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

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

"""

import numpy as np

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


[docs]class TwoPlusTwo(Cage): """ Represents a tetrahedron 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.TwoPlusTwo((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.TwoPlusTwo( 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 3 See :class:`.Cage` for more details and examples. """ _x = 1 _vertex_prototypes = ( NonLinearVertex(0, [_x, 0, -_x / np.sqrt(2)], False), NonLinearVertex(1, [-_x, 0, -_x / np.sqrt(2)], False), NonLinearVertex(2, [0, _x, _x / np.sqrt(2)], False), NonLinearVertex(3, [0, -_x, _x / np.sqrt(2)], 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[3]), Edge(3, _vertex_prototypes[1], _vertex_prototypes[2]), Edge(4, _vertex_prototypes[1], _vertex_prototypes[3]), Edge(5, _vertex_prototypes[2], _vertex_prototypes[3]), ) _num_windows = 4 _num_window_types = 1