"""
M4L4 Tetrahedron
================
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import NonLinearVertex
[docs]
class M4L4Tetrahedron(Cage):
"""
Represents a cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
iron_atom = stk.BuildingBlock(
smiles='[Fe+2]',
functional_groups=(
stk.SingleAtom(stk.Fe(0, charge=2))
for i in range(6)
),
position_matrix=[[0, 0, 0]],
)
bb2 = stk.BuildingBlock(
smiles='C1=NC(C=NBr)=CC=C1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#35]',
bonders=(1, ),
deleters=(),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
complex = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.OctahedralDelta(
metals=iron_atom,
ligands=bb2,
optimizer=stk.MCHammer(),
),
)
# Assign Bromo functional groups to the metal complex.
iron_oct_delta = stk.BuildingBlock.init_from_molecule(
molecule=complex,
functional_groups=[stk.BromoFactory()],
)
# Define building blocks.
bb3 = stk.BuildingBlock(
smiles=(
'C1=C(C=C(C=C1Br)Br)Br'
),
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M4L4Tetrahedron(
building_blocks={
iron_oct_delta: (0, 1, 2, 3),
bb3: (4, 5, 6, 7),
},
),
)
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
iron_atom = stk.BuildingBlock(
smiles='[Fe+2]',
functional_groups=(
stk.SingleAtom(stk.Fe(0, charge=2))
for i in range(6)
),
position_matrix=[[0, 0, 0]],
)
bb2 = stk.BuildingBlock(
smiles='C1=NC(C=NBr)=CC=C1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#35]',
bonders=(1, ),
deleters=(),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
complex = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.OctahedralDelta(
metals=iron_atom,
ligands=bb2,
optimizer=stk.MCHammer(),
),
)
# Assign Bromo functional groups to the metal complex.
iron_oct_delta = stk.BuildingBlock.init_from_molecule(
molecule=complex,
functional_groups=[stk.BromoFactory()],
)
# Define building blocks.
bb3 = stk.BuildingBlock(
smiles=(
'C1=C(C=C(C=C1Br)Br)Br'
),
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M4L4Tetrahedron(
building_blocks={
iron_oct_delta: (0, 1, 2, 3),
bb3: (4, 5, 6, 7),
},
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()
),
)
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 (metal): 0 to 3
| 3-functional groups (linker): 4 to 7
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])),
)
_vertex_prototypes = (
*_non_linears,
NonLinearVertex.init_at_center(
id=4,
vertices=(
_non_linears[0],
_non_linears[1],
_non_linears[2],
),
),
NonLinearVertex.init_at_center(
id=5,
vertices=(
_non_linears[0],
_non_linears[1],
_non_linears[3],
),
),
NonLinearVertex.init_at_center(
id=6,
vertices=(
_non_linears[0],
_non_linears[2],
_non_linears[3],
),
),
NonLinearVertex.init_at_center(
id=7,
vertices=(
_non_linears[1],
_non_linears[2],
_non_linears[3],
),
),
)
_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[1], _vertex_prototypes[4]),
Edge(4, _vertex_prototypes[1], _vertex_prototypes[5]),
Edge(5, _vertex_prototypes[1], _vertex_prototypes[7]),
Edge(6, _vertex_prototypes[2], _vertex_prototypes[4]),
Edge(7, _vertex_prototypes[2], _vertex_prototypes[6]),
Edge(8, _vertex_prototypes[2], _vertex_prototypes[7]),
Edge(9, _vertex_prototypes[3], _vertex_prototypes[5]),
Edge(10, _vertex_prototypes[3], _vertex_prototypes[6]),
Edge(11, _vertex_prototypes[3], _vertex_prototypes[7]),
)
_num_windows = 4
_num_window_types = 1