Source code for stk.molecular.topology_graphs.metal_complex.porphyrin.porphyrin

"""
Porphyrin
=========

"""

from ...topology_graph 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), ), )