"""
Two Plus Four
=============
"""
import numpy as np
from stk._internal.topology_graphs.cage.cage import Cage
from stk._internal.topology_graphs.cage.vertices import (
LinearVertex,
NonLinearVertex,
)
from stk._internal.topology_graphs.edge import Edge
[docs]
class TwoPlusFour(Cage):
"""
Represents a capsule cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='C1=CC=C(C(=C1)Br)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.TwoPlusFour((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=C(C(=C1)Br)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.TwoPlusFour(
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, 1)
| 2-functional groups: (2, 3, 4, 5)
See :class:`.Cage` for more details and examples.
"""
_vertex_prototypes = (
NonLinearVertex(0, np.array([0, 0, -1])),
NonLinearVertex(1, np.array([0, 0, 1])),
LinearVertex(2, np.array([2, 0, 0]), False),
LinearVertex(3, np.array([-2, 0, 0]), False),
LinearVertex(4, np.array([0, 2, 0]), False),
LinearVertex(5, np.array([0, -2, 0]), False),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[2], _vertex_prototypes[0]),
Edge(1, _vertex_prototypes[2], _vertex_prototypes[1]),
Edge(2, _vertex_prototypes[3], _vertex_prototypes[0]),
Edge(3, _vertex_prototypes[3], _vertex_prototypes[1]),
Edge(4, _vertex_prototypes[4], _vertex_prototypes[0]),
Edge(5, _vertex_prototypes[4], _vertex_prototypes[1]),
Edge(6, _vertex_prototypes[5], _vertex_prototypes[0]),
Edge(7, _vertex_prototypes[5], _vertex_prototypes[1]),
)
_num_windows = 4
_num_window_types = 1