import pickle
from ase import Atoms
# load qm9 dataset and download if necessary
data = QM9("qm9.db", collect_triples=True)
loader = spk.data.AtomsLoader(data, batch_size=1, num_workers=2)
reps = rep.BehlerSFBlock()
# get wACSF feature
reps_dict = {}
for i,x in enumerate(loader):
reps_dict[data.get_atoms(i).__repr__()] = reps(x).squeeze(0)
structures = pd.read_csv('/home/will/Desktop/kaggle/QM/Data/structures.csv')
structures_gb = structures.groupby(['molecule_name'])
atoms_structures = {}
for k,v in structures_gb:
atom_dict = {'positions':v[['x','y','z']].values.tolist(),
'symbols':[i[0] for i in v[['atom']].values.tolist()]
}
atom = Atoms(**atom_dict)
atoms_structures[k] = atom.__repr__()
final_dict = {}
for k,v in atoms_structures.items():
final_dict[k] = reps_dict[v].numpy().astype(np.float32)
with open('/home/will/Desktop/kaggle/QM/Data/structures_dict_wACSF.pickle', 'wb') as handle:
pickle.dump(final_dict, handle, protocol=pickle.HIGHEST_PROTOCOL)
