old_contents: import numpy as np
  import os
  import yaml
  import itertools
  import copy
  
  substituted_benzene_names = ['benzene', 'chlorobenzene', 'dichlorobenzene', 'bromobenzene',
                               'naphthalene', 'ethylbenzene', 'propylbenzene', 'pentylbenzene']
  
  
  def create_yaml_file(mol_a, mol_b, yaml_dict):
      yaml_dict['molecules'] = [mol_a, mol_b]
      yaml_dict['traj_prefix'] = "{}_{}".format(mol_a, mol_b)
      yaml_dict['lengths'] = [5000]
  
      return yaml_dict
  
  def create_submit_script(template_script_file, yaml_filename):
      with open(template_script_file, "r") as templatefile:
          template_script = templatefile.read()
          template_script.format(yaml_filename)
  
  if __name__=="__main__":
      template_script_file_eq = "submit-eq.sh"
      template_script_file_neq = "submit-neq.sh"
  
      with open("rj_neq_template.yaml", "r") as yamlfile:
          template_yamldict = yaml.load(yamlfile)
  
      for pair in itertools.permutations(substituted_benzene_names, 2):
          if pair[0] == pair[1]:
              continue
  
          new_yaml_dict = create_yaml_file(pair[0], pair[1], copy.deepcopy(template_yamldict))
  
          new_yaml_filename = "{}_{}_rjneq.yaml".format(pair[0], pair[1])
  
          with open(new_yaml_filename, 'w') as yaml_outfile:
              yaml.dump(new_yaml_dict, yaml_outfile)
  
          with open("submit_{}_{}_eq.sh".format(pair[0], pair[1])) as submiteqfile:
              submit_eq = create_submit_script(template_script_file_eq, new_yaml_filename)
              submiteqfile.write(submit_eq)
  
          with open("submit_{}_{}_neq.sh".format(pair[0], pair[1])) as submitneqfile:
              submit_neq = create_submit_script(template_script_file_neq, new_yaml_filename)
              submitneqfile.write(submit_neq)
  
new_contents: import numpy as np
  import os
  import yaml
  import itertools
  import copy
  
  substituted_benzene_names = ['benzene', 'chlorobenzene', 'dichlorobenzene', 'bromobenzene',
                               'naphthalene', 'ethylbenzene', 'propylbenzene', 'pentylbenzene']
  
  
  def create_yaml_file(mol_a, mol_b, yaml_dict):
      yaml_dict['molecules'] = [mol_a, mol_b]
      yaml_dict['traj_prefix'] = "{}_{}".format(mol_a, mol_b)
      yaml_dict['lengths'] = [5000]
  
      return yaml_dict
  
  def create_submit_script(template_script_file, yaml_filename):
      with open(template_script_file, "r") as templatefile:
          template_script = templatefile.read()
          template_script.format(yaml_filename)
  
  if __name__=="__main__":
      template_script_file_eq = "submit-eq.sh"
      template_script_file_neq = "submit-neq.sh"
  
      with open("rj_neq_template.yaml", "r") as yamlfile:
          template_yamldict = yaml.load(yamlfile)
  
      for pair in itertools.permutations(substituted_benzene_names, 2):
          if pair[0] == pair[1]:
              continue
  
          new_yaml_dict = create_yaml_file(pair[0], pair[1], copy.deepcopy(template_yamldict))
  
          new_yaml_filename = "{}_{}_rjneq.yaml".format(pair[0], pair[1])
  
          with open(new_yaml_filename, 'w') as yaml_outfile:
              yaml.dump(new_yaml_dict, yaml_outfile)
  
          with open("submit_{}_{}_eq.sh".format(pair[0], pair[1]), 'w') as submiteqfile:
              submit_eq = create_submit_script(template_script_file_eq, new_yaml_filename)
              submiteqfile.write(submit_eq)
  
          with open("submit_{}_{}_neq.sh".format(pair[0], pair[1]), 'w') as submitneqfile:
              submit_neq = create_submit_script(template_script_file_neq, new_yaml_filename)
              submitneqfile.write(submit_neq)
  
subject: Fix typo