old_contents: import numpy as np
  import os
  import glob
  import mdtraj as md
  import fahmunge
  import pandas as pd
  
  projects = pd.read_csv("./projects.csv", index_col=0)
  output_path = "/data/choderalab/fah/munged/"
  
  for (project, location, pdb) in projects.itertuples():
      print(project, location, pdb)
      allatom_output_path = os.path.join(output_path, str(project), "allatoms/")
      protein_output_path = os.path.join(output_path, str(project), "protein/")
      fahmunge.automation.make_path(allatom_output_path)
      fahmunge.automation.make_path(protein_output_path)
      fahmunge.automation.merge_fah_trajectories(location, allatom_output_path, pdb)
      trj0 = md.load(pdb)  # Hacky temporary solution.
      top, bonds = trj0.top.to_dataframe()
      protein_atom_indices = top.index[top.chainID == 0].values    
      fahmunge.automation.strip_water(allatom_output_path, protein_output_path, protein_atom_indices)
  
new_contents: import numpy as np
  import os
  import glob
  import mdtraj as md
  import fahmunge
  import pandas as pd
  
  projects = pd.read_csv("./projects.csv", index_col=0)
  output_path = "/data/choderalab/fah/munged/"
  
  for (project, location, pdb) in projects.itertuples():
      print(project, location, pdb)
      allatom_output_path = os.path.join(output_path, "allatoms/", "%s/" % project)
      protein_output_path = os.path.join(output_path, "protein/", "%s/" % project)
      fahmunge.automation.make_path(allatom_output_path)
      fahmunge.automation.make_path(protein_output_path)
      fahmunge.automation.merge_fah_trajectories(location, allatom_output_path, pdb)
      trj0 = md.load(pdb)  # Hacky temporary solution.
      top, bonds = trj0.top.to_dataframe()
      protein_atom_indices = top.index[top.chainID == 0].values    
      fahmunge.automation.strip_water(allatom_output_path, protein_output_path, protein_atom_indices)
  
subject: Change output data structure to support faster rsync