"""
Six Plus Eight
==============
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import NonLinearVertex
[docs]
class SixPlusEight(Cage):
"""
Represents a cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='Brc1c(Br)cc(Br)c(Br)c1',
functional_groups=[stk.BromoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='Brc1cc(Br)cc(Br)c1',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.SixPlusEight((bb1, bb2)),
)
moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
cage.get_atoms(),
cage.get_position_matrix(),
)
),
bonds=(
molecule.Bond(
atom1_id=bond.get_atom1().get_id(),
atom2_id=bond.get_atom2().get_id(),
order=bond.get_order(),
) for bond in cage.get_bonds()
),
)
:class:`.MCHammer` optimized consturction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='Brc1c(Br)cc(Br)c(Br)c1',
functional_groups=[stk.BromoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='Brc1cc(Br)cc(Br)c1',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.SixPlusEight(
building_blocks=(bb1, bb2),
optimizer=stk.MCHammer(),
),
)
moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
cage.get_atoms(),
cage.get_position_matrix(),
)
),
bonds=(
molecule.Bond(
atom1_id=bond.get_atom1().get_id(),
atom2_id=bond.get_atom2().get_id(),
order=bond.get_order(),
) for bond in cage.get_bonds()
),
)
Building blocks with three and four functional groups are required
for this topology graph.
When using a :class:`dict` for the `building_blocks` parameter,
as in :ref:`cage-topology-graph-examples`:
*Multi-Building Block Cage Construction*, a
:class:`.BuildingBlock`, with the following number of functional
groups, needs to be assigned to each of the following vertex ids:
| 4-functional groups: 0 to 5
| 3-functional groups: 6 to 13
See :class:`.Cage` for more details and examples.
"""
_x = 1
_non_linears = (
NonLinearVertex(0, np.array([-_x, _x, 0])),
NonLinearVertex(1, np.array([-_x, -_x, 0])),
NonLinearVertex(2, np.array([_x, _x, 0])),
NonLinearVertex(3, np.array([_x, -_x, 0])),
NonLinearVertex(4, np.array([0, 0, _x])),
NonLinearVertex(5, np.array([0, 0, -_x])),
)
_vertex_prototypes = (
*_non_linears,
NonLinearVertex.init_at_center(
id=6,
vertices=(
_non_linears[0],
_non_linears[4],
_non_linears[1],
),
),
NonLinearVertex.init_at_center(
id=7,
vertices=(
_non_linears[1],
_non_linears[4],
_non_linears[3],
),
),
NonLinearVertex.init_at_center(
id=8,
vertices=(
_non_linears[4],
_non_linears[3],
_non_linears[2],
),
),
NonLinearVertex.init_at_center(
id=9,
vertices=(
_non_linears[4],
_non_linears[2],
_non_linears[0],
),
),
NonLinearVertex.init_at_center(
id=10,
vertices=(
_non_linears[0],
_non_linears[5],
_non_linears[1],
),
),
NonLinearVertex.init_at_center(
id=11,
vertices=(
_non_linears[5],
_non_linears[1],
_non_linears[3],
),
),
NonLinearVertex.init_at_center(
id=12,
vertices=(
_non_linears[3],
_non_linears[5],
_non_linears[2],
),
),
NonLinearVertex.init_at_center(
id=13,
vertices=(
_non_linears[2],
_non_linears[5],
_non_linears[0],
),
),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[6], _vertex_prototypes[0]),
Edge(1, _vertex_prototypes[6], _vertex_prototypes[4]),
Edge(2, _vertex_prototypes[6], _vertex_prototypes[1]),
Edge(3, _vertex_prototypes[7], _vertex_prototypes[1]),
Edge(4, _vertex_prototypes[7], _vertex_prototypes[4]),
Edge(5, _vertex_prototypes[7], _vertex_prototypes[3]),
Edge(6, _vertex_prototypes[8], _vertex_prototypes[4]),
Edge(7, _vertex_prototypes[8], _vertex_prototypes[3]),
Edge(8, _vertex_prototypes[8], _vertex_prototypes[2]),
Edge(9, _vertex_prototypes[9], _vertex_prototypes[4]),
Edge(10, _vertex_prototypes[9], _vertex_prototypes[2]),
Edge(11, _vertex_prototypes[9], _vertex_prototypes[0]),
Edge(12, _vertex_prototypes[10], _vertex_prototypes[0]),
Edge(13, _vertex_prototypes[10], _vertex_prototypes[5]),
Edge(14, _vertex_prototypes[10], _vertex_prototypes[1]),
Edge(15, _vertex_prototypes[11], _vertex_prototypes[5]),
Edge(16, _vertex_prototypes[11], _vertex_prototypes[1]),
Edge(17, _vertex_prototypes[11], _vertex_prototypes[3]),
Edge(18, _vertex_prototypes[12], _vertex_prototypes[3]),
Edge(19, _vertex_prototypes[12], _vertex_prototypes[5]),
Edge(20, _vertex_prototypes[12], _vertex_prototypes[2]),
Edge(21, _vertex_prototypes[13], _vertex_prototypes[2]),
Edge(22, _vertex_prototypes[13], _vertex_prototypes[5]),
Edge(23, _vertex_prototypes[13], _vertex_prototypes[0]),
)
_num_windows = 12
_num_window_types = 1