"""
Octahedral Delta
================
"""
from stk._internal.topology_graphs.edge import Edge
from .metal_complex import MetalComplex
from .vertices import BiDentateLigandVertex, MetalVertex
[docs]
class OctahedralDelta(MetalComplex):
"""
Represents a metal complex topology graph.
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = 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=CC=NC(C2=CC=CC(C3=C'
'C=CC=N3)=C2)=C1'
),
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
complex = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.OctahedralDelta(
metals=bb1,
ligands=bb2,
),
)
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 six 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, )
| ligands: (0, 1, 2)
See :class:`.MetalComplex` for more details and examples.
"""
_metal_vertex_prototypes = (MetalVertex(0, (0, 0, 0)),)
_ligand_vertex_prototypes = (
BiDentateLigandVertex(1, (2.5, 2.5, 0)),
BiDentateLigandVertex(2, (0, -2.5, 2.5)),
BiDentateLigandVertex(3, (-2.5, 0, -2.5)),
)
# The ordering here matters for the stereochemistry.
# The first edge to appear between two vertices determines the
# directionality of the binding ligand.
_edge_prototypes = (
Edge(
id=0,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[0],
position=(2.5, 0, 0),
),
Edge(
id=1,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[0],
position=(0, 2.5, 0),
),
Edge(
id=4,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[1],
position=(0, -2.5, 0),
),
Edge(
id=2,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[1],
position=(0, 0, 2.5),
),
Edge(
id=5,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[2],
position=(0, 0, -2.5),
),
Edge(
id=3,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[2],
position=(-2.5, 0, 0),
),
)