Source code for stk.molecular.topology_graphs.cage.three_plus_four.six_plus_eight

"""
Six Plus Eight
==============

"""

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


[docs]class SixPlusEight(Cage): """ Represents a cage topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='Brc1c(Br)cc(Br)c(Br)c1', functional_groups=[stk.BromoFactory()], ) bb2 = stk.BuildingBlock( smiles='Brc1cc(Br)cc(Br)c1', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.SixPlusEight((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:`.MCHammer` optimized consturction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='Brc1c(Br)cc(Br)c(Br)c1', functional_groups=[stk.BromoFactory()], ) bb2 = stk.BuildingBlock( smiles='Brc1cc(Br)cc(Br)c1', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.SixPlusEight( building_blocks=(bb1, bb2), 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 and four functional groups are required for this topology graph. 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 5 | 3-functional groups: 6 to 13 See :class:`.Cage` for more details and examples. """ _x = 1 _non_linears = ( NonLinearVertex(0, [-_x, _x, 0]), NonLinearVertex(1, [-_x, -_x, 0]), NonLinearVertex(2, [_x, _x, 0]), NonLinearVertex(3, [_x, -_x, 0]), NonLinearVertex(4, [0, 0, _x]), NonLinearVertex(5, [0, 0, -_x]), ) _vertex_prototypes = ( *_non_linears, NonLinearVertex.init_at_center( id=6, vertices=( _non_linears[0], _non_linears[4], _non_linears[1] ), ), NonLinearVertex.init_at_center( id=7, vertices=( _non_linears[1], _non_linears[4], _non_linears[3] ), ), NonLinearVertex.init_at_center( id=8, vertices=( _non_linears[4], _non_linears[3], _non_linears[2] ), ), NonLinearVertex.init_at_center( id=9, vertices=( _non_linears[4], _non_linears[2], _non_linears[0] ), ), NonLinearVertex.init_at_center( id=10, vertices=( _non_linears[0], _non_linears[5], _non_linears[1] ), ), NonLinearVertex.init_at_center( id=11, vertices=( _non_linears[5], _non_linears[1], _non_linears[3] ), ), NonLinearVertex.init_at_center( id=12, vertices=( _non_linears[3], _non_linears[5], _non_linears[2] ), ), NonLinearVertex.init_at_center( id=13, vertices=( _non_linears[2], _non_linears[5], _non_linears[0] ), ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[6], _vertex_prototypes[0]), Edge(1, _vertex_prototypes[6], _vertex_prototypes[4]), Edge(2, _vertex_prototypes[6], _vertex_prototypes[1]), Edge(3, _vertex_prototypes[7], _vertex_prototypes[1]), Edge(4, _vertex_prototypes[7], _vertex_prototypes[4]), Edge(5, _vertex_prototypes[7], _vertex_prototypes[3]), Edge(6, _vertex_prototypes[8], _vertex_prototypes[4]), Edge(7, _vertex_prototypes[8], _vertex_prototypes[3]), Edge(8, _vertex_prototypes[8], _vertex_prototypes[2]), Edge(9, _vertex_prototypes[9], _vertex_prototypes[4]), Edge(10, _vertex_prototypes[9], _vertex_prototypes[2]), Edge(11, _vertex_prototypes[9], _vertex_prototypes[0]), Edge(12, _vertex_prototypes[10], _vertex_prototypes[0]), Edge(13, _vertex_prototypes[10], _vertex_prototypes[5]), Edge(14, _vertex_prototypes[10], _vertex_prototypes[1]), Edge(15, _vertex_prototypes[11], _vertex_prototypes[5]), Edge(16, _vertex_prototypes[11], _vertex_prototypes[1]), Edge(17, _vertex_prototypes[11], _vertex_prototypes[3]), Edge(18, _vertex_prototypes[12], _vertex_prototypes[3]), Edge(19, _vertex_prototypes[12], _vertex_prototypes[5]), Edge(20, _vertex_prototypes[12], _vertex_prototypes[2]), Edge(21, _vertex_prototypes[13], _vertex_prototypes[2]), Edge(22, _vertex_prototypes[13], _vertex_prototypes[5]), Edge(23, _vertex_prototypes[13], _vertex_prototypes[0]), ) _num_windows = 12 _num_window_types = 1