"""
Eight Plus Twelve
=================
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import LinearVertex, NonLinearVertex
[docs]
class EightPlusTwelve(Cage):
"""
Represents a cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='NC1CCCCC1N',
functional_groups=[stk.PrimaryAminoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='O=Cc1cc(C=O)cc(C=O)c1',
functional_groups=[stk.AldehydeFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.EightPlusTwelve((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 construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='NC1CCCCC1N',
functional_groups=[stk.PrimaryAminoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='O=Cc1cc(C=O)cc(C=O)c1',
functional_groups=[stk.AldehydeFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.EightPlusTwelve(
building_blocks=(bb1, bb2),
optimizer=stk.MCHammer(num_steps=1000),
),
)
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()
),
)
Nonlinear building blocks with three functional groups are
required for this topology.
Linear building blocks with two functional groups are required for
this topology.
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:
| 3-functional groups: 0 to 7
| 2-functional groups: 8 to 19
See :class:`.Cage` for more details and examples.
"""
_non_linears = (
NonLinearVertex(0, np.array([-1, 1, -1])),
NonLinearVertex(1, np.array([-1, -1, -1])),
NonLinearVertex(2, np.array([1, 1, -1])),
NonLinearVertex(3, np.array([1, -1, -1])),
NonLinearVertex(4, np.array([-1, 1, 1])),
NonLinearVertex(5, np.array([-1, -1, 1])),
NonLinearVertex(6, np.array([1, 1, 1])),
NonLinearVertex(7, np.array([1, -1, 1])),
)
_vertex_prototypes = (
*_non_linears,
LinearVertex.init_at_center(
id=8,
vertices=(_non_linears[0], _non_linears[2]),
),
LinearVertex.init_at_center(
id=9,
vertices=(_non_linears[0], _non_linears[1]),
),
LinearVertex.init_at_center(
id=10,
vertices=(_non_linears[1], _non_linears[3]),
),
LinearVertex.init_at_center(
id=11,
vertices=(_non_linears[2], _non_linears[3]),
),
LinearVertex.init_at_center(
id=12,
vertices=(_non_linears[4], _non_linears[6]),
),
LinearVertex.init_at_center(
id=13,
vertices=(_non_linears[4], _non_linears[5]),
),
LinearVertex.init_at_center(
id=14,
vertices=(_non_linears[5], _non_linears[7]),
),
LinearVertex.init_at_center(
id=15,
vertices=(_non_linears[6], _non_linears[7]),
),
LinearVertex.init_at_center(
id=16,
vertices=(_non_linears[0], _non_linears[4]),
),
LinearVertex.init_at_center(
id=17,
vertices=(_non_linears[1], _non_linears[5]),
),
LinearVertex.init_at_center(
id=18,
vertices=(_non_linears[2], _non_linears[6]),
),
LinearVertex.init_at_center(
id=19,
vertices=(_non_linears[3], _non_linears[7]),
),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[8], _vertex_prototypes[0]),
Edge(1, _vertex_prototypes[8], _vertex_prototypes[2]),
Edge(2, _vertex_prototypes[9], _vertex_prototypes[0]),
Edge(3, _vertex_prototypes[9], _vertex_prototypes[1]),
Edge(4, _vertex_prototypes[10], _vertex_prototypes[1]),
Edge(5, _vertex_prototypes[10], _vertex_prototypes[3]),
Edge(6, _vertex_prototypes[11], _vertex_prototypes[2]),
Edge(7, _vertex_prototypes[11], _vertex_prototypes[3]),
Edge(8, _vertex_prototypes[12], _vertex_prototypes[4]),
Edge(9, _vertex_prototypes[12], _vertex_prototypes[6]),
Edge(10, _vertex_prototypes[13], _vertex_prototypes[4]),
Edge(11, _vertex_prototypes[13], _vertex_prototypes[5]),
Edge(12, _vertex_prototypes[14], _vertex_prototypes[5]),
Edge(13, _vertex_prototypes[14], _vertex_prototypes[7]),
Edge(14, _vertex_prototypes[15], _vertex_prototypes[6]),
Edge(15, _vertex_prototypes[15], _vertex_prototypes[7]),
Edge(16, _vertex_prototypes[16], _vertex_prototypes[0]),
Edge(17, _vertex_prototypes[16], _vertex_prototypes[4]),
Edge(18, _vertex_prototypes[17], _vertex_prototypes[1]),
Edge(19, _vertex_prototypes[17], _vertex_prototypes[5]),
Edge(20, _vertex_prototypes[18], _vertex_prototypes[2]),
Edge(21, _vertex_prototypes[18], _vertex_prototypes[6]),
Edge(22, _vertex_prototypes[19], _vertex_prototypes[3]),
Edge(23, _vertex_prototypes[19], _vertex_prototypes[7]),
)
_num_windows = 6
_num_window_types = 1