diff options
| -rw-r--r-- | ml_exp/representations.py | 26 |
1 files changed, 13 insertions, 13 deletions
diff --git a/ml_exp/representations.py b/ml_exp/representations.py index 937268d0c..4a685d388 100644 --- a/ml_exp/representations.py +++ b/ml_exp/representations.py @@ -239,19 +239,19 @@ the current compound.') instead of (size).') size = n - am = np.zeros((size, size), dtype=np.float64) - - for i, bond_i in enumerate(bonds_i): - for j, bond_j in enumerate(bonds_i): - # Ignore the diagonal. - if i != j: - if (bond_i[0] in bond_j) or (bond_i[1] in bond_j): - if use_forces: - am[i, j] = np.dot(bonds_f[i], bonds_f[j]) - else: - am[i, j] = bonds_k[i] - - return am + am = np.zeros((n, n), dtype=np.float64) + + for i in range(n - 1): + for j in range(i + 1, n): + if (bonds_i[i][0] in bonds_i[j]) or (bonds_i[i][1] in bonds_i[j]): + if use_forces: + am[i, j] = np.dot(bonds_f[i], bonds_f[j]) + am[j, i] = am[i, j] + else: + am[i, j] = bonds_k[i] + am[j, i] = am[i, j] + + return np.pad(am, ((0, size - n), (0, size - n)), 'constant') def check_bond(bags, |