Source code for stk.molecular.topology_graphs.cage.two_plus_four.two_plus_four

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

"""

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


[docs]class TwoPlusFour(Cage): """ Represents a capsule cage topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='C1=CC=C(C(=C1)Br)Br', functional_groups=[stk.BromoFactory()], ) bb2 = stk.BuildingBlock( smiles='C1(=C(C(=C1Br)Br)Br)Br', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.TwoPlusFour((bb1, bb2)), ) 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:`.Collapser` optimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='C1=CC=C(C(=C1)Br)Br', functional_groups=[stk.BromoFactory()], ) bb2 = stk.BuildingBlock( smiles='C1(=C(C(=C1Br)Br)Br)Br', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.TwoPlusFour( building_blocks=(bb1, bb2), optimizer=stk.Collapser(), ), ) 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() ), ) Nonlinear building blocks with four functional groups are required for this topology. Linear building blocks with two 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: | 4-functional groups: (0, 1) | 2-functional groups: (2, 3, 4, 5) See :class:`.Cage` for more details and examples. """ _vertex_prototypes = ( NonLinearVertex(0, [0, 0, -1]), NonLinearVertex(1, [0, 0, 1]), LinearVertex(2, [2, 0, 0], False), LinearVertex(3, [-2, 0, 0], False), LinearVertex(4, [0, 2, 0], False), LinearVertex(5, [0, -2, 0], False), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[2], _vertex_prototypes[0]), Edge(1, _vertex_prototypes[2], _vertex_prototypes[1]), Edge(2, _vertex_prototypes[3], _vertex_prototypes[0]), Edge(3, _vertex_prototypes[3], _vertex_prototypes[1]), Edge(4, _vertex_prototypes[4], _vertex_prototypes[0]), Edge(5, _vertex_prototypes[4], _vertex_prototypes[1]), Edge(6, _vertex_prototypes[5], _vertex_prototypes[0]), Edge(7, _vertex_prototypes[5], _vertex_prototypes[1]), ) _num_windows = 4 _num_window_types = 1