def ranking(D, perm_mode='normal1'):
r""" Compute the ranking vector."""
_check_input(D)
R_hat = _rank_differential(D)
res = permutation_2sided(D, R_hat,
remove_zero_col=False,
remove_zero_row=False,
mode=perm_mode)
# Compute the rank
_, rank = np.where(res["array_u"] == 1)
rank += 1
return rank
def mol_align(A, B):
r"""Align two molecules using two sided permutation Procrustes with one
transformation.
"""
# Compute the permutation matrix
_, _, U, e_opt = permutation_2sided(A,
B,
transform_mode='single_undirected',
remove_zero_col=False,
remove_zero_row=False)
# Compute the transformed molecule A
A = _utils._get_input_arrays(A)
new_A = np.dot(U.T, np.dot(A, U))
# B
new_B = B
return new_A, new_B, U, e_opt
def mol_align(A, B):
r"""Align two molecules using two sided permutation Procrustes with one
transformation.
"""
# Compute the permutation matrix
res = permutation_2sided(A,
B,
transform_mode='single_undirected',
remove_zero_col=False,
remove_zero_row=False)
# Compute the transformed coordinates of molecule A
A = utils.setup_input_arrays(A)
new_A = np.dot(res["array_u"].T, np.dot(A, res["array_u"]))
# coordinates of molecule B
new_B = B
return new_A, new_B, res["array_u"], res["e_opt"]