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

"""
Six Plus Nine
=============

"""

import numpy as np

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


[docs]class SixPlusNine(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.SixPlusNine((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.SixPlusNine( 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() ), ) 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 5 | 2-functional groups: 5 to 14 See :class:`.Cage` for more details and examples. """ # source: http://eusebeia.dyndns.org/4d/prism3 _non_linears = ( NonLinearVertex(0, [-1, -1/np.sqrt(3), -1]), NonLinearVertex(1, [-1, -1/np.sqrt(3), 1]), NonLinearVertex(2, [1, -1/np.sqrt(3), -1]), NonLinearVertex(3, [1, -1/np.sqrt(3), 1]), NonLinearVertex(4, [0, 2/np.sqrt(3), -1]), NonLinearVertex(5, [0, 2/np.sqrt(3), 1]) ) _vertex_prototypes = ( *_non_linears, LinearVertex.init_at_center( id=6, vertices=(_non_linears[0], _non_linears[1]), ), LinearVertex.init_at_center( id=7, vertices=(_non_linears[0], _non_linears[2]), ), LinearVertex.init_at_center( id=8, vertices=(_non_linears[2], _non_linears[3]), ), LinearVertex.init_at_center( id=9, vertices=(_non_linears[1], _non_linears[3]), ), LinearVertex.init_at_center( id=10, vertices=(_non_linears[0], _non_linears[4]), ), LinearVertex.init_at_center( id=11, vertices=(_non_linears[2], _non_linears[4]), ), LinearVertex.init_at_center( id=12, vertices=(_non_linears[1], _non_linears[5]), ), LinearVertex.init_at_center( id=13, vertices=(_non_linears[3], _non_linears[5]), ), LinearVertex.init_at_center( id=14, vertices=(_non_linears[4], _non_linears[5]), ), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[6], _vertex_prototypes[0]), Edge(1, _vertex_prototypes[6], _vertex_prototypes[1]), Edge(2, _vertex_prototypes[7], _vertex_prototypes[0]), Edge(3, _vertex_prototypes[7], _vertex_prototypes[2]), Edge(4, _vertex_prototypes[8], _vertex_prototypes[2]), Edge(5, _vertex_prototypes[8], _vertex_prototypes[3]), Edge(6, _vertex_prototypes[9], _vertex_prototypes[1]), Edge(7, _vertex_prototypes[9], _vertex_prototypes[3]), Edge(8, _vertex_prototypes[10], _vertex_prototypes[0]), Edge(9, _vertex_prototypes[10], _vertex_prototypes[4]), Edge(10, _vertex_prototypes[11], _vertex_prototypes[2]), Edge(11, _vertex_prototypes[11], _vertex_prototypes[4]), Edge(12, _vertex_prototypes[12], _vertex_prototypes[1]), Edge(13, _vertex_prototypes[12], _vertex_prototypes[5]), Edge(14, _vertex_prototypes[13], _vertex_prototypes[3]), Edge(15, _vertex_prototypes[13], _vertex_prototypes[5]), Edge(16, _vertex_prototypes[14], _vertex_prototypes[4]), Edge(17, _vertex_prototypes[14], _vertex_prototypes[5]), ) _num_windows = 5 _num_window_types = 1