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

"""
Five Plus Ten
=============

"""

import numpy as np

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


[docs]class FivePlusTen(Cage): """ Represents a cage topology graph. Unoptimized construction .. moldoc:: import moldoc.molecule as molecule import stk bb1 = stk.BuildingBlock( smiles='C1=CC(=CC=C1Br)Br', functional_groups=[stk.BromoFactory()], ) bb2 = stk.BuildingBlock( smiles='C1(=C(C(=C1Br)Br)Br)Br', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.FivePlusTen((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='C1=CC(=CC=C1Br)Br', functional_groups=[stk.BromoFactory()], ) bb2 = stk.BuildingBlock( smiles='C1(=C(C(=C1Br)Br)Br)Br', functional_groups=[stk.BromoFactory()], ) cage = stk.ConstructedMolecule( topology_graph=stk.cage.FivePlusTen( 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 4 | 2-functional groups: 5 to 14 See :class:`.Cage` for more details and examples. """ _c1 = np.cos(2*np.pi/5) _c2 = np.cos(np.pi/5) _s1 = np.sin(2*np.pi/5) _s2 = np.sin(4*np.pi/5) _vertex_prototypes = ( NonLinearVertex(0, [0, 1, 0], False), NonLinearVertex(1, [_s1, _c1, 0], False), NonLinearVertex(2, [_s2, -_c2, 0], False), NonLinearVertex(3, [-_s2, -_c2, 0], False), NonLinearVertex(4, [-_s1, _c1, 0], False), LinearVertex(5, [_s1, 1+_c1, 0.5], False), LinearVertex(6, [_s1, 1+_c1, -0.5], False), LinearVertex(7, [_s1+_s2, _c1-_c2, 0.5], False), LinearVertex(8, [_s1+_s2, _c1-_c2, -0.5], False), LinearVertex(9, [0, -2*_c2, 0.5], False), LinearVertex(10, [0, -2*_c2, -0.5], False), LinearVertex(11, [-_s2-_s1, -_c2+_c1, 0.5], False), LinearVertex(12, [-_s2-_s1, -_c2+_c1, -0.5], False), LinearVertex(13, [-_s1, 1+_c1, 0.5], False), LinearVertex(14, [-_s1, 1+_c1, -0.5], False), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[5], _vertex_prototypes[0]), Edge(1, _vertex_prototypes[5], _vertex_prototypes[1]), Edge(2, _vertex_prototypes[6], _vertex_prototypes[0]), Edge(3, _vertex_prototypes[6], _vertex_prototypes[1]), Edge(4, _vertex_prototypes[7], _vertex_prototypes[1]), Edge(5, _vertex_prototypes[7], _vertex_prototypes[2]), Edge(6, _vertex_prototypes[8], _vertex_prototypes[1]), Edge(7, _vertex_prototypes[8], _vertex_prototypes[2]), Edge(8, _vertex_prototypes[9], _vertex_prototypes[2]), Edge(9, _vertex_prototypes[9], _vertex_prototypes[3]), Edge(10, _vertex_prototypes[10], _vertex_prototypes[2]), Edge(11, _vertex_prototypes[10], _vertex_prototypes[3]), Edge(12, _vertex_prototypes[11], _vertex_prototypes[3]), Edge(13, _vertex_prototypes[11], _vertex_prototypes[4]), Edge(14, _vertex_prototypes[12], _vertex_prototypes[3]), Edge(15, _vertex_prototypes[12], _vertex_prototypes[4]), Edge(16, _vertex_prototypes[13], _vertex_prototypes[4]), Edge(17, _vertex_prototypes[13], _vertex_prototypes[0]), Edge(18, _vertex_prototypes[14], _vertex_prototypes[4]), Edge(19, _vertex_prototypes[14], _vertex_prototypes[0]), ) _num_windows = 7 _num_window_types = 2