"""
Porphyrin
=========
"""
from stk._internal.topology_graphs.edge import Edge
from .metal_complex import MetalComplex
from .vertices import MetalVertex, UnaligningVertex
[docs]
class Porphyrin(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=CC2=CC3=CC=C([N]3)C=C4C=CC'
'(=N4)C=C5C=CC(=N5)C=C1[N]2'
),
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7]~[#6]',
bonders=(1, ),
deleters=(),
),
],
)
complex = stk.ConstructedMolecule(
topology_graph=stk.metal_complex.Porphyrin(
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 four functional groups are
required for this topology.
Ligand building blocks with at least four functional group 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, )
See :class:`.MetalComplex` for more details and examples.
"""
_metal_vertex_prototypes = (MetalVertex(0, (0, 0, 0)),)
_ligand_vertex_prototypes = (UnaligningVertex(1, (0, 0, 0)),)
_edge_prototypes = (
Edge(
id=0,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[0],
position=(0.1, 0, 0),
),
Edge(
id=1,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[0],
position=(0, 0.1, 0),
),
Edge(
id=2,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[0],
position=(-0.1, 0, 0),
),
Edge(
id=3,
vertex1=_metal_vertex_prototypes[0],
vertex2=_ligand_vertex_prototypes[0],
position=(0, -0.1, 0),
),
)