input.ini' %(systemName), 'wb') as of:
          of.write(scriptText)
          
  with open('runAll.sh', 'wb') as of:
      for systemName in systemNames:
          newLine = 'POVME3.py povme_%s_input.ini  \n' %(systemName)
          of.write(newLine)
  
new_contents: 
  import glob
  systemNames = [i.split('/')[-1].replace('_aligned.pdb','') for i in glob.glob('../1-trajectories/*_aligned.pdb')]
  
  
  povmeInputTemplate = '''
  PDBFileName	../1-trajectories/!!!SYSTEM NAME!!!_aligned.pdb
  GridSpacing	1.0
  #InclusionSphere	25.400 37.100 34.200 12.0
  InclusionSphere		38.2 -47.5 63.7 15
  #SeedSphere	25.400 37.100 34.200 4.0 
  #SeedBox	27.472 19.570 40.038 6.0 6.0 6.0
  #SeedBox	13.487 23.673 36.818 6.0 6.0 6.0
  ContiguousPointsCriteria 3
  DistanceCutoff	1.09
  ConvexHullExclusion	none
  OutputFilenamePrefix	./!!!SYSTEM NAME!!!/!!!SYSTEM NAME!!!_
  CompressOutput	false
  NumProcessors	1
  
  
  '''
  
  for systemName in systemNames:
      scriptText = povmeInputTemplate.replace('!!!SYSTEM NAME!!!',systemName)
      with open('povme_%s_input.ini' %(systemName), 'wb') as of:
          of.write(scriptText)
          
  with open('runAll.sh', 'wb') as of:
      for systemName in systemNames:
          newLine = 'POVME3.py povme_%s_input.ini  \n' %(systemName)
          of.write(newLine)
  
subject: Update makeRunAllScript.py