old_contents: #!/usr/bin/env python
  
  # =============================================================================
  # MODULE DOCSTRING
  # =============================================================================
  
  """
  Test pipeline functions in pipeline.py.
  
  """
  
  # =============================================================================
  # GLOBAL IMPORTS
  # =============================================================================
  
  from yank.pipeline import find_components
  
  
  # =============================================================================
  # TESTS
  # =============================================================================
  
  def test_method_find_components():
      """Test find_components() function."""
      data_dir = utils.get_data_filename(os.path.join('tests', 'data'))
      ben_tol_dir = os.path.join(data_dir, 'benzene-toluene-explicit')
      ben_tol_complex_path = os.path.join(ben_tol_dir, 'complex.prmtop')
      ben_tol_prmtop = openmm.app.AmberPrmtopFile(ben_tol_complex_path)
  
      topology = ben_tol_prmtop.topology
      system = ben_tol_prmtop.createSystem(nonbondedMethod=openmm.app.PME)
      n_atoms = system.getNumParticles()
  
      # Standard selection.
      atom_indices = find_components(system, topology, ligand_dsl='resname BEN')
      assert len(atom_indices['ligand']) == 12
      assert len(atom_indices['receptor']) == 15
      assert len(atom_indices['solvent']) == n_atoms - 12 - 15
  
      # Select toluene as solvent to test solvent_dsl.
      atom_indices = find_components(system, topology, ligand_dsl='resname BEN',
                                     solvent_dsl='resname TOL')
      assert len(atom_indices['ligand']) == 12
      assert len(atom_indices['solvent']) == 15
      assert len(atom_indices['receptor']) == n_atoms - 12 - 15
  
new_contents: #!/usr/bin/env python
  
  # =============================================================================
  # MODULE DOCSTRING
  # =============================================================================
  
  """
  Test pipeline functions in pipeline.py.
  
  """
  
  # =============================================================================
  # GLOBAL IMPORTS
  # =============================================================================
  
  import os
  
  from simtk import openmm
  
  from yank import utils
  from yank.pipeline import find_components
  
  
  # =============================================================================
  # TESTS
  # =============================================================================
  
  def test_method_find_components():
      """Test find_components() function."""
      data_dir = utils.get_data_filename(os.path.join('tests', 'data'))
      ben_tol_dir = os.path.join(data_dir, 'benzene-toluene-explicit')
      ben_tol_complex_path = os.path.join(ben_tol_dir, 'complex.prmtop')
      ben_tol_prmtop = openmm.app.AmberPrmtopFile(ben_tol_complex_path)
  
      topology = ben_tol_prmtop.topology
      system = ben_tol_prmtop.createSystem(nonbondedMethod=openmm.app.PME)
      n_atoms = system.getNumParticles()
  
      # Standard selection.
      atom_indices = find_components(system, topology, ligand_dsl='resname BEN')
      assert len(atom_indices['ligand']) == 12
      assert len(atom_indices['receptor']) == 15
      assert len(atom_indices['solvent']) == n_atoms - 12 - 15
  
      # Select toluene as solvent to test solvent_dsl.
      atom_indices = find_components(system, topology, ligand_dsl='resname BEN',
                                     solvent_dsl='resname TOL')
      assert len(atom_indices['ligand']) == 12
      assert len(atom_indices['solvent']) == 15
      assert len(atom_indices['receptor']) == n_atoms - 12 - 15
  
subject: Fix test imports