Fixing binding pocket tests

  cutoff: int, optional

    The distance in angstroms from the protein pocket to

    consider for featurization.

  Returns

  -------

  A tuple of `(CoordinateBox, np.ndarray)` where the second entry is

  of shape `(N, 3)` with `N` the number of atoms in the active site.

  """

  protein = rdkit_util.load_molecule(

      protein_file, add_hydrogens=False)

    for pocket in boxes:

      assert isinstance(pocket, box_utils.CoordinateBox)

  def test_boxes_to_atoms(self):

    """Test that mapping of protein atoms to boxes is meaningful."""

    current_dir = os.path.dirname(os.path.realpath(__file__))

    protein_file = os.path.join(current_dir, "1jld_protein.pdb")

    ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")

    coords = rdkit_util.load_molecule(protein_file)[0]

    boxes = box_utils.get_face_boxes(coords)

    mapping = dc.dock.binding_pocket.boxes_to_atoms(coords, boxes)

    assert isinstance(mapping, dict)

    for box, box_atoms in mapping.items():

      (x_min, x_max), (y_min, y_max), (z_min, z_max) = box.x_range, box.y_range, box.z_range

      for atom_ind in box_atoms:

        atom = coords[atom_ind]

        assert x_min <= atom[0] and atom[0] <= x_max

        assert y_min <= atom[1] and atom[1] <= y_max

        assert z_min <= atom[2] and atom[2] <= z_max

  def test_convex_find_pockets(self):

    """Test that some pockets are filtered out."""

    current_dir = os.path.dirname(os.path.realpath(__file__))

    finder = dc.dock.ConvexHullPocketFinder()

    all_pockets = finder.find_all_pockets(protein_file)

    pockets = finder.find_pockets(

        protein_file, ligand_file)

    pockets = finder.find_pockets(protein_file)

    # Test that every atom in pocket maps exists

    n_protein_atoms = protein.xyz.shape[1]

    for pocket in pockets:

    active_site_box, active_site_coords = (

        dc.dock.binding_pocket.extract_active_site(protein_file, ligand_file))

    finder = dc.dock.ConvexHullPocketFinder()

    pockets = finder.find_pockets(protein_file, ligand_file)

    pockets = finder.find_pockets(protein_file)

    assert len(pockets) > 0

        str(molecule_file), sanitize=False, removeHs=False)

    from_pdb = True

  else:

    raise ValueError("Unrecognized file type")

    raise ValueError("Unrecognized file type for %s" % str(molecule_file))

  if my_mol is None:

    raise ValueError("Unable to read non None Molecule Object")