"""
Paddlewheel
===========
"""
from stk._internal.topology_graphs.edge import Edge
from .metal_complex import MetalComplex
from .vertices import BiDentateLigandVertex, MetalVertex
[docs]
class Paddlewheel(MetalComplex):
"""
Represents a metal complex topology graph.
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='[Cu+2]',
functional_groups=(
stk.SingleAtom(stk.Cu(0, charge=2))
for i in range(4)
),
position_matrix=([0, 0, 0], ),
)
bb2 = stk.BuildingBlock(
smiles='O=C(O)c1ccc(Br)cc1',
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#8]~[#1]',
bonders=(1, ),
deleters=(2, ),
),
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#8X1]',
bonders=(1, ),
deleters=(),
),
],
)
complex = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.Paddlewheel(
metals=bb1,
ligands=bb2,
reaction_factory=stk.DativeReactionFactory(
stk.GenericReactionFactory(
bond_orders={
frozenset({
stk.GenericFunctionalGroup,
stk.SingleAtom,
}): 9,
},
),
),
),
)
moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
complex.get_atoms(),
complex.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 complex.get_bonds()
),
)
Metal building blocks with at least four functional groups are
required for this topology.
Ligand building blocks with two functional groups are required for
this topology graph.
When using a :class:`dict` for initialization, a
:class:`.BuildingBlock` needs to be assigned to each of the
following numbers:
| metals: (0, 1)
| ligands: (0, 1, 2, 3)
See :class:`.MetalComplex` for more details and examples.
"""
_metal_vertex_prototypes = (
MetalVertex(0, (0, 1, 0)),
MetalVertex(1, (0, -1, 0)),
)
_ligand_vertex_prototypes = (
BiDentateLigandVertex(2, (2, 0, 0)),
BiDentateLigandVertex(3, (0, 0, 2)),
BiDentateLigandVertex(4, (-2, 0, 0)),
BiDentateLigandVertex(5, (0, 0, -2)),
)
_edge_prototypes = (
Edge(
id=0,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[0],
position=(0.1, 0.5, 0),
),
Edge(
id=1,
vertex1=_metal_vertex_prototypes[1],
vertex2=_ligand_vertex_prototypes[0],
position=(0.1, -0.5, 0),
),
Edge(
id=2,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[1],
position=(0, 0.5, 0.1),
),
Edge(
id=3,
vertex1=_metal_vertex_prototypes[1],
vertex2=_ligand_vertex_prototypes[1],
position=(0, -0.5, 0.1),
),
Edge(
id=4,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[2],
position=(-0.1, 0.5, 0),
),
Edge(
id=5,
vertex1=_metal_vertex_prototypes[1],
vertex2=_ligand_vertex_prototypes[2],
position=(-0.1, -0.5, 0),
),
Edge(
id=6,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[3],
position=(0, 0.5, -0.1),
),
Edge(
id=7,
vertex1=_metal_vertex_prototypes[1],
vertex2=_ligand_vertex_prototypes[3],
position=(0, -0.5, -0.1),
),
)