def values(zma, angstrom=False, degree=False):
""" coordinate values, by coordinate name
"""
vma, val_dct = zma
# post-processing for unit convertions
dist_names = _v_.distance_names(vma)
ang_names = _v_.angle_names(vma)
orig_val_dct = val_dct
val_dct = {}
for name, val in orig_val_dct.items():
if angstrom and name in dist_names:
val *= qcc.conversion_factor('bohr', 'angstrom')
if degree and name in ang_names:
val *= qcc.conversion_factor('radian', 'degree')
val_dct[name] = val
return val_dct
def from_geometry(vma, geo):
""" determine z-matrix from v-matrix and geometry
"""
assert _v_.symbols(vma) == automol.geom.symbols(geo)
val_dct = {}
coo_dct = _v_.coordinates(vma, multi=False)
dist_names = _v_.distance_names(vma)
cent_names = _v_.central_angle_names(vma)
dih_names = _v_.dihedral_angle_names(vma)
for name, coo in coo_dct.items():
if name in dist_names:
val_dct[name] = automol.geom.distance(geo, *coo)
elif name in cent_names:
val_dct[name] = automol.geom.central_angle(geo, *coo)
elif name in dih_names:
val_dct[name] = automol.geom.dihedral_angle(geo, *coo)
zma = automol.create.zmatrix.from_data(
symbols=_v_.symbols(vma), key_matrix=_v_.key_matrix(vma),
name_matrix=_v_.name_matrix(vma), values=val_dct)
return zma
def distance_names(zma):
""" distance coordinate names
"""
return _v_.distance_names(var_(zma))