hydrogen1=stk.H(14),
hydrogen2=stk.H(15),
atom=stk.C(4),
bonders=(stk.C(5), ),
deleters=(stk.N(7), stk.H(14), stk.H(15)),
),
),
),
lambda: CaseData(
factory=stk.ThioacidFactory(),
molecule=stk.BuildingBlock('O=C(S)CC(S)=O'),
functional_groups=(
stk.Thioacid(
carbon=stk.C(1),
oxygen=stk.O(0),
sulfur=stk.S(2),
hydrogen=stk.H(7),
atom=stk.C(3),
bonders=(stk.C(1), ),
deleters=(stk.S(2), stk.H(7)),
),
stk.Thioacid(
carbon=stk.C(4),
oxygen=stk.O(6),
sulfur=stk.S(5),
hydrogen=stk.H(10),
atom=stk.C(3),
bonders=(stk.C(4), ),
deleters=(stk.S(5), stk.H(10)),
),
),
atom=stk.C(4),
bonders=(stk.C(4), ),
deleters=(stk.N(0), stk.H(2), stk.H(3)),
),
stk.SecondaryAmino(
nitrogen=stk.N(12),
hydrogen=stk.H(21),
atom1=stk.C(0),
atom2=stk.C(12),
bonders=(stk.N(12), ),
deleters=(stk.H(21), ),
),
stk.Thioacid(
carbon=stk.C(0),
oxygen=stk.O(12),
sulfur=stk.S(21),
hydrogen=stk.H(2),
atom=stk.C(1),
bonders=(stk.C(0), ),
deleters=(stk.S(21), stk.H(2)),
),
stk.Thiol(
sulfur=stk.S(12),
hydrogen=stk.H(21),
atom=stk.C(32),
bonders=(stk.C(32), ),
deleters=(stk.S(12), stk.H(21)),
),
stk.SingleAtom(atom=stk.Fe(0)),
), )
def functional_group1(request):
hydrogen2=stk.H(2),
atom=stk.C(3),
bonders=(stk.C(3), ),
deleters=(stk.N(0), stk.H(1), stk.H(2)),),
lambda: stk.SecondaryAmino(
nitrogen=stk.N(0),
hydrogen=stk.H(1),
atom1=stk.C(2),
atom2=stk.C(3),
bonders=(stk.N(0), ),
deleters=(stk.H(1), ),
),
lambda: stk.Thioacid(
carbon=stk.C(0),
oxygen=stk.O(1),
sulfur=stk.S(2),
hydrogen=stk.H(3),
atom=stk.C(4),
bonders=(stk.C(0), ),
deleters=(stk.S(2), stk.H(3)),
),
lambda: stk.Thiol(
sulfur=stk.S(0),
hydrogen=stk.H(1),
atom=stk.C(2),
bonders=(stk.C(2), ),
deleters=(stk.S(0), stk.H(1)),
),
lambda: stk.SingleAtom(atom=stk.Fe(0)),
),
)
def thiol(get_atom_ids):
a, b, c = get_atom_ids(3)
return _thiol(stk.S(a), stk.H(b), stk.C(c))
)
),
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,
),
stk.AtomInfo(
)
),
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,
),
stk.AtomInfo(
atom=stk.O(1, 1),
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,
},
),
)
import pytest
import stk
@pytest.fixture(
params=[
lambda bond: {},
lambda bond: {
bond.get_atom1().get_id(): stk.Be(33)
},
lambda bond: {
bond.get_atom2().get_id(): stk.Bi(122)
},
lambda bond: {
bond.get_atom1().get_id(): stk.K(4),
bond.get_atom2().get_id(): stk.S(7),
},
], )
def get_atom_map(request):
"""
Return a valid `atom_map` parameter for a bond.
Parameters
----------
bond : :class:`.Bond`
The bond, for which the `atom_map` parameter needs to be
created.
Returns
-------
:class:`dict`