def zmatrix_with_conversion_info(geo, ts_bnds=()):
""" Generate a corresponding Z-Matrix for a molecular geometry
using internal autochem procedures.
: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))
:returns: automol Z-Matrix data structure, Z-Matrix atom ordering, and
a dictionary mapping linear atoms onto their associated dummy atoms
"""
if ts_bnds:
raise NotImplementedError
if is_atom(geo):
symbs = symbols(geo)
key_mat = [[None, None, None]]
val_mat = [[None, None, None]]
zma = automol.zmat.base.from_data(symbs, key_mat, val_mat)
zma_keys = [0]
dummy_key_dct = {}
else:
geo, dummy_key_dct = insert_dummies_on_linear_atoms(geo)
gra = connectivity_graph(geo)
bnd_keys = tuple(dummy_key_dct.items())
ord_dct = {k: 0 for k in bnd_keys}
gra = automol.graph.add_bonds(gra, bnd_keys, ord_dct=ord_dct)
vma, zma_keys = automol.graph.vmat.vmatrix(gra)
geo = from_subset(geo, zma_keys)
zma = automol.zmat.base.from_geometry(vma, geo)
return zma, zma_keys, dummy_key_dct
def external_symmetry_factor(geo):
""" Obtain the external symmetry factor for a geometry using x2z interface
which determines the initial symmetry factor and then divides by the
enantiomeric factor.
:param geo: molecular geometry
:type geo: automol geometry data structure
:rtype: float
"""
if is_atom(geo):
ext_sym_fac = 1.
else:
oriented_geom = _pyx2z.to_oriented_geometry(geo)
ext_sym_fac = oriented_geom.sym_num()
if oriented_geom.is_enantiomer():
ext_sym_fac *= 0.5
return ext_sym_fac
def x2z_zmatrix(geo, ts_bnds=()):
""" Generate a corresponding Z-Matrix for a molecular geometry
using x2z interface.
: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))
"""
if is_atom(geo):
symbs = automol.geom.base.symbols(geo)
key_mat = [[None, None, None]]
val_mat = [[None, None, None]]
zma = automol.zmat.base.from_data(symbs, key_mat, val_mat)
else:
x2m = _pyx2z.from_geometry(geo, ts_bnds=ts_bnds)
zma = _pyx2z.to_zmatrix(x2m)
zma = automol.zmat.base.standard_form(zma)
return zma