old_contents: """Cluster based on RMSD between conformations
  
  {{header}}
  
  Meta
  ----
  depends:
    - meta.pandas.pickl
    - trajs
    - top.pdb
  """
  import mdtraj as md
  
  from msmbuilder.cluster import MiniBatchKMedoids
  from msmbuilder.io import load_meta, itertrajs, save_trajs, preload_top
  
  ## Set up parameters
  kmed = MiniBatchKMedoids(
      n_clusters=500,
      metric='rmsd',
  )
  
  ## Load
  meta = load_meta()
  centroids = md.load("centroids.xtc", top=preload_top(meta))
  
  ## Kernel
  SIGMA = 0.3  # nm
  from msmbuilder.featurizer import RMSDFeaturizer
  import numpy as np
  
  featurizer = RMSDFeaturizer(centroids)
  lfeats = {}
  for i, traj in itertrajs(meta):
      lfeat = featurizer.partial_transform(traj)
      lfeat = np.exp(-lfeat ** 2 / (2 * (SIGMA ** 2)))
      lfeats[i] = lfeat
  save_trajs(lfeats, 'ftrajs', meta)
  
new_contents: """Cluster based on RMSD between conformations
  
  {{header}}
  
  Meta
  ----
  depends:
    - meta.pandas.pickl
    - trajs
    - top.pdb
  """
  import mdtraj as md
  
  from msmbuilder.io import load_meta, itertrajs, save_trajs, preload_top
  
  ## Load
  meta = load_meta()
  centroids = md.load("centroids.xtc", top=preload_top(meta))
  
  ## Kernel
  SIGMA = 0.3  # nm
  from msmbuilder.featurizer import RMSDFeaturizer
  import numpy as np
  
  featurizer = RMSDFeaturizer(centroids)
  lfeats = {}
  for i, traj in itertrajs(meta):
      lfeat = featurizer.partial_transform(traj)
      lfeat = np.exp(-lfeat ** 2 / (2 * (SIGMA ** 2)))
      lfeats[i] = lfeat
  save_trajs(lfeats, 'ftrajs', meta)
  
subject: remove redundant code