"""
Five Plus Ten
=============
"""
import numpy as np
from stk._internal.topology_graphs.edge import Edge
from .cage import Cage
from .vertices import LinearVertex, NonLinearVertex
[docs]
class FivePlusTen(Cage):
"""
Represents a cage topology graph.
Unoptimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='C1=CC(=CC=C1Br)Br',
functional_groups=[stk.BromoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='C1(=C(C(=C1Br)Br)Br)Br',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.FivePlusTen((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:`.Collapser` optimized construction
.. moldoc::
import moldoc.molecule as molecule
import stk
bb1 = stk.BuildingBlock(
smiles='C1=CC(=CC=C1Br)Br',
functional_groups=[stk.BromoFactory()],
)
bb2 = stk.BuildingBlock(
smiles='C1(=C(C(=C1Br)Br)Br)Br',
functional_groups=[stk.BromoFactory()],
)
cage = stk.ConstructedMolecule(
topology_graph=stk.cage.FivePlusTen(
building_blocks=(bb1, bb2),
optimizer=stk.Collapser(),
),
)
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 four 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:
| 4-functional groups: 0 to 4
| 2-functional groups: 5 to 14
See :class:`.Cage` for more details and examples.
"""
_c1 = np.cos(2 * np.pi / 5)
_c2 = np.cos(np.pi / 5)
_s1 = np.sin(2 * np.pi / 5)
_s2 = np.sin(4 * np.pi / 5)
_vertex_prototypes = (
NonLinearVertex(0, np.array([0, 1, 0]), False),
NonLinearVertex(1, np.array([_s1, _c1, 0]), False),
NonLinearVertex(2, np.array([_s2, -_c2, 0]), False),
NonLinearVertex(3, np.array([-_s2, -_c2, 0]), False),
NonLinearVertex(4, np.array([-_s1, _c1, 0]), False),
LinearVertex(5, np.array([_s1, 1 + _c1, 0.5]), False),
LinearVertex(6, np.array([_s1, 1 + _c1, -0.5]), False),
LinearVertex(7, np.array([_s1 + _s2, _c1 - _c2, 0.5]), False),
LinearVertex(8, np.array([_s1 + _s2, _c1 - _c2, -0.5]), False),
LinearVertex(9, np.array([0, -2 * _c2, 0.5]), False),
LinearVertex(10, np.array([0, -2 * _c2, -0.5]), False),
LinearVertex(11, np.array([-_s2 - _s1, -_c2 + _c1, 0.5]), False),
LinearVertex(12, np.array([-_s2 - _s1, -_c2 + _c1, -0.5]), False),
LinearVertex(13, np.array([-_s1, 1 + _c1, 0.5]), False),
LinearVertex(14, np.array([-_s1, 1 + _c1, -0.5]), False),
)
_edge_prototypes = (
Edge(0, _vertex_prototypes[5], _vertex_prototypes[0]),
Edge(1, _vertex_prototypes[5], _vertex_prototypes[1]),
Edge(2, _vertex_prototypes[6], _vertex_prototypes[0]),
Edge(3, _vertex_prototypes[6], _vertex_prototypes[1]),
Edge(4, _vertex_prototypes[7], _vertex_prototypes[1]),
Edge(5, _vertex_prototypes[7], _vertex_prototypes[2]),
Edge(6, _vertex_prototypes[8], _vertex_prototypes[1]),
Edge(7, _vertex_prototypes[8], _vertex_prototypes[2]),
Edge(8, _vertex_prototypes[9], _vertex_prototypes[2]),
Edge(9, _vertex_prototypes[9], _vertex_prototypes[3]),
Edge(10, _vertex_prototypes[10], _vertex_prototypes[2]),
Edge(11, _vertex_prototypes[10], _vertex_prototypes[3]),
Edge(12, _vertex_prototypes[11], _vertex_prototypes[3]),
Edge(13, _vertex_prototypes[11], _vertex_prototypes[4]),
Edge(14, _vertex_prototypes[12], _vertex_prototypes[3]),
Edge(15, _vertex_prototypes[12], _vertex_prototypes[4]),
Edge(16, _vertex_prototypes[13], _vertex_prototypes[4]),
Edge(17, _vertex_prototypes[13], _vertex_prototypes[0]),
Edge(18, _vertex_prototypes[14], _vertex_prototypes[4]),
Edge(19, _vertex_prototypes[14], _vertex_prototypes[0]),
)
_num_windows = 7
_num_window_types = 2