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Update generic structures for topology graphs using single atom representations. #495

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Update generic structures for topology graphs using single atom representations. #495

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f8c67ac
WIP: Setup topology structures for three examples.
andrewtarzia Jun 26, 2023
70112eb
WIP: try to fix unicode.
andrewtarzia Jun 26, 2023
4211963
Run Black.
andrewtarzia Jun 29, 2023
9685b9e
Test colours.
andrewtarzia Jul 7, 2023
f6c15c2
Test colours.
andrewtarzia Jul 7, 2023
1514f64
Test colours.
andrewtarzia Jul 7, 2023
b026170
Revert some.
andrewtarzia Jul 7, 2023
eca2826
Fix.
andrewtarzia Jul 7, 2023
686c3b6
Fix.
andrewtarzia Jul 7, 2023
26c70f3
Fix.
andrewtarzia Jul 7, 2023
64825db
Fix.
andrewtarzia Jul 7, 2023
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80 changes: 27 additions & 53 deletions src/stk/_internal/topology_graphs/cage/four_plus_six.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,64 +16,36 @@ class FourPlusSix(Cage):
"""
Represents a cage topology graph.

Unoptimized construction
Vertex connectivities:

.. 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.FourPlusSix((bb1, bb2)),
three_c_bb = stk.BuildingBlock(
smiles="[Br][C]([Br])[Br]",
position_matrix=[
[-2, 0, -1],
[0, 0, 1],
[0, -2, -1],
[2, 0, 1],
],
functional_groups=(stk.BromoFactory(placers=(0, 1)),),
)

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()
),
two_c_bb = stk.BuildingBlock(
smiles="[Br][N][Br]",
position_matrix=[
[-2, 0, -1],
[0, 0, 1],
[0, -2, -1],
],
functional_groups=(stk.BromoFactory(placers=(0, 1)),),
)

: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.FourPlusSix(
building_blocks=(bb1, bb2),
optimizer=stk.MCHammer(),
),
topology_graph=stk.cage.FourPlusSix((three_c_bb, two_c_bb)),
)

moldoc_display_molecule = molecule.Molecule(
Expand All @@ -95,20 +67,22 @@ class FourPlusSix(Cage):
),
)

Nonlinear building blocks with three functional groups are
required for this topology.
Nonlinear building blocks (COLOUR1) with three functional groups
are required for this topology.

Linear building blocks (COLOUR2) with two functional groups
are required for this topology.

Linear building blocks with two functional groups are required for
this topology.
:class:`.MCHammer` optimization is recommended for construction.

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 3
| 2-functional groups: 4 to 9
| 3-functional groups (COLOUR1): 0 to 3
| 2-functional groups (COLOUR2): 4 to 9

See :class:`.Cage` for more details and examples.

Expand Down
73 changes: 47 additions & 26 deletions src/stk/_internal/topology_graphs/cage/m24l48.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,43 +19,62 @@ class M24L48(Cage):
import moldoc.molecule as molecule
import stk

bb1 = stk.BuildingBlock(
smiles='[Pd+2]',
functional_groups=(
stk.SingleAtom(stk.Pd(0, charge=2))
for i in range(4)
),
position_matrix=[[0, 0, 0]],
four_c_bb = stk.BuildingBlock(
smiles="[Br][C]([Br])([Br])[Br]",
position_matrix=[
[-2, 0, -1],
[0, 0, 1],
[0, -2, -1],
[2, 0, 1],
[0, 2, 1],
],
functional_groups=(stk.BromoFactory(placers=(0, 1)),),
)

bb2 = stk.BuildingBlock(
smiles=(
'C1=NC=CC(C2=CC=CC(C3=C'
'C=NC=C3)=C2)=C1'
),
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
two_c_bb = stk.BuildingBlock(
smiles="[Br][N][Br]",
position_matrix=[
[-2, 0, -1],
[0, 0, 1],
[0, -2, -1],
],
functional_groups=(stk.BromoFactory(placers=(0, 1)),),
)

cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M24L48(
building_blocks=(bb1, bb2),
building_blocks=(four_c_bb, two_c_bb),
),
)
rgb1 = [192, 87, 161]
rgb2 = [97, 201, 217]
points = cage.get_num_atoms()
colour_list = [
[
int(rgb1[0] + ((rgb2[0]-rgb1[0])/points)*i),
int(rgb1[1] + ((rgb2[1]-rgb1[1])/points)*i),
int(rgb1[2] + ((rgb2[2]-rgb1[2])/points)*i),
]
for i in range(points)
]

moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
config=molecule.AtomConfig(
color=molecule.Color(
red=col[0],
green=col[1],
blue=col[2],
),
size=2.0,
)
) for atom, position, col in zip(
cage.get_atoms(),
cage.get_position_matrix(),
colour_list,
)
),
bonds=(
Expand All @@ -71,20 +90,22 @@ class M24L48(Cage):
),
)

Metal building blocks with four functional groups are
required for this topology.
Metal building blocks (COLOUR1) with four functional groups
are required for this topology.

Ligand building blocks (COLOUR2) with two functional groups
are required for this topology.

Ligand building blocks with two functional groups are required for
this topology.
:class:`.MCHammer` optimization is recommended for construction.

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 23
| 2-functional groups: 24 to 71
| 4-functional groups (\u25FC, COLOUR1): 0 to 23
| 2-functional groups (u'\u25FC', COLOUR2): 24 to 71

See :class:`.Cage` for more details and examples.

Expand Down
74 changes: 47 additions & 27 deletions src/stk/_internal/topology_graphs/cage/m2l4_lantern.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,44 +80,62 @@ class M2L4Lantern(Cage):
import moldoc.molecule as molecule
import stk

bb1 = stk.BuildingBlock(
smiles='[Pd+2]',
functional_groups=(
stk.SingleAtom(stk.Pd(0, charge=2))
for i in range(4)
),
position_matrix=[[0, 0, 0]],
four_c_bb = stk.BuildingBlock(
smiles="[Br][C]([Br])([Br])[Br]",
position_matrix=[
[-2, 0, -1],
[0, 0, 1],
[0, -2, -1],
[2, 0, 1],
[0, 2, 1],
],
functional_groups=(stk.BromoFactory(placers=(0, 1)),),
)

bb2 = stk.BuildingBlock(
smiles=(
'C1=NC=CC(C2=CC=CC(C3=C'
'C=NC=C3)=C2)=C1'
),
functional_groups=[
stk.SmartsFunctionalGroupFactory(
smarts='[#6]~[#7X2]~[#6]',
bonders=(1, ),
deleters=(),
),
two_c_bb = stk.BuildingBlock(
smiles="[Br][N][Br]",
position_matrix=[
[-2, 0, -1],
[0, 0, 1],
[0, -2, -1],
],
functional_groups=(stk.BromoFactory(placers=(0, 1)),),
)

cage = stk.ConstructedMolecule(
topology_graph=stk.cage.M2L4Lantern(
building_blocks=(bb1, bb2),
optimizer=stk.MCHammer(),
building_blocks=(four_c_bb, two_c_bb),
),
)
rgb1 = [192, 87, 161]
rgb2 = [97, 201, 217]
points = cage.get_num_atoms()
colour_list = [
[
int(rgb1[0] + ((rgb2[0]-rgb1[0])/points)*i),
int(rgb1[1] + ((rgb2[1]-rgb1[1])/points)*i),
int(rgb1[2] + ((rgb2[2]-rgb1[2])/points)*i),
]
for i in range(points)
]

moldoc_display_molecule = molecule.Molecule(
atoms=(
molecule.Atom(
atomic_number=atom.get_atomic_number(),
position=position,
) for atom, position in zip(
config=molecule.AtomConfig(
color=molecule.Color(
red=col[0],
green=col[1],
blue=col[2],
),
size=2.0,
)
) for atom, position, col in zip(
cage.get_atoms(),
cage.get_position_matrix(),
colour_list,
)
),
bonds=(
Expand All @@ -133,20 +151,22 @@ class M2L4Lantern(Cage):
),
)

Metal building blocks with four functional groups are
required for this topology.
Metal building blocks (COLOUR1) with four functional groups
are required for this topology.

Ligand building blocks (COLOUR2) with two functional groups
are required for this topology.

Ligand building blocks with two functional groups are required for
this topology.
:class:`.MCHammer` optimization is recommended for construction.

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 1
| 2-functional groups: 2 to 5
| 4-functional groups (COLOUR1): 0 to 1
| 2-functional groups (COLOUR2): 2 to 5

See :class:`.Cage` for more details and examples.

Expand Down