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 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_molec_geom(mgeo):
x2zmg = pyx2z.MolecGeom()
for asymb, xyz in mgeo:
x2zatm = _pyx2z_atom(asymb, xyz)
x2zmg.push_back(x2zatm)
return x2zmg
def test__MolecGeom_push_back():
""" test pyx2z.MolecGeom.push_back()
"""
m = pyx2z.MolecGeom()
m.push_back(pyx2z.Atom('C'))
assert m.size() == 1
def _molec_geom_obj(asymbs, coords):
_mg = pyx2z.MolecGeom()
for asymb, xyz in zip(asymbs, coords):
_a = _atom_obj(asymb, xyz)
_mg.push_back(_a)
return _mg
def test__MolecGeom_size():
""" test pyx2z.MolecGeom.size()
"""
m = pyx2z.MolecGeom()
assert m.size() == 0