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 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 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),
)
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),
nitrogen=stk.N(4),
hydrogen=stk.H(15),
atom1=stk.C(3),
atom2=stk.C(5),
bonders=(stk.N(4), ),
deleters=(stk.H(15), ),
),
),
),
lambda: CaseData(
factory=stk.AldehydeFactory(),
molecule=stk.BuildingBlock('O=CCC=O'),
functional_groups=(
stk.Aldehyde(
carbon=stk.C(1),
oxygen=stk.O(0),
hydrogen=stk.H(5),
atom=stk.C(2),
bonders=(stk.C(1), ),
deleters=(stk.O(0), ),
),
stk.Aldehyde(
carbon=stk.C(3),
oxygen=stk.O(4),
hydrogen=stk.H(8),
atom=stk.C(2),
bonders=(stk.C(3), ),
deleters=(stk.O(4), ),
),
),
),
import pytest
from pytest_lazyfixture import lazy_fixture
import stk
# Fixtures must be visible for lazy_fixture() calls.
from .fixtures import * # noqa
@pytest.fixture(
scope='session',
params=(
lambda: stk.Alcohol(
oxygen=stk.O(0),
hydrogen=stk.H(1),
atom=stk.C(2),
bonders=(stk.C(2), ),
deleters=(stk.O(0), stk.H(1)),
),
lambda: 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),),
),
lambda: stk.Alkene(
carbon1=stk.C(0),
atom1=stk.H(1),
atom2=stk.H(2),
carbon2=stk.C(3),
),
placer_ids=(1, ),
)
),
lambda: 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,
def alcohol(get_atom_ids):
a, b, c = get_atom_ids(3)
return _alcohol(stk.O(a), stk.H(b), stk.C(c))
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))
),
placer_ids=(1, ),
)
),
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=bb1,
building_block_id=0,
),
def thioacid(get_atom_ids):
a, b, c, d, e = get_atom_ids(5)
return _thioacid(stk.C(a), stk.O(b), stk.S(c), stk.H(d), stk.C(e))
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,
},
),
)
