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, ), ) )
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)), ), stk.Bromo( bromine=stk.Br(0), atom=stk.C(1), bonders=(stk.C(1), ), deleters=(stk.Br(0), ), ), stk.CarboxylicAcid( carbon=stk.C(0), oxygen1=stk.O(1), oxygen2=stk.O(5), hydrogen=stk.H(6), atom=stk.C(8), bonders=(stk.C(0), ), deleters=(stk.O(5), stk.H(6)), ), stk.Fluoro( fluorine=stk.F(12),
def dibromo(get_atom_ids): a, b, c, d = get_atom_ids(4) return _dibromo(stk.Br(a), stk.C(b), stk.Br(c), stk.C(d))
deleters=(stk.F(3), ), ), stk.Fluoro( fluorine=stk.F(6), atom=stk.C(5), bonders=(stk.C(5), ), deleters=(stk.F(6), ), ), ), ), lambda: CaseData( factory=stk.BromoFactory(), molecule=stk.BuildingBlock('BrCC(Br)CCBr'), functional_groups=( stk.Bromo( bromine=stk.Br(0), atom=stk.C(1), bonders=(stk.C(1), ), deleters=(stk.Br(0), ), ), 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), ),
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), 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), ),
params=( lambda: CaseData( building_block=stk.BuildingBlock.init_from_molecule( molecule=stk.BuildingBlock('Br[C+2][C+2]Br'), ), functional_groups=(), core_atom_ids=(0, 1, 2, 3), placer_ids=(0, 1, 2, 3), ), lambda: CaseData( building_block=stk.BuildingBlock.init_from_molecule( molecule=stk.BuildingBlock('Br[C+2][C+2]Br'), functional_groups=[stk.BromoFactory()], ), 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=(1, 2), ), lambda: CaseData(
def bromo(get_atom_ids): a, b = get_atom_ids(2) return _bromo(stk.Br(a), stk.C(b))
import pytest import numpy as np import stk from ..case_data import CaseData @pytest.fixture( scope='session', params=( lambda: CaseData( building_block=stk.BuildingBlock.init( atoms=(stk.Br(0), stk.C(1, 2), stk.C(2, 2), stk.Br(3)), bonds=( stk.Bond(stk.Br(0), stk.C(1, 2), 1), stk.Bond(stk.C(1, 2), stk.C(2, 2), 1), stk.Bond(stk.C(2, 2), stk.Br(3), 1), ), position_matrix=np.array([ [0., 0., 0.], [1., 1., 1.], [2., 2., 2.], [3., 3., 3.], ]), ), functional_groups=(), core_atom_ids=(0, 1, 2, 3), placer_ids=(0, 1, 2, 3), ), lambda: CaseData( building_block=stk.BuildingBlock.init(