stk.Bromo(
bromine=stk.Br(3),
atom=stk.C(2),
bonders=(stk.C(2), ),
deleters=(stk.Br(3), ),
),
stk.Bromo(
bromine=stk.Br(6),
atom=stk.C(5),
bonders=(stk.C(5), ),
deleters=(stk.Br(6), ),
),
),
),
lambda: CaseData(
factory=stk.IodoFactory(),
molecule=stk.BuildingBlock('ICC(I)CCI'),
functional_groups=(
stk.Iodo(
iodine=stk.I(0),
atom=stk.C(1),
bonders=(stk.C(1), ),
deleters=(stk.I(0), ),
),
stk.Iodo(
iodine=stk.I(3),
atom=stk.C(2),
bonders=(stk.C(2), ),
deleters=(stk.I(3), ),
),
stk.Iodo(
import numpy as np
import pytest
import stk
from .case_data import 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()
@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),
54,
55,
56,
57,
58,
59,
31,
62,
63,
),
stk.BuildingBlock(
smiles=('Br[C+]1[C+]2[N+][C+2]C2(Br)[C+](I)[C+'
'](I)[C+](Br)[C+]1Br'),
functional_groups=[
stk.BromoFactory(),
stk.IodoFactory(),
stk.FluoroFactory(),
],
): (0, 1, 18, 50, 51),
stk.BuildingBlock(
smiles=('Br[C+]1[C+]2[S][C+2]C2(Br)[C+](I)[C+]'
'(I)[C+](Br)[C+]1Br'),
functional_groups=[
stk.BromoFactory(),
stk.IodoFactory(),
stk.FluoroFactory(),
],
): (2, 16, 34, 49),
stk.BuildingBlock(
smiles=('Br[C+]1[C+]2[S][O]C2(Br)[C+](I)[C+](I'
')[C+](Br)[C+]1Br'),
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=(0, 3),
),
lambda: CaseData(
building_block=stk.BuildingBlock.init_from_molecule(
molecule=stk.BuildingBlock('Br[C+2][C+2]Br'),
functional_groups=[stk.IodoFactory()],
),
functional_groups=(),
core_atom_ids=(0, 1, 2, 3),
placer_ids=(0, 1, 2, 3),
),
),
)
def init_from_molecule(request) -> CaseData:
return request.param()
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,
},
),
)
