chao1224
commented
2 weeks ago Hi @EchoShoot , this should be the issue with OGB version. Can you downgrade your OGB package? Like 1.2.1.
Open EchoShoot opened 2 weeks ago
chao1224
commented
2 weeks ago Hi @EchoShoot , this should be the issue with OGB version. Can you downgrade your OGB package? Like 1.2.1.
3795548it [35:35, 2047.74it/s][17:51:48] WARNING: not removing hydrogen atom without neighbors 3803453it [35:40, 1777.16it/s] Extracting 3D positions from SDF files for Training Data... 25308it [00:18, 1335.28it/s] Traceback (most recent call last): File "generate_PCQM4Mv2.py", line 6, in
test_dataset = PCQM4Mv2(root=root_dir, transform=None)
File "/data/temp/GTAM/modules/datasets/dataset_PCQM4Mv2.py", line 74, in init
super(PCQM4Mv2, self).init(root, transform, pre_transform, pre_filter)
File "/usr/local/anaconda3/envs/gRisk/lib/python3.7/site-packages/torch_geometric/data/in_memory_dataset.py", line 57, in init
super().init(root, transform, pre_transform, pre_filter, log)
File "/usr/local/anaconda3/envs/gRisk/lib/python3.7/site-packages/torch_geometric/data/dataset.py", line 97, in init
self._process()
File "/usr/local/anaconda3/envs/gRisk/lib/python3.7/site-packages/torch_geometric/data/dataset.py", line 230, in _process
self.process()
File "/data/temp/GTAM/modules/datasets/datasetPCQM4Mv2.py", line 137, in process
data, = mol_to_graph_data_obj_simple_3D(mol)
File "/data/temp/GTAM/modules/datasets/dataset_utils.py", line 121, in mol_to_graph_data_obj_simple_3D
atom_feature = atom_to_feature_vector(atom)
File "/usr/local/anaconda3/envs/gRisk/lib/python3.7/site-packages/ogb/utils/features.py", line 60, in atom_to_feature_vector
allowable_features['possible_chirality_list'].index(str(atom.GetChiralTag())),
ValueError: 'CHI_TRIGONALBIPYRAMIDAL' is not in list