def test__MolecStruct_is_radical():
""" test pyx2z.MolecStruct.is_radical()
"""
asymbs = ['O', 'H']
coords = [(-1.2516025626, 2.3683550357, 0.0000000000),
(-1.5749323743, 3.2380324089, -0.2828764736)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(m, [])
assert s.is_radical(0) is True
assert s.is_radical(1) is False
asymbs = ['H']
coords = [(0., 0., 0.)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(m, [])
assert s.is_radical(0) is True
def test__MolecStruct_size():
""" test pyx2z.MolecStruct.size()
"""
asymbs = ['O', 'H', 'H']
coords = [(-1.2516025626, 2.3683550357, 0.0000000000),
(-0.2816025626, 2.3683550357, 0.0000000000),
(-1.5749323743, 3.2380324089, -0.2828764736)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(m, [])
assert s.size() == 3
asymbs = ['H']
coords = [(0., 0., 0.)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(m, [])
assert s.size() == 1
def from_geometry(geo):
""" x2z molecule object from a geometry
"""
_mg = pyx2z.MolecGeom()
for sym, xyz in geo:
_atm = pyx2z.Atom(sym)
_atm[0], _atm[1], _atm[2] = xyz
_mg.push_back(_atm)
_ps = pyx2z.PrimStruct(_mg)
x2m = pyx2z.MolecStruct(_ps)
return x2m
def test__MolecStruct_resonance_count():
""" test pyx2z.MolecStruct.resonance_count()
"""
asymbs = ['C', 'C', 'C', 'H', 'H', 'H', 'H', 'H']
coords = [(1.10206, 0.05263, 0.02517), (2.44012, 0.03045, 0.01354),
(3.23570, 0.06292, 1.20436), (2.86296, -0.38925, 2.11637),
(4.29058, 0.30031, 1.12619), (0.54568, -0.01805, -0.90370),
(0.53167, 0.14904, 0.94292), (2.97493, -0.03212, -0.93001)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(m, [])
assert s.resonance_count() == 2
def from_geometry(geo, ts_bnds=()):
""" x2z molecule object from a geometry
"""
_mg = pyx2z.MolecGeom()
for sym, xyz in geo:
_atm = pyx2z.Atom(sym)
_atm[0], _atm[1], _atm[2] = xyz
_mg.push_back(_atm)
ts_bnds = list(map(list, ts_bnds))
x2m = pyx2z.MolecStruct(_mg, ts_bnds)
return x2m
def test__MolecStruct_resonance_averaged_bond_order():
""" test pyx2z.MolecStruct.resonance_averaged_bond_order()
"""
asymbs = ['O', 'H', 'H']
coords = [(-1.2516025626, 2.3683550357, 0.0000000000),
(-0.2816025626, 2.3683550357, 0.0000000000),
(-1.5749323743, 3.2380324089, -0.2828764736)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(m, [])
assert s.resonance_averaged_bond_order(0, 1) == 1.
assert s.resonance_averaged_bond_order(0, 2) == 1.
assert s.resonance_averaged_bond_order(1, 2) == 0.
def test__MolecStruct_bond_order():
""" test pyx2z.MolecStruct.bond_order()
"""
asymbs = ['C', 'C', 'C', 'H', 'H', 'H', 'H', 'H']
coords = [(1.10206, 0.05263, 0.02517), (2.44012, 0.03045, 0.01354),
(3.23570, 0.06292, 1.20436), (2.86296, -0.38925, 2.11637),
(4.29058, 0.30031, 1.12619), (0.54568, -0.01805, -0.90370),
(0.53167, 0.14904, 0.94292), (2.97493, -0.03212, -0.93001)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(pyx2z.PrimStruct(m))
assert s.bond_order(0, 1, 0) == 2
assert s.bond_order(1, 2, 0) == 1
assert s.bond_order(0, 1, 1) == 1
assert s.bond_order(1, 2, 1) == 2
def test__rotational_group_indices():
""" test pyx2z.rotational_group_indices()
"""
asymbs = ['C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
coords = [
(-1.232983, -0.321673, -0.105358), (1.243527, 0.070589, -0.288927),
(-0.013971, 0.332706, 0.522469), (-1.409212, 0.063988, -1.114625),
(-1.106163, -1.407114, -0.169728), (-2.124468, -0.118860, 0.496321),
(1.145567, 0.468640, -1.303997), (2.106311, 0.551275, 0.182712),
(1.448625, -1.002453, -0.359095), (-0.179317, 1.412994, 0.600234),
(0.122085, -0.050093, 1.539995)
]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(m, [])
indices = pyx2z.rotational_group_indices(s)
print(indices)
def test__MolecStruct_atom_ordering():
""" test pyx2z.MolecStruct.atom_ordering()
"""
asymbs = ['C', 'O', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H']
coords = [(-2.2704178657, 2.9586871732, -0.0000000000),
(-2.0230332171, 1.7537576097, 0.0000000000),
(-1.3903791691, 3.9451234997, 0.7188849720),
(-0.5605839137, 3.4182459749, 1.1980823377),
(-1.9710320856, 4.4623547554, 1.4866301464),
(-0.9857357677, 4.6646475866, 0.0028769813),
(-3.4679340657, 3.5185797384, -0.7188849720),
(-4.0230068872, 2.7073743052, -1.1980823377),
(-3.1380484986, 4.2227540733, -1.4866301464),
(-4.1233452839, 4.0204635187, -0.0028769813)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(m, [])
assert s.atom_ordering() == [0, 1, 2, 6, 3, 4, 5, 7, 8, 9]
def test__rotational_bond_coordinates():
""" test pyx2z.rotational_bond_coordinates()
"""
asymbs = ['C', 'O', 'C', 'H', 'H', 'H', 'C', 'H', 'H', 'H']
coords = [(-2.2704178657, 2.9586871732, -0.0000000000),
(-2.0230332171, 1.7537576097, 0.0000000000),
(-1.3903791691, 3.9451234997, 0.7188849720),
(-0.5605839137, 3.4182459749, 1.1980823377),
(-1.9710320856, 4.4623547554, 1.4866301464),
(-0.9857357677, 4.6646475866, 0.0028769813),
(-3.4679340657, 3.5185797384, -0.7188849720),
(-4.0230068872, 2.7073743052, -1.1980823377),
(-3.1380484986, 4.2227540733, -1.4866301464),
(-4.1233452839, 4.0204635187, -0.0028769813)]
m = _molec_geom_obj(asymbs, coords)
s = pyx2z.MolecStruct(pyx2z.PrimStruct(m))
coords = pyx2z.rotational_bond_coordinates(s)
assert coords == ['D4', 'D7']
def from_geometry(geo, ts_bnds=()):
""" Generate an x2z molecule object from a geometry.
:param geo: molecular geometry
:type geo: automol geometry data structure
:param ts_bnds: keys for the breaking/forming bonds in a TS
:type ts_bnds: tuple(frozenset(int))
:rtype: x2z molecule object
"""
_mg = pyx2z.MolecGeom()
for sym, xyz in geo:
_atm = pyx2z.Atom(sym)
_atm[0], _atm[1], _atm[2] = xyz
_mg.push_back(_atm)
ts_bnds = list(map(list, ts_bnds))
x2m = pyx2z.MolecStruct(_mg, ts_bnds)
return x2m
def _pyx2z_molec_struct(mgeo):
x2zps = _pyx2z_prim_struct(mgeo)
return pyx2z.MolecStruct(x2zps)
