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

"""
Eight Plus Sixteen
==================

"""

import numpy as np

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


[docs]class EightPlusSixteen(Cage): """ Represents a cage topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='BrCCBr', functional_groups=[stk.BromoFactory()], ) bb2 = stk.BuildingBlock( smiles='Brc1c(Br)cc(Br)c(Br)c1', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.EightPlusSixteen((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='BrCCBr', functional_groups=[stk.BromoFactory()], ) bb2 = stk.BuildingBlock( smiles='Brc1c(Br)cc(Br)c(Br)c1', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.EightPlusSixteen( 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 to 7 | 2-functional groups: 8 to 23 See :class:`.Cage` for more details and examples. """ _x = 2 _non_linears = ( NonLinearVertex(0, [-0.5*_x, 0.5*_x, -0.35*_x]), NonLinearVertex(1, [-0.5*_x, -0.5*_x, -0.35*_x]), NonLinearVertex(2, [0.5*_x, -0.5*_x, -0.35*_x]), NonLinearVertex(3, [0.5*_x, 0.5*_x, -0.35*_x]), NonLinearVertex(4, [-_x*np.sqrt(2)/2, 0, _x*0.35]), NonLinearVertex(5, [0, -_x*np.sqrt(2)/2, _x*0.35]), NonLinearVertex(6, [_x*np.sqrt(2)/2, 0, _x*0.35]), NonLinearVertex(7, [0, _x*np.sqrt(2)/2, _x*0.35]), ) _vertex_prototypes = ( *_non_linears, LinearVertex.init_at_center( id=8, vertices=(_non_linears[1], _non_linears[5]), ), LinearVertex.init_at_center( id=9, vertices=(_non_linears[2], _non_linears[5]), ), LinearVertex.init_at_center( id=10, vertices=(_non_linears[0], _non_linears[4]), ), LinearVertex.init_at_center( id=11, vertices=(_non_linears[1], _non_linears[4]), ), LinearVertex.init_at_center( id=12, vertices=(_non_linears[2], _non_linears[6]), ), LinearVertex.init_at_center( id=13, vertices=(_non_linears[3], _non_linears[6]), ), LinearVertex.init_at_center( id=14, vertices=(_non_linears[0], _non_linears[7]), ), LinearVertex.init_at_center( id=15, vertices=(_non_linears[3], _non_linears[7]), ), LinearVertex.init_at_center( id=16, vertices=(_non_linears[0], _non_linears[1]), ), LinearVertex.init_at_center( id=17, vertices=(_non_linears[1], _non_linears[2]), ), LinearVertex.init_at_center( id=18, vertices=(_non_linears[2], _non_linears[3]), ), LinearVertex.init_at_center( id=19, vertices=(_non_linears[3], _non_linears[0]), ), LinearVertex.init_at_center( id=20, vertices=(_non_linears[4], _non_linears[5]), ), LinearVertex.init_at_center( id=21, vertices=(_non_linears[5], _non_linears[6]), ), LinearVertex.init_at_center( id=22, vertices=(_non_linears[6], _non_linears[7]), ), LinearVertex.init_at_center( id=23, vertices=(_non_linears[7], _non_linears[4]), ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[8], _vertex_prototypes[1]), Edge(1, _vertex_prototypes[8], _vertex_prototypes[5]), Edge(2, _vertex_prototypes[9], _vertex_prototypes[2]), Edge(3, _vertex_prototypes[9], _vertex_prototypes[5]), Edge(4, _vertex_prototypes[10], _vertex_prototypes[0]), Edge(5, _vertex_prototypes[10], _vertex_prototypes[4]), Edge(6, _vertex_prototypes[11], _vertex_prototypes[1]), Edge(7, _vertex_prototypes[11], _vertex_prototypes[4]), Edge(8, _vertex_prototypes[12], _vertex_prototypes[2]), Edge(9, _vertex_prototypes[12], _vertex_prototypes[6]), Edge(10, _vertex_prototypes[13], _vertex_prototypes[3]), Edge(11, _vertex_prototypes[13], _vertex_prototypes[6]), Edge(12, _vertex_prototypes[14], _vertex_prototypes[0]), Edge(13, _vertex_prototypes[14], _vertex_prototypes[7]), Edge(14, _vertex_prototypes[15], _vertex_prototypes[3]), Edge(15, _vertex_prototypes[15], _vertex_prototypes[7]), Edge(16, _vertex_prototypes[16], _vertex_prototypes[0]), Edge(17, _vertex_prototypes[16], _vertex_prototypes[1]), Edge(18, _vertex_prototypes[17], _vertex_prototypes[1]), Edge(19, _vertex_prototypes[17], _vertex_prototypes[2]), Edge(20, _vertex_prototypes[18], _vertex_prototypes[2]), Edge(21, _vertex_prototypes[18], _vertex_prototypes[3]), Edge(22, _vertex_prototypes[19], _vertex_prototypes[3]), Edge(23, _vertex_prototypes[19], _vertex_prototypes[0]), Edge(24, _vertex_prototypes[20], _vertex_prototypes[4]), Edge(25, _vertex_prototypes[20], _vertex_prototypes[5]), Edge(26, _vertex_prototypes[21], _vertex_prototypes[5]), Edge(27, _vertex_prototypes[21], _vertex_prototypes[6]), Edge(28, _vertex_prototypes[22], _vertex_prototypes[6]), Edge(29, _vertex_prototypes[22], _vertex_prototypes[7]), Edge(30, _vertex_prototypes[23], _vertex_prototypes[7]), Edge(31, _vertex_prototypes[23], _vertex_prototypes[4]), ) _num_windows = 10 _num_window_types = 2