class_docstr: Adjacency list of neighbors for protein-ligand complexes in 3-space.
  Neighbors dtermined by user-defined distance cutoff.
  Currently only compatible with pdb files.
  
  Example:
  
  >>> frag1_n_atoms = 3
  >>> frag2_n_atoms = 3
  >>> complex_n_atoms = 6
  >>> n_neighbors = 6
  >>> cutoff = 12.0
  >>> boxsize = None
  >>> featurizer = ComplexNeighborListFragmentAtomicCoordinates(frag1_n_atoms,
                    frag2_n_atoms, complex_n_atoms, n_neighbors, cutoff, boxsize)
  >>> frag1 = "frag1.pdb"
  >>> frag2 = "frag2.pdb"
  >>> feature = featurizer._featurize_complex(str(frag1), str(frag2))
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docstr: Featurize fragments and complex.
  
  Parameters
  ----------
  frag1_pdb_file: string
    Location of frag1_pdb_file.
  frag2_pdb_file: string
    Location of frag2_pdb_file.
  
  Returns
  -------
  retval: tuple
    Tuple containing coordinates, neighbor list, and atomic number for
    fragment 1, fragment 2, and complex
docstr_tok: ["Featurize","fragments","and","complex",".","Parameters","--","--","--","--","--","frag1_pdb_file",":","string","Location","of","frag1_pdb_file",".","frag2_pdb_file",":","string","Location","of","frag2_pdb_file",".","Returns","--","--","--","-","retval",":","tuple","Tuple","containing","coordinates",",","neighbor","list",",","and","atomic","number","for","fragment","1",",","fragment","2",",","and","complex"]
code: def _featurize_complex(self, frag1_pdb_file, frag2_pdb_file):
      """Featurize fragments and complex.
  
      Parameters
      ----------
      frag1_pdb_file: string
        Location of frag1_pdb_file.
      frag2_pdb_file: string
        Location of frag2_pdb_file.
  
      Returns
      -------
      retval: tuple
        Tuple containing coordinates, neighbor list, and atomic number for
        fragment 1, fragment 2, and complex
  
      """
  
      try:
          frag1_mol = Chem.MolFromPDBFile(
              frag1_pdb_file, sanitize=False, removeHs=False
          )
          frag2_mol = Chem.MolFromPDBFile(
              frag2_pdb_file, sanitize=False, removeHs=False
          )
      except:
          frag1_mol = None
          frag2_mol = None
      if frag1_mol and frag2_mol:
          (
              frag1_coords,
              frag1_neighbor_list,
              frag1_z,
          ) = self.frag1_featurizer._featurize(frag1_mol)
          (
              frag2_coords,
              frag2_neighbor_list,
              frag2_z,
          ) = self.frag2_featurizer._featurize(frag2_mol)
          complex_mol = Chem.rdmolops.CombineMols(frag1_mol, frag2_mol)
          (
              complex_coords,
              complex_neighbor_list,
              complex_z,
          ) = self.complex_featurizer._featurize(complex_mol)
          return (
              frag1_coords,
              frag1_neighbor_list,
              frag1_z,
              frag2_coords,
              frag2_neighbor_list,
              frag2_z,
              complex_coords,
              complex_neighbor_list,
              complex_z,
          )
      else:
          print("failed to featurize")
          return (None, None, None, None, None, None, None, None, None)
  
file_path: deepchem/contrib/atomicconv/feat/atomicnet_coordinates.py
imports: from __future__ import print_function
  from __future__ import division
  from __future__ import unicode_literals
  import numpy
  from rdkit import Chem
  from deepchem.feat import Featurizer
  from deepchem.feat import ComplexFeaturizer
  from deepchem.utils import pad_array
label_desc: Use image node_id 2 for calling the ComplexNeighborListFragmentAtomicCoordinates obj's underlying member method code with example usage: obj._featurize_complex(frag1_pdb_file, frag2_pdb_file) and returns: frag1_coords,  frag1_neighbor_list,  frag1_z,  frag2_coords,  frag2_neighbor_list,  frag2_z,  complex_coords,  complex_neighbor_list,  complex_z, None,  None,  None,  None,  None,  None,  None,  None,  None