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: Initialize ComplexNeighborListFragmentAtomicCoordinates featurizer
  
  Parameters
  ----------
  frag1_num_atoms: int
    Maximum number of atoms in frag1
  frag2_num_atoms: int
    Maximum number of atoms in frag2
  complex_num_atoms: int
    Maximum number of atoms in complex
  max_num_neighbors: int
    Maximum number of neighbors per atom
  neighbor_cutoff: float
    Threshold distance [Angstroms] for counting neighbors.
  boxsize: float, optional (default None)
    Size of periodic box. If None, no periodic boundary conditions.
docstr_tok: ["Initialize","ComplexNeighborListFragmentAtomicCoordinates","featurizer","Parameters","--","--","--","--","--","frag1_num_atoms",":","int","Maximum","number","of","atoms","in","frag1","frag2_num_atoms",":","int","Maximum","number","of","atoms","in","frag2","complex_num_atoms",":","int","Maximum","number","of","atoms","in","complex","max_num_neighbors",":","int","Maximum","number","of","neighbors","per","atom","neighbor_cutoff",":","float","Threshold","distance","[","Angstroms","]","for","counting","neighbors",".","boxsize",":","float",",","optional","(","default","None",")","Size","of","periodic","box",".","If","None",",","no","periodic","boundary","conditions","."]
code: def __init__(
      self,
      frag1_num_atoms,
      frag2_num_atoms,
      complex_num_atoms,
      max_num_neighbors,
      neighbor_cutoff=12.0,
      boxsize=None,
  ):
      """Initialize ComplexNeighborListFragmentAtomicCoordinates featurizer
  
      Parameters
      ----------
      frag1_num_atoms: int
        Maximum number of atoms in frag1
      frag2_num_atoms: int
        Maximum number of atoms in frag2
      complex_num_atoms: int
        Maximum number of atoms in complex
      max_num_neighbors: int
        Maximum number of neighbors per atom
      neighbor_cutoff: float
        Threshold distance [Angstroms] for counting neighbors.
      boxsize: float, optional (default None)
        Size of periodic box. If None, no periodic boundary conditions.
  
      """
  
      self.frag1_num_atoms = frag1_num_atoms
      self.frag2_num_atoms = frag2_num_atoms
      self.complex_num_atoms = complex_num_atoms
      self.max_num_neighbors = max_num_neighbors
      self.neighbor_cutoff = neighbor_cutoff
      self.boxsize = boxsize
      # Type of data created by this featurizer
      self.dtype = object
      self.frag1_featurizer = NeighborListAtomicCoordinates(
          self.frag1_num_atoms,
          self.max_num_neighbors,
          self.neighbor_cutoff,
          self.boxsize,
      )
      self.frag2_featurizer = NeighborListAtomicCoordinates(
          self.frag2_num_atoms,
          self.max_num_neighbors,
          self.neighbor_cutoff,
          self.boxsize,
      )
      self.complex_featurizer = NeighborListAtomicCoordinates(
          self.complex_num_atoms,
          self.max_num_neighbors,
          self.neighbor_cutoff,
          self.boxsize,
      )
  
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 1 to create a new ComplexNeighborListFragmentAtomicCoordinates object from inherited base classes: ComplexFeaturizer with example: obj = ComplexNeighborListFragmentAtomicCoordinates(frag1_num_atoms, frag2_num_atoms, complex_num_atoms, max_num_neighbors, neighbor_cutoff, boxsize)