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 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 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))
atom4=stk.C(6),
bonders=(stk.C(1), ),
deleters=(stk.C(5), stk.C(6)),
),
stk.Alkyne(
carbon1=stk.C(0),
atom1=stk.C(1),
carbon2=stk.C(2),
atom2=stk.H(3),
bonders=(stk.C(0), ),
deleters=(stk.C(2), stk.H(3)),
),
stk.Amide(
carbon=stk.C(0),
oxygen=stk.O(1),
nitrogen=stk.N(2),
hydrogen1=stk.H(3),
hydrogen2=stk.H(4),
atom=stk.C(5),
bonders=(stk.C(0), ),
deleters=(stk.N(2), stk.H(3), stk.H(4)),
),
stk.BoronicAcid(
boron=stk.B(0),
oxygen1=stk.O(1),
hydrogen1=stk.H(2),
oxygen2=stk.O(3),
hydrogen2=stk.H(4),
atom=stk.C(5),
bonders=(stk.B(0), ),
deleters=(stk.O(1), stk.H(2), stk.O(3), stk.H(4)),
import pytest
import stk
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)),
),
),
),
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
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()
@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(
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
def single_atom(get_atom_ids):
a, = get_atom_ids(1)
return _single_atom(stk.N(a))
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
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`.
"""
@pytest.fixture(
params=(
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), ),
),
def primary_amino(get_atom_ids):
a, b, c, d = get_atom_ids(4)
return _primary_amino(stk.N(a), stk.H(b), stk.H(c), stk.C(d))
def get_case_data_2() -> CaseData:
bb1 = stk.BuildingBlock('[C+2][N+]Br', [stk.BromoFactory()])
canonical_bb1 = bb1.with_canonical_atom_ordering()
bb2 = stk.BuildingBlock('IS[O+]', [stk.IodoFactory()])
canonical_bb2 = bb2.with_canonical_atom_ordering()
return CaseData(
molecule=stk.ConstructedMolecule(
topology_graph=stk.polymer.Linear(
building_blocks=(bb1, bb2),
repeating_unit='AB',
num_repeating_units=1,
),
),
result=stk.ConstructedMolecule.init(
atoms=(
stk.C(0, 2),
stk.O(1, 1),
stk.N(2, 1),
stk.S(3),
),
bonds=(
stk.Bond(stk.C(0, 2), stk.N(2, 1), 1),
stk.Bond(stk.O(1, 1), stk.S(3), 1),
stk.Bond(stk.N(2, 1), stk.S(3), 1),
),
position_matrix=np.array([]),
atom_infos=(
stk.AtomInfo(
atom=stk.C(0, 2),
building_block_atom=stk.C(0, 2),
building_block=canonical_bb1,
building_block_id=0,
),
stk.AtomInfo(
atom=stk.O(1, 1),
building_block_atom=stk.O(0, 1),
building_block=canonical_bb2,
building_block_id=1,
),
stk.AtomInfo(
atom=stk.N(2, 1),
building_block_atom=stk.N(2, 1),
building_block=canonical_bb1,
building_block_id=0,
),
stk.AtomInfo(
atom=stk.S(3),
building_block_atom=stk.S(2),
building_block=canonical_bb2,
building_block_id=1,
),
),
bond_infos=(
stk.BondInfo(
bond=stk.Bond(stk.C(0, 2), stk.N(2, 1), 1),
building_block=canonical_bb1,
building_block_id=0,
),
stk.BondInfo(
bond=stk.Bond(stk.O(1, 1), stk.S(3), 1),
building_block=canonical_bb2,
building_block_id=1,
),
stk.BondInfo(
bond=stk.Bond(stk.N(2, 1), stk.S(3), 1),
building_block=None,
building_block_id=None,
),
),
num_building_blocks={
canonical_bb1: 1,
canonical_bb2: 1,
},
),
)
