def __init__(self, atom, building_block, building_block_id):
"""
Initialize a :class:`.CaseData` instance.
Parameters
----------
atom : :class:`.Atom`
The atom, which should be held by an :class:`.AtomInfo`.
building_block : :class:`.BuildingBlock`
The building block, which should be held by an
:class:`.AtomInfo`.
building_block_id : :class:`int`
The building block id, which should be held by an
:class:`.AtomInfo`.
"""
self.atom_info = stk.AtomInfo(
atom=atom,
building_block=building_block,
building_block_id=building_block_id,
)
self.atom = atom
self.building_block = building_block
self.building_block_id = building_block_id
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(
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),
building_block=bb2,
building_block_id=1,
),
stk.AtomInfo(
atom=stk.N(2, 1),
building_block=bb1,
building_block_id=0,
),
stk.AtomInfo(
atom=stk.S(3),
building_block=bb2,
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,
},
),
)