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class ComplexNeighborListFragmentAtomicCoordinates(ComplexFeaturizer):

  """This class computes the featurization that corresponds to AtomicConvModel.

  This class computes featurizations needed for AtomicConvModel. Given a two molecular structures, it computes a number of useful geometric features.

  This class computes featurizations needed for AtomicConvModel. Given a

  two molecular structures, it computes a number of useful geometric

  features. In particular, for each molecule and the global complex, it

  computes a coordinates matrix of size (N_atoms, 3) where N_atoms is the

  number of atoms. It also computes a neighbor-list, a dictionary with

  N_atoms elements where neighbor-list[i] is a list of the atoms the i-th

  atom has as neighbors. In addition, it computes a z-matrix for the

  molecule which is an array of shape (N_atoms,) that contains the atomic

  number of that atom.

  Since the featurization computes these three quantities for each of the

  two molecules and the complex, a total of 9 quantities are returned for

  each complex. Note that for efficiency, fragments of the molecules can be

  provided rather than the full molecules themselves.

  """

  def __init__(self,

           system_coords, system_neighbor_list, system_z

  def get_Z_matrix(self, mol, max_atoms):

    ################################################### DEBUG

    print("len(mol.GetAtoms())")

    print(len(mol.GetAtoms()))

    print("max_atoms")

    print(max_atoms)

    ################################################### DEBUG

    return pad_array(

        np.array([atom.GetAtomicNum() for atom in mol.GetAtoms()]), max_atoms)

    max_num_neighbors = 4

    # Cutoff in angstroms

    neighbor_cutoff = 4

    complex_featurizer = ComplexNeighborListFragmentAtomicCoordinates(frag1_num_atoms, frag2_num_atoms, complex_num_atoms, max_num_neighbors, neighbor_cutoff)

    complex_featurizer = ComplexNeighborListFragmentAtomicCoordinates(

        frag1_num_atoms, frag2_num_atoms, complex_num_atoms, max_num_neighbors,

        neighbor_cutoff)

    (frag1_coords, frag1_neighbor_list, frag1_z, frag2_coords,

    frag2_neighbor_list, frag2_z, complex_coords, complex_neighbor_list,

    complex_z) = complex_featurizer._featurize_complex(ligand_file, protein_file)

     frag2_neighbor_list, frag2_z, complex_coords,

     complex_neighbor_list, complex_z) = complex_featurizer._featurize_complex(

         ligand_file, protein_file)

    self.assertEqual(frag1_coords.shape, (frag1_num_atoms, 3))

    self.assertEqual(sorted(list(frag1_neighbor_list.keys())), list(range(frag1_num_atoms)))

    print("type(frag1_z)")

    print(type(frag1_z))

    print("frag1_z.shape")

    print(frag1_z.shape)

    self.assertEqual(

        sorted(list(frag1_neighbor_list.keys())), list(range(frag1_num_atoms)))

    self.assertEqual(frag1_z.shape, (frag1_num_atoms,))

    self.assertEqual(frag2_coords.shape, (frag2_num_atoms, 3))

    self.assertEqual(sorted(list(frag2_neighbor_list.keys())), list(range(frag2_num_atoms)))

    self.assertEqual(

        sorted(list(frag2_neighbor_list.keys())), list(range(frag2_num_atoms)))

    self.assertEqual(frag2_z.shape, (frag2_num_atoms,))

    self.assertEqual(complex_coords.shape, (complex_num_atoms, 3))

    self.assertEqual(sorted(list(complex_neighbor_list.keys())), list(range(complex_num_atoms)))

    self.assertEqual(

        sorted(list(complex_neighbor_list.keys())),

        list(range(complex_num_atoms)))

    self.assertEqual(complex_z.shape, (complex_num_atoms,))