4270c3dae0b80b384c4a0026e2043345904b4fe5,deepchem/featurizers/atomic_coordinates.py,NeighborListAtomicCoordinates,_featurize,#NeighborListAtomicCoordinates#Any#,161

Before Change

    ----------
    
    N = mol.GetNumAtoms()
    coords = np.zeros((N,3))

    coords_raw = [mol.GetConformer(0).GetAtomPosition(i) for i in range(N)]
    for atom in range(N):
      coords[atom,0] = coords_raw[atom].x
      coords[atom,1] = coords_raw[atom].y
      coords[atom,2] = coords_raw[atom].z

    x_bins, y_bins, z_bins = get_cells(coords, self.neighbor_cutoff)

After Change

      // result in neighboring cells being seen multiple times. Use a set() to
      // make sure duplicate neighbors are ignored. Convert back to list before
      // returning. 
      neighbor_list[atom] = set()
      ////////////////////////////////////////////////////////////////////////////////////////////////////////////// DEBUG
      all_nbrs = set()
      print("self.neighbor_cutoff")
      print(self.neighbor_cutoff)
      ////////////////////////////////////////////////////////////////////////////////////////////////////////////// DEBUG
      for neighbor_cell in neighbor_cells:
        atoms_in_cell = cell_to_atoms[neighbor_cell]
        for neighbor_atom in atoms_in_cell:
          if neighbor_atom == atom:
            continue
          // TODO(rbharath): How does distance need to be modified here to
          // account for periodic boundary conditions?
          if np.linalg.norm(coords[atom] - coords[neighbor_atom]) < self.neighbor_cutoff:
            neighbor_list[atom].add(neighbor_atom)
          ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// DEBUG
          all_nbrs.add(neighbor_atom)
          ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// DEBUG
          
      ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// DEBUG
      print("All neighbor-cell atoms for %d = %s" % (atom, str(all_nbrs)))
      neighbor_list[atom] = list(neighbor_list[atom])
        
    return neighbor_list

Instances