diff options
Diffstat (limited to 'ml_exp/representations.py')
| -rw-r--r-- | ml_exp/representations.py | 20 |
1 files changed, 12 insertions, 8 deletions
diff --git a/ml_exp/representations.py b/ml_exp/representations.py index 1fe55aa5f..ea079595e 100644 --- a/ml_exp/representations.py +++ b/ml_exp/representations.py @@ -310,8 +310,8 @@ def check_bond(bags, def bag_of_stuff(cm, atoms, - stuff='bonds', - size=23): + size=23, + stuff='bonds'): """ Creates the Bag of Bonds using the Coulomb Matrix. cm: coulomb matrix. @@ -322,6 +322,10 @@ def bag_of_stuff(cm, raise ValueError('Coulomb Matrix hasn\'t been initialized for the \ current compound.') + if cm.ndim == 1: + raise ValueError('Coulomb Matrix (CM) dimension is 1. Maybe it was \ +generated as the vector of eigenvalues, try (re-)generating the CM.') + n = len(atoms) if size < n: @@ -330,7 +334,7 @@ current compound.') size = n # Bond max length, calculated using only the upper triangular matrix. - bond_size = (size * size - size)/2 + size + bond_size = int((size * size - size)/2 + size) # List where each bag data is stored. bags = [] @@ -362,19 +366,19 @@ current compound.') bonds.append(''.join(sorted([a_i, a_j]))) bonds = atom_list + bonds - # Create the final vector for the bob. - bob = np.zeros(bond_size, dtype=float) + # Create the final vector for the bos. + bos = np.zeros(bond_size, dtype=float) c_i = 0 for i, bond in enumerate(bonds): checker = check_bond(bags, bond) if checker[0]: for j, num in enumerate(sorted(bags[checker[1]][1:])[::-1]): - # Use c_i as the index for bob if the zero padding should + # Use c_i as the index for bos if the zero padding should # be at the end of the vector instead of between each bond. - bob[i*size + j] = num + bos[i*size + j] = num c_i += 1 else: print(f'Error. Bond {bond} from bond list coudn\'t be found', 'in the bags list. This could be a case where the atom', 'is only present oncce in the molecule.') - return bob + return bos |