Source code for stk.molecular.topology_graphs.cage.two_plus_five.twelve_plus_thirty

"""
Twelve Plus Thirty
==================

"""

from scipy.constants import golden

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


[docs]class TwelvePlusThirty(Cage): """ Represents a icosahedron 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)C(Br)C(Br)C1Br', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.TwelvePlusThirty((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)C(Br)C(Br)C1Br', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.TwelvePlusThirty( 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 five 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: | 5-functional groups: 0 to 11 | 2-functional groups: 12 to 41 See :class:`.Cage` for more details and examples. """ # Vertices of a regular origin-centred icosahedron # Source: http://eusebeia.dyndns.org/4d/icosahedron _non_linears = ( NonLinearVertex(0, [0, 1, golden]), NonLinearVertex(1, [0, -1, golden]), NonLinearVertex(2, [0, 1, -golden]), NonLinearVertex(3, [0, -1, -golden]), NonLinearVertex(4, [1, golden, 0]), NonLinearVertex(5, [-1, golden, 0]), NonLinearVertex(6, [1, -golden, 0]), NonLinearVertex(7, [-1, -golden, 0]), NonLinearVertex(8, [golden, 0, 1]), NonLinearVertex(9, [-golden, 0, 1]), NonLinearVertex(10, [golden, 0, -1]), NonLinearVertex(11, [-golden, 0, -1]) ) _vertex_prototypes = ( *_non_linears, LinearVertex.init_at_center( id=12, vertices=(_non_linears[0], _non_linears[1]), ), LinearVertex.init_at_center( id=13, vertices=(_non_linears[0], _non_linears[9]), ), LinearVertex.init_at_center( id=14, vertices=(_non_linears[0], _non_linears[5]), ), LinearVertex.init_at_center( id=15, vertices=(_non_linears[0], _non_linears[4]), ), LinearVertex.init_at_center( id=16, vertices=(_non_linears[0], _non_linears[8]), ), LinearVertex.init_at_center( id=17, vertices=(_non_linears[8], _non_linears[1]),), LinearVertex.init_at_center( id=18, vertices=(_non_linears[1], _non_linears[9]), ), LinearVertex.init_at_center( id=19, vertices=(_non_linears[9], _non_linears[5]), ), LinearVertex.init_at_center( id=20, vertices=(_non_linears[5], _non_linears[4]), ), LinearVertex.init_at_center( id=21, vertices=(_non_linears[4], _non_linears[8]), ), LinearVertex.init_at_center( id=22, vertices=(_non_linears[5], _non_linears[2]), ), LinearVertex.init_at_center( id=23, vertices=(_non_linears[5], _non_linears[11]), ), LinearVertex.init_at_center( id=24, vertices=(_non_linears[9], _non_linears[11]), ), LinearVertex.init_at_center( id=25, vertices=(_non_linears[9], _non_linears[7]), ), LinearVertex.init_at_center( id=26, vertices=(_non_linears[1], _non_linears[7]), ), LinearVertex.init_at_center( id=27, vertices=(_non_linears[1], _non_linears[6]), ), LinearVertex.init_at_center( id=28, vertices=(_non_linears[8], _non_linears[6]), ), LinearVertex.init_at_center( id=29, vertices=(_non_linears[8], _non_linears[10]), ), LinearVertex.init_at_center( id=30, vertices=(_non_linears[4], _non_linears[10]), ), LinearVertex.init_at_center( id=31, vertices=(_non_linears[4], _non_linears[2]), ), LinearVertex.init_at_center( id=32, vertices=(_non_linears[2], _non_linears[11]), ), LinearVertex.init_at_center( id=33, vertices=(_non_linears[11], _non_linears[7]), ), LinearVertex.init_at_center( id=34, vertices=(_non_linears[7], _non_linears[6]), ), LinearVertex.init_at_center( id=35, vertices=(_non_linears[6], _non_linears[10]), ), LinearVertex.init_at_center( id=36, vertices=(_non_linears[10], _non_linears[2]), ), LinearVertex.init_at_center( id=37, vertices=(_non_linears[2], _non_linears[3]), ), LinearVertex.init_at_center( id=38, vertices=(_non_linears[11], _non_linears[3]), ), LinearVertex.init_at_center( id=39, vertices=(_non_linears[7], _non_linears[3]), ), LinearVertex.init_at_center( id=40, vertices=(_non_linears[6], _non_linears[3]), ), LinearVertex.init_at_center( id=41, vertices=(_non_linears[10], _non_linears[3]), ) ) _edge_prototypes = ( Edge(0, _vertex_prototypes[12], _vertex_prototypes[0]), Edge(1, _vertex_prototypes[12], _vertex_prototypes[1]), Edge(2, _vertex_prototypes[13], _vertex_prototypes[0]), Edge(3, _vertex_prototypes[13], _vertex_prototypes[9]), Edge(4, _vertex_prototypes[14], _vertex_prototypes[0]), Edge(5, _vertex_prototypes[14], _vertex_prototypes[5]), Edge(6, _vertex_prototypes[15], _vertex_prototypes[0]), Edge(7, _vertex_prototypes[15], _vertex_prototypes[4]), Edge(8, _vertex_prototypes[16], _vertex_prototypes[0]), Edge(9, _vertex_prototypes[16], _vertex_prototypes[8]), Edge(10, _vertex_prototypes[17], _vertex_prototypes[8]), Edge(11, _vertex_prototypes[17], _vertex_prototypes[1]), Edge(12, _vertex_prototypes[18], _vertex_prototypes[1]), Edge(13, _vertex_prototypes[18], _vertex_prototypes[9]), Edge(14, _vertex_prototypes[19], _vertex_prototypes[9]), Edge(15, _vertex_prototypes[19], _vertex_prototypes[5]), Edge(16, _vertex_prototypes[20], _vertex_prototypes[5]), Edge(17, _vertex_prototypes[20], _vertex_prototypes[4]), Edge(18, _vertex_prototypes[21], _vertex_prototypes[4]), Edge(19, _vertex_prototypes[21], _vertex_prototypes[8]), Edge(20, _vertex_prototypes[22], _vertex_prototypes[5]), Edge(21, _vertex_prototypes[22], _vertex_prototypes[2]), Edge(22, _vertex_prototypes[23], _vertex_prototypes[5]), Edge(23, _vertex_prototypes[23], _vertex_prototypes[11]), Edge(24, _vertex_prototypes[24], _vertex_prototypes[9]), Edge(25, _vertex_prototypes[24], _vertex_prototypes[11]), Edge(26, _vertex_prototypes[25], _vertex_prototypes[9]), Edge(27, _vertex_prototypes[25], _vertex_prototypes[7]), Edge(28, _vertex_prototypes[26], _vertex_prototypes[1]), Edge(29, _vertex_prototypes[26], _vertex_prototypes[7]), Edge(30, _vertex_prototypes[27], _vertex_prototypes[1]), Edge(31, _vertex_prototypes[27], _vertex_prototypes[6]), Edge(32, _vertex_prototypes[28], _vertex_prototypes[8]), Edge(33, _vertex_prototypes[28], _vertex_prototypes[6]), Edge(34, _vertex_prototypes[29], _vertex_prototypes[8]), Edge(35, _vertex_prototypes[29], _vertex_prototypes[10]), Edge(36, _vertex_prototypes[30], _vertex_prototypes[4]), Edge(37, _vertex_prototypes[30], _vertex_prototypes[10]), Edge(38, _vertex_prototypes[31], _vertex_prototypes[4]), Edge(39, _vertex_prototypes[31], _vertex_prototypes[2]), Edge(40, _vertex_prototypes[32], _vertex_prototypes[2]), Edge(41, _vertex_prototypes[32], _vertex_prototypes[11]), Edge(42, _vertex_prototypes[33], _vertex_prototypes[11]), Edge(43, _vertex_prototypes[33], _vertex_prototypes[7]), Edge(44, _vertex_prototypes[34], _vertex_prototypes[7]), Edge(45, _vertex_prototypes[34], _vertex_prototypes[6]), Edge(46, _vertex_prototypes[35], _vertex_prototypes[6]), Edge(47, _vertex_prototypes[35], _vertex_prototypes[10]), Edge(48, _vertex_prototypes[36], _vertex_prototypes[10]), Edge(49, _vertex_prototypes[36], _vertex_prototypes[2]), Edge(50, _vertex_prototypes[37], _vertex_prototypes[2]), Edge(51, _vertex_prototypes[37], _vertex_prototypes[3]), Edge(52, _vertex_prototypes[38], _vertex_prototypes[11]), Edge(53, _vertex_prototypes[38], _vertex_prototypes[3]), Edge(54, _vertex_prototypes[39], _vertex_prototypes[7]), Edge(55, _vertex_prototypes[39], _vertex_prototypes[3]), Edge(56, _vertex_prototypes[40], _vertex_prototypes[6]), Edge(57, _vertex_prototypes[40], _vertex_prototypes[3]), Edge(58, _vertex_prototypes[41], _vertex_prototypes[10]), Edge(59, _vertex_prototypes[41], _vertex_prototypes[3]), ) _num_windows = 20 _num_window_types = 1