def to_zmatrix_old(x2m):
""" Generate a Z-Natrix from an x2z molecule object (old).
:param x2m: molecule object
:type x2m: x2z molecule object
:rtype: automol Z-Matrix data structure
"""
zma_str = pyx2z.zmatrix_string(x2m)
syms, key_mat, name_mat, val_mat = ar.zmat.read(
zma_str,
mat_entry_sep_ptt=',',
mat_entry_start_ptt=',',
setv_sep_ptt=app.padded(app.one_of_these(['', app.NEWLINE])))
zma = automol.create.zmat.from_data(syms,
key_mat,
name_mat,
val_mat,
one_indexed=True,
angstrom=False,
degree=True)
return zma
def test__zmatrix_string():
""" test pyx2z.zmatrix_sring()
"""
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, [])
string = pyx2z.zmatrix_string(s)
print(string)
def to_zmatrix(x2m):
""" z-matrix from an x2z molecule object
"""
zma_str = pyx2z.zmatrix_string(x2m)
syms, key_mat, name_mat, val_dct = ar.zmatrix.read(
zma_str,
mat_entry_sep_ptt=',',
mat_entry_start_ptt=',',
setv_sep_ptt=app.padded(app.one_of_these(['', app.NEWLINE])))
zma = _zmatrix_from_data(syms,
key_mat,
name_mat,
val_dct,
one_indexed=True,
angstrom=False,
degree=True)
return zma