Reorganize rdkitgridfeaturizer module

      # voxels_per_edge, num_feat) so we should concatenate on the last

      # axis.

      return np.concatenate(pairwise_features, axis=-1)

def compute_all_sybyl(mol, indices=None):

  """Computes Sybyl atom types for atoms in molecule."""

  raise NotImplementedError("This function is not implemented yet")

def featurize_binding_pocket_sybyl(protein_xyz,

                                   protein,

                                   ligand_xyz,

                                   ligand,

                                   pairwise_distances=None,

                                   cutoff=7.0):

  """Computes Sybyl dicts for ligand and binding pocket of the protein.

  Parameters

  ----------

  protein_xyz: np.ndarray

    Of shape (N_protein_atoms, 3)

  protein: Rdkit Molecule

    Contains more metadata.

  ligand_xyz: np.ndarray

    Of shape (N_ligand_atoms, 3)

  ligand: Rdkit Molecule

    Contains more metadata

  pairwise_distances: np.ndarray

    Array of pairwise protein-ligand distances (Angstroms)

  cutoff: float

    Cutoff distance for contact consideration.

  """

  features_dict = {}

  if pairwise_distances is None:

    pairwise_distances = compute_pairwise_distances(protein_xyz, ligand_xyz)

  contacts = np.nonzero((pairwise_distances < cutoff))

  protein_atoms = set([int(c) for c in contacts[0].tolist()])

  protein_sybyl_dict = compute_all_sybyl(protein, indices=protein_atoms)

  ligand_sybyl_dict = compute_all_sybyl(ligand)

  return (protein_sybyl_dict, ligand_sybyl_dict)