def to_oriented_geometry(geo):
""" obtain an oriented 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)
orient_mg = pyx2z.MolecOrient(_mg)
return orient_mg
def test__Atom___getitem__():
""" test pyx2z.Atom.__getitem__() and __setitem()
"""
a = pyx2z.Atom('C', 13)
a[0] = 1.0
a[1] = 1.1
a[2] = 1.2
assert numpy.allclose(a[0], 1.0)
assert numpy.allclose(a[1], 1.1)
assert numpy.allclose(a[2], 1.2)
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 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 to_oriented_geometry(geo):
""" Generate an oriented x2z molecule object from a geometry.
:param geo: molecular geometry
:type geo: automol geometry data structure
: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)
orient_mg = pyx2z.MolecOrient(_mg)
return orient_mg
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_atom(asymb, xyz):
ang2bohr = 1.8897259886
x2zatm = pyx2z.Atom(asymb)
x2zatm[0], x2zatm[1], x2zatm[2] = numpy.multiply(xyz, ang2bohr)
return x2zatm
def _atom_obj(asymb, xyz):
_ang2bohr = 1.8897259886
_a = pyx2z.Atom(asymb)
_a[0], _a[1], _a[2] = numpy.multiply(xyz, _ang2bohr)
return _a
def test__MolecGeom_push_back():
""" test pyx2z.MolecGeom.push_back()
"""
m = pyx2z.MolecGeom()
m.push_back(pyx2z.Atom('C'))
assert m.size() == 1