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

"""
Two Plus Three
==============

"""

import numpy as np

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


[docs]class TwoPlusThree(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.TwoPlusThree((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.TwoPlusThree( 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, 1) | 2-functional groups: (2, 3, 4) See :class:`.Cage` for more details and examples. """ _vertex_prototypes = ( NonLinearVertex(0, [0, 0, 1]), NonLinearVertex(1, [0, 0, -1]), LinearVertex(2, [-1, -0.5 * np.sqrt(3), 0], False), LinearVertex(3, [1, -0.5 * np.sqrt(3), 0], False), LinearVertex(4, [0, 0.5 * np.sqrt(3), 0], False), ) _edge_prototypes = ( Edge(0, _vertex_prototypes[0], _vertex_prototypes[2]), Edge(1, _vertex_prototypes[0], _vertex_prototypes[3]), Edge(2, _vertex_prototypes[0], _vertex_prototypes[4]), Edge(3, _vertex_prototypes[1], _vertex_prototypes[2]), Edge(4, _vertex_prototypes[1], _vertex_prototypes[3]), Edge(5, _vertex_prototypes[1], _vertex_prototypes[4]), ) _num_windows = 3 _num_window_types = 1