def test__from_data():
""" test vmatrix.from_data
"""
vma = vmatrix.from_data(
syms=vmatrix.symbols(CH4O_VMA),
key_mat=vmatrix.key_matrix(CH4O_VMA),
name_mat=vmatrix.name_matrix(CH4O_VMA),
)
assert vma == CH4O_VMA
def string(zma):
""" write a z-matrix to a string
"""
zma_str = aw.zmatrix.write(
syms=_v_.symbols(var_(zma)),
key_mat=_v_.key_matrix(var_(zma), shift=1),
name_mat=_v_.name_matrix(var_(zma)),
val_dct=values(zma, angstrom=True, degree=True)
)
return zma_str
def string(zma, one_indexed=True, angstrom=True, degree=True):
""" write a z-matrix to a string
"""
shift = 1 if one_indexed else 0
zma_str = aw.zmatrix.write(
syms=_v_.symbols(var_(zma)),
key_mat=_v_.key_matrix(var_(zma), shift=shift),
name_mat=_v_.name_matrix(var_(zma)),
val_dct=values(zma, angstrom=angstrom, degree=degree)
)
return zma_str
def set_values(zma, val_dct):
""" set coordinate values for the z-matrix
"""
vma = var_(zma)
_names = _v_.names(vma)
assert set(val_dct.keys()) <= set(_names)
new_val_dct = values(zma).copy()
new_val_dct.update(val_dct)
return automol.create.zmatrix.from_data(
_v_.symbols(vma), _v_.key_matrix(vma), _v_.name_matrix(vma),
new_val_dct)
def set_names(zma, name_dct):
""" set coordinate names for the z-matrix
"""
orig_vma = var_(zma)
vma = _v_.set_names(orig_vma, name_dct)
name_mat = _v_.name_matrix(vma)
name_dct = dict(zip(numpy.ravel(_v_.name_matrix(orig_vma)),
numpy.ravel(name_mat)))
val_dct = {name_dct[orig_name]: val
for orig_name, val in values(zma).items()}
return automol.create.zmatrix.from_data(
_v_.symbols(vma), _v_.key_matrix(vma), name_mat, val_dct)
def is_valid(zma):
""" is this a valid zmatrix?
"""
ret = hasattr(zma, '__len__') and len(zma) == 2
if ret:
vma, val_dct = zma
ret = _v_.is_valid(vma) and set(_v_.names(vma)) == set(val_dct)
if ret:
try:
automol.create.zmatrix.from_data(
_v_.symbols(vma), _v_.key_matrix(vma),
_v_.name_matrix(vma), val_dct)
except AssertionError:
ret = False
return ret
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 key_matrix(zma, shift=0):
""" coordinate atom keys, by z-matrix row and column
"""
return _v_.key_matrix(var_(zma), shift=shift)