"""
Square
======
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cof import Cof
from .vertices import LinearVertex, NonLinearVertex
[docs]
class Square(Cof):
"""
Represents a sqaure COF topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
cof = stk.ConstructedMolecule(
topology_graph=stk.cof.PeriodicSquare(
building_blocks=(
stk.BuildingBlock(
smiles='BrCC(Br)',
functional_groups=[stk.BromoFactory()],
),
stk.BuildingBlock(
smiles='BrC1=C(Br)C(Br)=C1Br',
functional_groups=[stk.BromoFactory()],
),
),
lattice_size=(3, 3, 1),
),
)
moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
cof.get_atoms(),
cof.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 cof.get_bonds()
if all(p == 0 for p in bond.get_periodicity())
),
)
``Collapser(scale_steps=False)`` optimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
cof = stk.ConstructedMolecule(
topology_graph=stk.cof.PeriodicSquare(
building_blocks=(
stk.BuildingBlock(
smiles='BrCC(Br)',
functional_groups=[stk.BromoFactory()],
),
stk.BuildingBlock(
smiles='BrC1=C(Br)C(Br)=C1Br',
functional_groups=[stk.BromoFactory()],
),
),
lattice_size=(3, 3, 1),
optimizer=stk.Collapser(scale_steps=False),
),
)
moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
cof.get_atoms(),
cof.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 cof.get_bonds()
if all(p == 0 for p in bond.get_periodicity())
),
)
Building blocks with four and two functional groups are required
for this topology graph.
When using a :class:`dict` for the `building_blocks` parameter,
as in :ref:`cof-topology-graph-examples`:
*Multi-Building Block COF 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
| 2-functional groups: 1 to 2
See :class:`.Cof` for more details and examples.
"""
_lattice_constants = _a, _b, _c = (
np.array([1.0, 0.0, 0.0]),
np.array([0.0, 1.0, 0.0]),
np.array([0.0, 0.0, 1.0]),
)
_non_linears = (NonLinearVertex(0, (0.5) * _a + (0.5) * _b + (0.5) * _c),)
_vertex_prototypes = (
*_non_linears,
LinearVertex.init_at_shifted_center(
id=1,
vertices=(_non_linears[0], _non_linears[0]),
cell_shifts=((0, 0, 0), (1, 0, 0)),
lattice_constants=_lattice_constants,
),
LinearVertex.init_at_shifted_center(
id=2,
vertices=(_non_linears[0], _non_linears[0]),
cell_shifts=((0, 0, 0), (0, 1, 0)),
lattice_constants=_lattice_constants,
),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[1], _vertex_prototypes[0]),
Edge(
id=1,
vertex1=_vertex_prototypes[1],
vertex2=_vertex_prototypes[0],
periodicity=(1, 0, 0),
),
Edge(2, _vertex_prototypes[2], _vertex_prototypes[0]),
Edge(
id=3,
vertex1=_vertex_prototypes[2],
vertex2=_vertex_prototypes[0],
periodicity=(0, 1, 0),
),
)