def count(zma):
""" Obtain the number of rows of the Z-Matrix, which corresponds to
the number of atoms defined in the Z-Matrix. This includes all
real and dummy atoms.
:param zma: Z-Matrix
:type zma: automol Z-Matrix data structure
:rtype: int
"""
return vmat.count(zma)
def shift_down(zma, vals):
"""
Build a remdummy list that tells how to shift the groups
"""
dummy_idxs = sorted(atom_indices(zma, 'X', match=True))
if dummy_idxs:
remdummy = [0 for _ in range(count(zma))]
for dummy in dummy_idxs:
for idx, _ in enumerate(remdummy):
if dummy < idx:
remdummy[idx] += 1
vals1 = tuple(val + 1 for val in vals)
vals2 = tuple(val - remdummy[val - 1] for val in vals1)
shift_vals = tuple(val - 1 for val in vals2)
else:
shift_vals = vals
return shift_vals
def count(zma):
""" the number of z-matrix rows (number of atoms or dummy atoms)
"""
return vmat.count(zma)