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, }, ), )