def get_case_data_1() -> CaseData:
return CaseData(
molecule=stk.BuildingBlock(
smiles='Br[C+2][N+]Cl',
functional_groups=[stk.BromoFactory()],
placer_ids=(0, ),
),
result=stk.BuildingBlock.init(
atoms=(
stk.Cl(0),
stk.Br(1),
stk.C(2, 2),
stk.N(3, 1),
),
bonds=(
stk.Bond(stk.Cl(0), stk.N(3, 1), 1),
stk.Bond(stk.Br(1), stk.C(2, 2), 1),
stk.Bond(stk.C(2, 2), stk.N(3, 1), 1),
),
position_matrix=np.array([
]),
functional_groups=(
stk.Bromo(
bromine=stk.Br(1),
atom=stk.C(2, 2),
bonders=(stk.C(2, 2), ),
deleters=(stk.Br(1), ),
),
),
placer_ids=(1, ),
)
)
def carboxylic_acid(get_atom_ids):
a, b, c, d, e = get_atom_ids(5)
return _carboxylic_acid(
carbon=stk.C(a),
oxygen1=stk.O(b),
oxygen2=stk.O(c),
hydrogen=stk.H(d),
atom=stk.C(e),
)
def diol(get_atom_ids):
a, b, c, d, e, f = get_atom_ids(6)
return _diol(
atom1=stk.C(a),
oxygen1=stk.O(b),
hydrogen1=stk.H(c),
atom2=stk.C(d),
oxygen2=stk.O(e),
hydrogen2=stk.H(f),
)
def amide(get_atom_ids):
a, b, c, d, e, f = get_atom_ids(6)
return _amide(
carbon=stk.C(a),
oxygen=stk.O(b),
nitrogen=stk.N(c),
hydrogen1=stk.H(d),
hydrogen2=stk.H(e),
atom=stk.C(f),
)
def ring_amine(get_atom_ids):
a, b, c, d, e, f, g = get_atom_ids(7)
return _ring_amine(
nitrogen=stk.N(a),
hydrogen1=stk.H(b),
hydrogen2=stk.H(c),
carbon1=stk.C(d),
carbon2=stk.C(e),
hydrogen3=stk.H(f),
carbon3=stk.C(g),
)
def make_xor_monomer(self, position=0):
# initialize building blocks
benzene = self.init_building_block(smiles='C1=CC=CC=C1')
acetaldehyde = self.init_building_block(smiles='CC=O')
benzene = benzene.with_functional_groups([stk.SingleAtom(stk.C(position))])
acetaldehyde = acetaldehyde.with_functional_groups(
[stk.SingleAtom(stk.C(1))])
# construct xor gate monomer
xor_gate = stk.ConstructedMolecule(
topology_graph=stk.polymer.Linear(
building_blocks=(benzene, acetaldehyde),
repeating_unit='AB',
num_repeating_units=1
)
)
# construct functional groups for xor gate monomer
# numbering starts at top and proceeds clockwise
c_0, c_1, c_2, c_3, c_4, c_5 = stk.C(0), stk.C(
1), stk.C(2), stk.C(3), stk.C(4), stk.C(5)
functional_groups = [stk.GenericFunctionalGroup(atoms=(c_0, c_1, c_2, c_3, c_4, c_5),
bonders=(c_0, c_3), deleters=(c_4, c_5)),
stk.GenericFunctionalGroup(atoms=(c_0, c_1, c_2, c_3, c_4, c_5),
bonders=(c_1, c_2), deleters=())]
return stk.BuildingBlock.init_from_molecule(xor_gate, functional_groups=functional_groups)
def boronic_acid(get_atom_ids):
a, b, c, d, e, f = get_atom_ids(6)
return _boronic_acid(
boron=stk.B(a),
oxygen1=stk.O(b),
hydrogen1=stk.H(c),
oxygen2=stk.O(d),
hydrogen2=stk.H(e),
atom=stk.C(f),
)
def test_torsion_matching():
"""
Confirm torsions are appropriately mapped.
Check corresponding torsion angles between building blocks and
constructed molecules to confirm that the angle is the same in
both.
"""
bb1 = stk.BuildingBlock('NCCNCCN', [stk.PrimaryAminoFactory()])
bb2 = stk.BuildingBlock('O=CCCC=O', [stk.AldehydeFactory()])
assert _polymer_angles_match(bb1, bb2)
# Test case designed such that default rdkit torsion for
# constructed molecule spans over both building blocks, requiring
# stko to correctly clean this up.
bonders3 = (stk.C(1), )
deleters3 = (stk.H(7), )
functional_group3 = stk.GenericFunctionalGroup(atoms=bonders3 + deleters3,
bonders=bonders3,
deleters=deleters3)
bb3 = stk.BuildingBlock('CCCC', [functional_group3])
bonders4 = (stk.C(0), )
deleters4 = (stk.H(1), )
functional_group4 = stk.GenericFunctionalGroup(atoms=bonders4 + deleters4,
bonders=bonders4,
deleters=deleters4)
bb4 = stk.BuildingBlock('C', [functional_group4])
assert _polymer_angles_match(bb3, bb4)
# Test case for an exterior atom of a building block torsion being
# deleted in construction.
bonders5 = (stk.C(1), )
deleters5 = (stk.C(0), stk.H(4), stk.H(5), stk.H(6))
functional_group5 = stk.GenericFunctionalGroup(atoms=bonders5 + deleters5,
bonders=bonders5,
deleters=deleters5)
bb5 = stk.BuildingBlock('CCCC', [functional_group5])
bb6 = bb4
assert not _polymer_angles_match(bb5, bb6)
def alkene(get_atom_ids):
a, b, c, d, e, f = get_atom_ids(6)
return _alkene(
carbon1=stk.C(a),
atom1=stk.C(b),
atom2=stk.C(c),
carbon2=stk.C(d),
atom3=stk.C(e),
atom4=stk.C(f),
)
def thiol(get_atom_ids):
a, b, c = get_atom_ids(3)
return _thiol(stk.S(a), stk.H(b), stk.C(c))
import pytest
import stk
from .case_data import CaseData
@pytest.fixture(
params=(CaseData(
molecule=stk.BuildingBlock('NCCN'),
bonds=(
stk.Bond(stk.N(0), stk.C(1), 1),
stk.Bond(stk.C(1), stk.C(2), 1),
stk.Bond(stk.C(2), stk.N(3), 1),
stk.Bond(stk.N(0), stk.H(4), 1),
stk.Bond(stk.N(0), stk.H(5), 1),
stk.Bond(stk.C(1), stk.H(6), 1),
stk.Bond(stk.C(1), stk.H(7), 1),
stk.Bond(stk.C(2), stk.H(8), 1),
stk.Bond(stk.C(2), stk.H(9), 1),
stk.Bond(stk.N(3), stk.H(10), 1),
stk.Bond(stk.N(3), stk.H(11), 1),
),
), ), )
def case_data(request):
return request.param
canonical_bb2 = bb2.with_canonical_atom_ordering()
@pytest.fixture(
params=(
lambda: CaseData(
molecule=stk.BuildingBlock(
smiles='Br[C+2][N+]Cl',
functional_groups=[stk.BromoFactory()],
placer_ids=(0, ),
),
result=stk.BuildingBlock.init(
atoms=(
stk.Cl(0),
stk.Br(1),
stk.C(2, 2),
stk.N(3, 1),
),
bonds=(
stk.Bond(stk.Cl(0), stk.N(3, 1), 1),
stk.Bond(stk.Br(1), stk.C(2, 2), 1),
stk.Bond(stk.C(2, 2), stk.N(3, 1), 1),
),
position_matrix=np.array([
]),
functional_groups=(
stk.Bromo(
bromine=stk.Br(1),
atom=stk.C(2, 2),
bonders=(stk.C(2, 2), ),
deleters=(stk.Br(1), ),
import pytest
import stk
from ..case_data import CaseData
@pytest.fixture(
scope='session',
params=(lambda: CaseData(
factory=stk.RingAmineFactory(),
molecule=stk.BuildingBlock('NCC(Br)c1c(Br)cccc1'),
functional_groups=(stk.RingAmine(
nitrogen=stk.N(0),
carbon1=stk.C(1),
carbon2=stk.C(2),
carbon3=stk.C(4),
hydrogen1=stk.H(11),
hydrogen2=stk.H(12),
hydrogen3=stk.H(15),
), ),
), ),
)
def case_data(request) -> CaseData:
"""
A :class:`.CaseData` instance.
"""
return request.param()
import pytest
import stk
from .case_data import CaseData
@pytest.fixture(params=[stk.C(0), stk.H(1), stk.K(12)])
def atom(request):
"""
An :class:`.Atom` instance.
"""
return request.param.clone()
@pytest.fixture
def atom1(atom):
"""
An :class:`.Atom` instance.
"""
return atom.clone()
@pytest.fixture
def atom2(atom):
"""
An :class:`.Atom` instance.
import re
import os
from pytest_lazyfixture import lazy_fixture
import stk
import numpy as np
from rdkit.Chem import AllChem as rdkit
from .case_data import CaseData
# Fixtures need to be visible for lazy_fixture() calls.
from .fixtures import * # noqa
@pytest.fixture(
params=[
stk.BuildingBlock.init(
atoms=(stk.C(0, 4), ),
bonds=(),
position_matrix=np.array([[0.0, 0.0, 0.0]]),
functional_groups=(),
),
stk.BuildingBlock.init(
atoms=(stk.C(0, 3), stk.H(1)),
bonds=(stk.Bond(stk.C(0, 3), stk.H(1), 1), ),
position_matrix=np.array([
[0.39382080513175644, 0.0, 0.0],
[-0.39382080513175644, 0.0, 0.0],
]),
functional_groups=(),
),
stk.BuildingBlock.init(
atoms=(stk.C(0, 2), stk.H(1), stk.H(2)),
import pytest
import stk
from .case_data import CaseData
@pytest.fixture(
params=(
stk.Bond(stk.C(0), stk.N(1), 1),
),
)
def bond(request):
"""
A :class:`.Bond` instance.
"""
return request.param
@pytest.fixture(
params=(
stk.BuildingBlock('NCCN'),
None,
),
)
def building_block(request):
"""
A valid building block for a :class:`.BondInfo`.
"""
def alcohol(get_atom_ids):
a, b, c = get_atom_ids(3)
return _alcohol(stk.O(a), stk.H(b), stk.C(c))
import pytest
from pytest_lazyfixture import lazy_fixture
import stk
# Fixtures need to visible for lazy_fixture() calls.
from .fixtures import * # noqa
@pytest.fixture(
params=(
stk.Alcohol(
oxygen=stk.O(1),
hydrogen=stk.H(2),
atom=stk.C(2),
bonders=(stk.C(2), ),
deleters=(stk.O(1), stk.H(2)),
),
stk.Aldehyde(
carbon=stk.C(0),
oxygen=stk.O(1),
hydrogen=stk.H(2),
atom=stk.C(3),
bonders=(stk.C(0), ),
deleters=(stk.O(1), ),
),
stk.Alkene(
carbon1=stk.C(1),
atom1=stk.C(2),
atom2=stk.C(3),
carbon2=stk.C(4),
atom3=stk.C(5),
import pytest
import stk
from .case_data import CaseData
@pytest.fixture(
params=(stk.Bond(stk.C(0), stk.N(1), 1), ), )
def bond(request):
"""
A :class:`.Bond` instance.
"""
return request.param
@pytest.fixture(
params=(
stk.BuildingBlock('NCCN'),
None,
), )
def building_block(request):
"""
A valid building block for a :class:`.BondInfo`.
"""
return request.param
from ..case_data import CaseData
@pytest.fixture(
scope='session',
params=(
lambda: CaseData(
factory=stk.PrimaryAminoFactory(),
molecule=stk.BuildingBlock('NCCN'),
functional_groups=(
stk.PrimaryAmino(
nitrogen=stk.N(0),
hydrogen1=stk.H(4),
hydrogen2=stk.H(5),
atom=stk.C(1),
bonders=(stk.N(0), ),
deleters=(stk.H(4), stk.H(5)),
),
stk.PrimaryAmino(
nitrogen=stk.N(3),
hydrogen1=stk.H(10),
hydrogen2=stk.H(11),
atom=stk.C(2),
bonders=(stk.N(3), ),
deleters=(stk.H(10), stk.H(11)),
),
),
),
lambda: CaseData(
factory=stk.PrimaryAminoFactory(),
def bromo(get_atom_ids):
a, b = get_atom_ids(2)
return _bromo(stk.Br(a), stk.C(b))
def fluoro(get_atom_ids):
a, b = get_atom_ids(2)
return _fluoro(stk.F(a), stk.C(b))
import pytest
import stk
from .case_data import CaseData
@pytest.fixture(
params=(CaseData(
molecule=stk.BuildingBlock('NCCN'),
atoms=(
stk.N(0),
stk.C(1),
stk.C(2),
stk.N(3),
stk.H(4),
stk.H(5),
stk.H(6),
stk.H(7),
stk.H(8),
stk.H(9),
stk.H(10),
stk.H(11),
),
), ), )
def case_data(request):
"""
A :class:`.CaseData` instance.
"""
return request.param
def alkyne(get_atom_ids):
a, b, c, d = get_atom_ids(4)
return _alkyne(stk.C(a), stk.C(b), stk.C(c), stk.C(d))
def difluoro(get_atom_ids):
a, b, c, d = get_atom_ids(4)
return _difluoro(stk.F(a), stk.C(b), stk.F(c), stk.C(d))
def aldehyde(get_atom_ids):
a, b, c, d = get_atom_ids(4)
return _aldehyde(stk.C(a), stk.O(b), stk.H(c), stk.C(d))
def dibromo(get_atom_ids):
a, b, c, d = get_atom_ids(4)
return _dibromo(stk.Br(a), stk.C(b), stk.Br(c), stk.C(d))
lambda: CaseData(
building_block=stk.BuildingBlock.init_from_molecule(
molecule=stk.BuildingBlock('Br[C+2][C+2]Br'), ),
functional_groups=(),
core_atom_ids=(0, 1, 2, 3),
placer_ids=(0, 1, 2, 3),
),
lambda: CaseData(
building_block=stk.BuildingBlock.init_from_molecule(
molecule=stk.BuildingBlock('Br[C+2][C+2]Br'),
functional_groups=[stk.BromoFactory()],
),
functional_groups=(
stk.Bromo(
bromine=stk.Br(0),
atom=stk.C(1, 2),
bonders=(stk.C(1, 2), ),
deleters=(stk.Br(0), ),
),
stk.Bromo(
bromine=stk.Br(3),
atom=stk.C(2, 2),
bonders=(stk.C(2, 2), ),
deleters=(stk.Br(3), ),
),
),
core_atom_ids=(1, 2),
placer_ids=(1, 2),
),
lambda: CaseData(
building_block=stk.BuildingBlock.init_from_molecule(
def secondary_amino(get_atom_ids):
a, b, c, d = get_atom_ids(4)
return _secondary_amino(stk.N(a), stk.H(b), stk.C(c), stk.C(d))
def carbon():
return stk.C(333, attr2=None, attr12='abc', _pattr=22.22)