[10:{'node':` <gym.core.Space object at 0x7effce1cd6a0>, 'adj': <gym.core.Space object at 0x7effce1cd438>}
WARN: Could not seed environment <MoleculeEnv<molecule-v0>>
ob_adj (?, 3, ?, ?) ob_node (?, 1, ?, 10)
logits_first (?, ?) logits_second (?, ?) logits_edge (?, 3)
ac_edge (?,)
ob_adj (?, 3, ?, ?) ob_node (?, 1, ?, 10)
logits_first (?, ?) logits_second (?, ?) logits_edge (?, 3)
ac_edge (?,)
[10:54:02] Explicit valence for atom # 2 O, 3, is greater than permitted
[10:54:02] Explicit valence for atom # 4 N, 4, is greater than permitted
[10:54:02] Explicit valence for atom # 1 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 5 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 4 N, 4, is greater than permitted
[10:54:02] Explicit valence for atom # 1 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 8 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 9 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 22 O, 3, is greater than permitted
[10:54:02] Explicit valence for atom # 7 N, 4, is greater than permitted
[10:54:02] Explicit valence for atom # 1 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 20 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 2 O, 3, is greater than permitted
[10:54:02] Explicit valence for atom # 0 Br, 2, is greater than permitted
[10:54:02] Explicit valence for atom # 1 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 14 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 20 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 14 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 2 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 3 O, 3, is greater than permitted
[10:54:02] Explicit valence for atom # 8 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 8 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 8 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 11 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 19 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 2 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 24 O, 3, is greater than permitted
[10:54:02] Explicit valence for atom # 0 N, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 30 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 2 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 30 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 7 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 19 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 2 N, 4, is greater than permitted
[10:54:02] Explicit valence for atom # 6 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 5 N, 4, is greater than permitted
[10:54:02] Explicit valence for atom # 2 N, 4, is greater than permitted
[10:54:02] Explicit valence for atom # 7 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 16 O, 3, is greater than permitted
[10:54:02] Explicit valence for atom # 3 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 1 C, 6, is greater than permitted
[10:54:02] Explicit valence for atom # 13 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 27 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 22 C, 5, is greater than permitted
[10:54:02] Explicit valence for atom # 14 N, 5, is greater than permitted
/home/bowen/anaconda3/envs/rl_graph_generation_apr_11_2018/lib/python3.5/site-packages/tensorflow/python/ops/gradients_impl.py:100: UserWarning: Converting sparse IndexedSlices to a dense Tensor of unknown shape. This may consume a large amount of memory.
"Converting sparse IndexedSlices to a dense Tensor of unknown shape. "
Traceback (most recent call last):
File "run_molecule.py", line 86, in main
train(args,args.env, num_timesteps=args.num_timesteps, seed=args.seed,writer=writer)
File "run_molecule.py", line 46, in train
schedule='linear', writer=writer
File "/home/bowen/pycharm_deployment_directory/rl_graph_generation/rl-baselines/baselines/ppo1/pposgd_simple_gcn.py", line 254, in learn
seg = seg_gen.__next__()
File "/home/bowen/pycharm_deployment_directory/rl_graph_generation/rl-baselines/baselines/ppo1/pposgd_simple_gcn.py", line 74, in traj_segment_generator
info = env.get_info()
File "/home/bowen/pycharm_deployment_directory/rl_graph_generation/gym-molecule/gym_molecule/envs/molecule.py", line 281, in get_info
info['reward_sa'] = calculateScore(m) * self.sa_ratio # lower better
File "/home/bowen/pycharm_deployment_directory/rl_graph_generation/gym-molecule/gym_molecule/envs/sascorer.py", line 59, in calculateScore
2) #<- 2 is the *radius* of the circular fingerprint
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdMolDescriptors.GetMorganFingerprint(NoneType, int)
did not match C++ signature:
GetMorganFingerprint(RDKit::ROMol mol, int radius, boost::python::api::object invariants=[], boost::python::api::object fromAtoms=[], bool useChirality=False, bool useBondTypes=True, bool useFeatures=False, bool useCounts=True, boost::python::api::object bitInfo=None)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "run_molecule.py", line 93, in <module>
main()
File "run_molecule.py", line 88, in main
writer.export_scalars_to_json("./all_scalars.json")
AttributeError: 'NoneType' object has no attribute 'export_scalars_to_json'