"""
M4L82
=====
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import LinearVertex, NonLinearVertex
[docs]
class M4L82(Cage):
"""
Represents a cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='[Pd+2]',
functional_groups=(
stk.SingleAtom(stk.Pd(0, charge=2))
for i in range(4)
),
position_matrix=[[0, 0, 0]],
)
bb2 = stk.BuildingBlock(
smiles='C1=NC=CC(C2=CC=CC(C3=CC=NC=C3)=C2)=C1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M4L82(
building_blocks=(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=(
1
if bond.get_order() == 9
else 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='[Pd+2]',
functional_groups=(
stk.SingleAtom(stk.Pd(0, charge=2))
for i in range(4)
),
position_matrix=[[0, 0, 0]],
)
bb2 = stk.BuildingBlock(
smiles='C1=NC=CC(C2=CC=CC(C3=CC=NC=C3)=C2)=C1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M4L82(
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=(
1
if bond.get_order() == 9
else bond.get_order()
),
) for bond in cage.get_bonds()
),
)
Metal building blocks with four functional groups are
required for this topology.
Ligand 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 to 3
| 2-functional groups: 4 to 11
See :class:`.Cage` for more details and examples.
"""
_non_linears = (
NonLinearVertex(0, np.array([0, 0, np.sqrt(6) / 2])),
NonLinearVertex(1, np.array([-1, -np.sqrt(3) / 3, -np.sqrt(6) / 6])),
NonLinearVertex(2, np.array([1, -np.sqrt(3) / 3, -np.sqrt(6) / 6])),
NonLinearVertex(3, np.array([0, 2 * np.sqrt(3) / 3, -np.sqrt(6) / 6])),
)
paired_wall_1_coord = (
sum(
vertex.get_position()
for vertex in (_non_linears[0], _non_linears[1])
)
/ 2
)
wall_1_shift = np.array((0.2, 0.2, 0))
paired_wall_2_coord = (
sum(
vertex.get_position()
for vertex in (_non_linears[2], _non_linears[3])
)
/ 2
)
wall_2_shift = np.array((0.2, 0.2, 0))
_vertex_prototypes = (
*_non_linears,
LinearVertex(
id=4,
position=paired_wall_1_coord + wall_1_shift,
use_neighbor_placement=False,
),
LinearVertex.init_at_center(
id=5,
vertices=(_non_linears[0], _non_linears[2]),
),
LinearVertex.init_at_center(
id=6,
vertices=(_non_linears[0], _non_linears[3]),
),
LinearVertex.init_at_center(
id=7,
vertices=(_non_linears[1], _non_linears[2]),
),
LinearVertex.init_at_center(
id=8,
vertices=(_non_linears[1], _non_linears[3]),
),
LinearVertex(
id=9,
position=paired_wall_2_coord + wall_2_shift,
use_neighbor_placement=False,
),
LinearVertex(
id=10,
position=paired_wall_1_coord - wall_1_shift,
use_neighbor_placement=False,
),
LinearVertex(
id=11,
position=paired_wall_2_coord - wall_2_shift,
use_neighbor_placement=False,
),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[0], _vertex_prototypes[4]),
Edge(1, _vertex_prototypes[0], _vertex_prototypes[5]),
Edge(2, _vertex_prototypes[0], _vertex_prototypes[6]),
Edge(3, _vertex_prototypes[0], _vertex_prototypes[10]),
Edge(4, _vertex_prototypes[1], _vertex_prototypes[4]),
Edge(5, _vertex_prototypes[1], _vertex_prototypes[7]),
Edge(6, _vertex_prototypes[1], _vertex_prototypes[8]),
Edge(7, _vertex_prototypes[1], _vertex_prototypes[10]),
Edge(8, _vertex_prototypes[2], _vertex_prototypes[5]),
Edge(9, _vertex_prototypes[2], _vertex_prototypes[7]),
Edge(10, _vertex_prototypes[2], _vertex_prototypes[9]),
Edge(11, _vertex_prototypes[2], _vertex_prototypes[11]),
Edge(12, _vertex_prototypes[3], _vertex_prototypes[6]),
Edge(13, _vertex_prototypes[3], _vertex_prototypes[8]),
Edge(14, _vertex_prototypes[3], _vertex_prototypes[9]),
Edge(15, _vertex_prototypes[3], _vertex_prototypes[11]),
)
_num_windows = 2
_num_window_types = 1