Source code for stk.molecular.topology_graphs.cage.two_plus_three.eight_plus_twelve

"""
Eight Plus Twelve
=================

"""

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


[docs]class EightPlusTwelve(Cage): """ Represents a cage topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='NC1CCCCC1N', functional_groups=[stk.PrimaryAminoFactory()], ) bb2 = stk.BuildingBlock( smiles='O=Cc1cc(C=O)cc(C=O)c1', functional_groups=[stk.AldehydeFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.EightPlusTwelve((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 construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='NC1CCCCC1N', functional_groups=[stk.PrimaryAminoFactory()], ) bb2 = stk.BuildingBlock( smiles='O=Cc1cc(C=O)cc(C=O)c1', functional_groups=[stk.AldehydeFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.EightPlusTwelve( building_blocks=(bb1, bb2), optimizer=stk.MCHammer(num_steps=1000), ), ) 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 three 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: | 3-functional groups: 0 to 7 | 2-functional groups: 8 to 19 See :class:`.Cage` for more details and examples. """ _non_linears = ( NonLinearVertex(0, [-1, 1, -1]), NonLinearVertex(1, [-1, -1, -1]), NonLinearVertex(2, [1, 1, -1]), NonLinearVertex(3, [1, -1, -1]), NonLinearVertex(4, [-1, 1, 1]), NonLinearVertex(5, [-1, -1, 1]), NonLinearVertex(6, [1, 1, 1]), NonLinearVertex(7, [1, -1, 1]), ) _vertex_prototypes = ( *_non_linears, LinearVertex.init_at_center( id=8, vertices=(_non_linears[0], _non_linears[2]), ), LinearVertex.init_at_center( id=9, vertices=(_non_linears[0], _non_linears[1]), ), LinearVertex.init_at_center( id=10, vertices=(_non_linears[1], _non_linears[3]), ), LinearVertex.init_at_center( id=11, vertices=(_non_linears[2], _non_linears[3]), ), LinearVertex.init_at_center( id=12, vertices=(_non_linears[4], _non_linears[6]), ), LinearVertex.init_at_center( id=13, vertices=(_non_linears[4], _non_linears[5]), ), LinearVertex.init_at_center( id=14, vertices=(_non_linears[5], _non_linears[7]), ), LinearVertex.init_at_center( id=15, vertices=(_non_linears[6], _non_linears[7]), ), LinearVertex.init_at_center( id=16, vertices=(_non_linears[0], _non_linears[4]), ), LinearVertex.init_at_center( id=17, vertices=(_non_linears[1], _non_linears[5]), ), LinearVertex.init_at_center( id=18, vertices=(_non_linears[2], _non_linears[6]), ), LinearVertex.init_at_center( id=19, vertices=(_non_linears[3], _non_linears[7]), ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[8], _vertex_prototypes[0]), Edge(1, _vertex_prototypes[8], _vertex_prototypes[2]), Edge(2, _vertex_prototypes[9], _vertex_prototypes[0]), Edge(3, _vertex_prototypes[9], _vertex_prototypes[1]), Edge(4, _vertex_prototypes[10], _vertex_prototypes[1]), Edge(5, _vertex_prototypes[10], _vertex_prototypes[3]), Edge(6, _vertex_prototypes[11], _vertex_prototypes[2]), Edge(7, _vertex_prototypes[11], _vertex_prototypes[3]), Edge(8, _vertex_prototypes[12], _vertex_prototypes[4]), Edge(9, _vertex_prototypes[12], _vertex_prototypes[6]), Edge(10, _vertex_prototypes[13], _vertex_prototypes[4]), Edge(11, _vertex_prototypes[13], _vertex_prototypes[5]), Edge(12, _vertex_prototypes[14], _vertex_prototypes[5]), Edge(13, _vertex_prototypes[14], _vertex_prototypes[7]), Edge(14, _vertex_prototypes[15], _vertex_prototypes[6]), Edge(15, _vertex_prototypes[15], _vertex_prototypes[7]), Edge(16, _vertex_prototypes[16], _vertex_prototypes[0]), Edge(17, _vertex_prototypes[16], _vertex_prototypes[4]), Edge(18, _vertex_prototypes[17], _vertex_prototypes[1]), Edge(19, _vertex_prototypes[17], _vertex_prototypes[5]), Edge(20, _vertex_prototypes[18], _vertex_prototypes[2]), Edge(21, _vertex_prototypes[18], _vertex_prototypes[6]), Edge(22, _vertex_prototypes[19], _vertex_prototypes[3]), Edge(23, _vertex_prototypes[19], _vertex_prototypes[7]), ) _num_windows = 6 _num_window_types = 1