def zmatrix_atom_ordering(geo, ts_bnds=()):
""" z-matrix atom ordering
"""
syms = automol.geom.symbols(geo)
if len(syms) == 1:
idxs = (0, )
else:
x2m = _pyx2z.from_geometry(geo, ts_bnds=ts_bnds)
idxs = _pyx2z.zmatrix_atom_ordering(x2m)
return idxs
def zmatrix_torsion_coordinate_names(geo, ts_bnds=()):
""" z-matrix torsional coordinate names
"""
syms = automol.geom.symbols(geo)
if len(syms) == 1:
names = ()
else:
x2m = _pyx2z.from_geometry(geo, ts_bnds=ts_bnds)
names = _pyx2z.zmatrix_torsion_coordinate_names(x2m)
zma = _pyx2z.to_zmatrix(x2m)
name_dct = automol.zmatrix.standard_names(zma)
names = tuple(map(name_dct.__getitem__, names))
return names
def zmatrix(geo, ts_bnds=()):
""" geometry => z-matrix
"""
syms = automol.geom.symbols(geo)
if len(syms) == 1:
key_mat = [[None, None, None]]
name_mat = [[None, None, None]]
val_dct = {}
zma = create.zmatrix.from_data(syms, key_mat, name_mat, val_dct)
else:
x2m = _pyx2z.from_geometry(geo, ts_bnds=ts_bnds)
zma = _pyx2z.to_zmatrix(x2m)
zma = automol.zmatrix.standard_form(zma)
return zma
def zmatrix_atom_ordering(geo, ts_bnds=()):
""" Generate a dictionary which maps the order of atoms from the input
molecular geometry to the order of atoms of the resulting Z-Matrix
that is generated by the 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))
:rtype: dict[int: int]
"""
symbs = geom_symbols(geo)
if len(symbs) == 1:
idxs = {0: 0}
else:
x2m = _pyx2z.from_geometry(geo, ts_bnds=ts_bnds)
idxs = _pyx2z.zmatrix_atom_ordering(x2m)
return idxs
def zmatrix_x2z(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 = geom_symbols(geo)
key_mat = [[None, None, None]]
val_mat = [[None, None, None]]
zma = create.zmat.from_data(symbs, key_mat, val_mat)
else:
x2m = _pyx2z.from_geometry(geo, ts_bnds=ts_bnds)
zma = _pyx2z.to_zmatrix(x2m)
zma = standard_form(zma)
return zma
def zmatrix_torsion_coordinate_names(geo, ts_bnds=()):
""" Generate a list of torsional coordinates using x2z interface. These
names corresond to the Z-Matrix generated using the same algorithm.
: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: tuple(str)
"""
symbs = geom_symbols(geo)
if len(symbs) == 1:
names = ()
else:
x2m = _pyx2z.from_geometry(geo, ts_bnds=ts_bnds)
names = _pyx2z.zmatrix_torsion_coordinate_names(x2m)
zma = _pyx2z.to_zmatrix(x2m)
name_dct = standard_names(zma)
names = tuple(map(name_dct.__getitem__, names))
return names