"""
Two Plus Two
============
"""
import numpy as np
from stk._internal.topology_graphs.cage.cage import Cage
from stk._internal.topology_graphs.edge import Edge
from .vertices import NonLinearVertex
[docs]
class TwoPlusTwo(Cage):
"""
Represents a tetrahedron cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb = stk.BuildingBlock(
smiles='Brc1cc(Br)cc(Br)c1',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.TwoPlusTwo((bb, )),
)
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
bb = stk.BuildingBlock(
smiles='Brc1cc(Br)cc(Br)c1',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.TwoPlusTwo(
building_blocks=(bb, ),
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()
),
)
Building blocks with three 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 3
See :class:`.Cage` for more details and examples.
"""
_x = 1
_vertex_prototypes = (
NonLinearVertex(0, np.array([_x, 0, -_x / np.sqrt(2)]), False),
NonLinearVertex(1, np.array([-_x, 0, -_x / np.sqrt(2)]), False),
NonLinearVertex(2, np.array([0, _x, _x / np.sqrt(2)]), False),
NonLinearVertex(3, np.array([0, -_x, _x / np.sqrt(2)]), False),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[0], _vertex_prototypes[1]),
Edge(1, _vertex_prototypes[0], _vertex_prototypes[2]),
Edge(2, _vertex_prototypes[0], _vertex_prototypes[3]),
Edge(3, _vertex_prototypes[1], _vertex_prototypes[2]),
Edge(4, _vertex_prototypes[1], _vertex_prototypes[3]),
Edge(5, _vertex_prototypes[2], _vertex_prototypes[3]),
)
_num_windows = 4
_num_window_types = 1