"""
M6L2L3 Prism
============
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import NonLinearVertex
[docs]
class M6L2L3Prism(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()],
)
bb4 = stk.BuildingBlock(
smiles=(
'C1=CC(=CC=C1C2=CC(=C(C=C2C3=CC=C(C=C3)Br)C4=CC=C(C=C'
'4)Br)C5=CC=C(C=C5)Br)Br'
),
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M6L2L3Prism(
building_blocks={
iron_oct_delta: range(6),
bb3: (6, 7),
bb4: range(8, 11),
},
),
)
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:`.Collapser` 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()],
)
bb4 = stk.BuildingBlock(
smiles=(
'C1=CC(=CC=C1C2=CC(=C(C=C2C3=CC=C(C=C3)Br)C4=CC=C(C=C'
'4)Br)C5=CC=C(C=C5)Br)Br'
),
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M6L2L3Prism(
building_blocks={
iron_oct_delta: range(6),
bb3: (6, 7),
bb4: range(8, 11),
},
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=(
1
if bond.get_order() == 9
else bond.get_order()
),
) for bond in cage.get_bonds()
),
)
Metal building blocks with three functional groups are
required for this topology.
Ligand building blocks with three and four functional groups are
required for ligand type A and B, respectively, on 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 5
| 3-functional groups (ligand A): 6, 7
| 4-functional groups (ligand B): 8 to 10
See :class:`.Cage` for more details and examples.
"""
_non_linears = (
NonLinearVertex(0, np.array([-1, -1 / np.sqrt(3), 1])),
NonLinearVertex(1, np.array([1, -1 / np.sqrt(3), 1])),
NonLinearVertex(2, np.array([0, 2 / np.sqrt(3), 1])),
NonLinearVertex(3, np.array([-1, -1 / np.sqrt(3), -1])),
NonLinearVertex(4, np.array([1, -1 / np.sqrt(3), -1])),
NonLinearVertex(5, np.array([0, 2 / np.sqrt(3), -1])),
)
_vertex_prototypes = (
*_non_linears,
NonLinearVertex.init_at_center(
id=6,
vertices=(
_non_linears[0],
_non_linears[1],
_non_linears[2],
),
),
NonLinearVertex.init_at_center(
id=7,
vertices=(
_non_linears[3],
_non_linears[4],
_non_linears[5],
),
),
NonLinearVertex.init_at_center(
id=8,
vertices=(
_non_linears[0],
_non_linears[1],
_non_linears[3],
_non_linears[4],
),
),
NonLinearVertex.init_at_center(
id=9,
vertices=(
_non_linears[1],
_non_linears[2],
_non_linears[4],
_non_linears[5],
),
),
NonLinearVertex.init_at_center(
id=10,
vertices=(
_non_linears[2],
_non_linears[0],
_non_linears[5],
_non_linears[3],
),
),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[0], _vertex_prototypes[6]),
Edge(1, _vertex_prototypes[0], _vertex_prototypes[8]),
Edge(2, _vertex_prototypes[0], _vertex_prototypes[10]),
Edge(3, _vertex_prototypes[1], _vertex_prototypes[6]),
Edge(4, _vertex_prototypes[1], _vertex_prototypes[8]),
Edge(5, _vertex_prototypes[1], _vertex_prototypes[9]),
Edge(6, _vertex_prototypes[2], _vertex_prototypes[6]),
Edge(7, _vertex_prototypes[2], _vertex_prototypes[9]),
Edge(8, _vertex_prototypes[2], _vertex_prototypes[10]),
Edge(9, _vertex_prototypes[3], _vertex_prototypes[7]),
Edge(10, _vertex_prototypes[3], _vertex_prototypes[8]),
Edge(11, _vertex_prototypes[3], _vertex_prototypes[10]),
Edge(12, _vertex_prototypes[4], _vertex_prototypes[7]),
Edge(13, _vertex_prototypes[4], _vertex_prototypes[8]),
Edge(14, _vertex_prototypes[4], _vertex_prototypes[9]),
Edge(15, _vertex_prototypes[5], _vertex_prototypes[7]),
Edge(16, _vertex_prototypes[5], _vertex_prototypes[9]),
Edge(17, _vertex_prototypes[5], _vertex_prototypes[10]),
)
_num_windows = 4
_num_window_types = 1