diff options
| -rw-r--r-- | ml_exp/bob.py | 16 |
1 files changed, 12 insertions, 4 deletions
diff --git a/ml_exp/bob.py b/ml_exp/bob.py index 5f45019a0..e3d54c5fa 100644 --- a/ml_exp/bob.py +++ b/ml_exp/bob.py @@ -43,6 +43,7 @@ def check_bond(bags, def bob(c_matrix, atoms, + max_n=25, max_bond_len=325): """ Creates the bag of bond using the coulomb matrix data. @@ -54,10 +55,15 @@ def bob(c_matrix, bond_n = (n * n - n) / 2 + n n_r = range(n) + if max_n < n: + print(''.join(['Error. Molecule matrix dimension (mol_n) is ', + 'greater than max_len. Using mol_n.'])) + max_n = n + if max_bond_len < bond_n: print(''.join(['Error. Molecule bond lenght (bond_n) is ', 'greater than max_bond_len. Using bond_n.'])) - max_bond_len = None + max_bond_len = bond_n # List where each bag data is stored. bags = [] @@ -90,11 +96,13 @@ def bob(c_matrix, # Create the final vector for the bob. bob = array(zeros(max_bond_len), dtype=float) c_i = 0 - for bond in bonds: + for i, bond in enumerate(bonds): checker = check_bond(bags, bond) if checker[0]: - for num in bags[checker[1]][1:]: - bob[c_i] = num + for j, num in enumerate(bags[checker[1]][1:]): + # Use c_i as the index for bob if the zero padding should + # be at the end of the vector instead of between each bond. + bob[i*max_n + j] = num c_i += 1 # This is set to false because this was a debugging measure. elif False: |