Source code for stk.molecular.topology_graphs.metal_complex.octahedral.octahedral_delta

"""
Octahedral Delta
================

"""

from ...topology_graph 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), ), )