Source code for stk.molecular.topology_graphs.cage.three_plus_three.four_plus_four

"""
Four Plus Four
==============

"""

from ...topology_graph import Edge
from ..cage import Cage
from ..vertices import NonLinearVertex


[docs]class FourPlusFour(Cage): """ Represents a cube cage topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb = stk.BuildingBlock( smiles='Brc1cc(Br)cc(Br)c1', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.FourPlusFour((bb, )), ) moldoc_display_molecule = molecule.Molecule( atoms=( molecule.Atom( atomic_number=atom.get_atomic_number(), position=position, ) for atom, position in zip( cage.get_atoms(), cage.get_position_matrix(), ) ), bonds=( molecule.Bond( atom1_id=bond.get_atom1().get_id(), atom2_id=bond.get_atom2().get_id(), order=bond.get_order(), ) for bond in cage.get_bonds() ), ) :class:`.MCHammer` optimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb = stk.BuildingBlock( smiles='Brc1cc(Br)cc(Br)c1', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.FourPlusFour( building_blocks=(bb, ), optimizer=stk.MCHammer(), ), ) moldoc_display_molecule = molecule.Molecule( atoms=( molecule.Atom( atomic_number=atom.get_atomic_number(), position=position, ) for atom, position in zip( cage.get_atoms(), cage.get_position_matrix(), ) ), bonds=( molecule.Bond( atom1_id=bond.get_atom1().get_id(), atom2_id=bond.get_atom2().get_id(), order=bond.get_order(), ) for bond in cage.get_bonds() ), ) Building blocks with three functional groups are required for this topology. When using a :class:`dict` for the `building_blocks` parameter, as in :ref:`cage-topology-graph-examples`: *Multi-Building Block Cage Construction*, a :class:`.BuildingBlock`, with the following number of functional groups, needs to be assigned to each of the following vertex ids: | 3-functional groups: 0 to 7 See :class:`.Cage` for more details and examples. """ _x = 1 _vertex_prototypes = ( NonLinearVertex(0, [-_x, _x, -_x], False), NonLinearVertex(1, [-_x, -_x, -_x], False), NonLinearVertex(2, [_x, _x, -_x], False), NonLinearVertex(3, [_x, -_x, -_x], False), NonLinearVertex(4, [-_x, _x, _x], False), NonLinearVertex(5, [-_x, -_x, _x], False), NonLinearVertex(6, [_x, _x, _x], False), NonLinearVertex(7, [_x, -_x, _x], False), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[0], _vertex_prototypes[1]), Edge(1, _vertex_prototypes[0], _vertex_prototypes[2]), Edge(2, _vertex_prototypes[0], _vertex_prototypes[4]), Edge(3, _vertex_prototypes[1], _vertex_prototypes[3]), Edge(4, _vertex_prototypes[1], _vertex_prototypes[5]), Edge(5, _vertex_prototypes[2], _vertex_prototypes[6]), Edge(6, _vertex_prototypes[2], _vertex_prototypes[3]), Edge(7, _vertex_prototypes[3], _vertex_prototypes[7]), Edge(8, _vertex_prototypes[4], _vertex_prototypes[6]), Edge(9, _vertex_prototypes[4], _vertex_prototypes[5]), Edge(10, _vertex_prototypes[5], _vertex_prototypes[7]), Edge(11, _vertex_prototypes[6], _vertex_prototypes[7]), ) _num_windows = 6 _num_window_types = 1