Example #1
0
 def get_vector(self, atom1, atom2, distance):
     if atom1 in atom2.yield_neighbors():
         return None
     bond_type = bonds.bonded(atom1.number, atom2.number, distance)
     if bond_type is None:
         return None
     else:
         return Bond(bond_type=bond_type, targets=[atom1, atom2])
Example #2
0
 def compare_function(positioned1, positioned2):
     delta = positioned2.coordinate - positioned1.coordinate
     if unit_cell is not None:
         delta = unit_cell.shortest_vector(delta)
     distance = numpy.linalg.norm(delta)
     if distance < binned_atoms.gridsize:
         bond_order = bonds.bonded(molecule.numbers[positioned1.id], molecule.numbers[positioned2.id], distance)
         if bond_order != None:
             return bond_order, distance