def test__from_data():
""" test vmat.from_data
"""
vma1 = vmat.from_data(
syms=vmat.symbols(CH4O_VMA),
key_mat=vmat.key_matrix(CH4O_VMA),
name_mat=vmat.name_matrix(CH4O_VMA),
)
assert vma1 == CH4O_VMA
vma2 = vmat.from_data(
syms=vmat.symbols(CH4O_VMA_NO_NONES),
key_mat=vmat.key_matrix(CH4O_VMA_NO_NONES),
name_mat=vmat.name_matrix(CH4O_VMA_NO_NONES),
)
assert vma2 == CH4O_VMA
vma1 = list(map(list, vma1))
vma2 = list(map(list, vma2))
assert vmat.is_valid(vma1)
assert vmat.is_valid(vma2)
vma1[0] += [None]
vma2[0][1] = vma2[0][1] + (None,)
assert not vmat.is_valid(vma1)
assert not vmat.is_valid(vma2)
def from_data(symbs,
key_mat,
val_mat,
name_mat=None,
one_indexed=False,
angstrom=False,
degree=False):
""" Z-Matrix constructor
:param symbs: atomic symbols
:type symbs: tuple[str]
:param key_mat: key/index columns of the z-matrix, zero-indexed
:type key_mat: tuple[tuple[float, float or None, float or None]]
:param val_mat: z-matrix coordinate values
:type val_mat: tuple[tuple[float, float or None, float or None]]
:param name_mat: coordinate name columns of the z-matrix
:type name_mat; tuple[tuple[str, str or None, str or None]]
:param one_indexed: are the keys in `key_mat` one-indexed?
:type one_indexed: bool
:param angstrom: are distance values in `val_mat` in angstroms?
:type angstrom: bool
:param degree: are angle values in `val_mat` in degrees?
:type degree: bool
:rtype: automol Z-Matrix data structure
"""
vma = vmat.from_data(symbs, key_mat, name_mat, one_indexed=one_indexed)
val_mat = _value_matrix(val_mat, angstrom=angstrom, degree=degree)
symbs, key_mat, name_mat = zip(*vma)
zma = tuple(zip(symbs, key_mat, name_mat, val_mat))
return zma
def vmatrix(zma):
""" Parse and return the V-Matrix component of a Z-Matrix.
:param zma: Z-Matrix
:type zma: automol Z-Matrix data structure
"""
return vmat.from_data(symbs=symbols(zma),
key_mat=key_matrix(zma),
name_mat=name_matrix(zma))
def test__from_data():
""" test vmat.from_data
"""
vma = vmat.from_data(
symbs=vmat.symbols(CH4O_VMA),
key_mat=vmat.key_matrix(CH4O_VMA),
name_mat=vmat.name_matrix(CH4O_VMA),
)
assert vma == CH4O_VMA
def vmatrix(zma):
""" convert z-matrix to v-matrix
"""
return vmat.from_data(syms=symbols(zma),
key_mat=key_matrix(zma),
name_mat=name_matrix(zma))