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Fenglei104 / DeepPROTACs

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AttributeError #11

Open Herbert0305 opened 10 months ago

Herbert0305 commented 10 months ago

This is a very interesting job. When I tried to run single_predict.py, I reported the following error: “AttributeError: 'GCNConv' object has no attribute 'explain'”. How can I solve this problem? thank you! Have you defined explain in the code?

Herbert0305 commented 10 months ago

Traceback (most recent call last): File "D:\Protac\DeepPROTACs-master\single_prediction.py", line 216, in data_sample['smiles_length'],) File "D:\Anaconda3\envs\DeepPROTACs\lib\site-packages\torch\nn\modules\module.py", line 1194, in _call_impl return forward_call(*input, kwargs) File "D:\Protac\DeepPROTACs-master\model.py", line 71, in forward v_0 = self.ligase_ligand_model(ligase_ligand) File "D:\Anaconda3\envs\DeepPROTACs\lib\site-packages\torch\nn\modules\module.py", line 1194, in _call_impl return forward_call(*input, *kwargs) File "D:\Protac\DeepPROTACs-master\model.py", line 18, in forward x = self.gcn1(x, edge_index, edge_attr) File "D:\Anaconda3\envs\DeepPROTACs\lib\site-packages\torch\nn\modules\module.py", line 1194, in _call_impl return forward_call(input, kwargs) File "D:\Anaconda3\envs\DeepPROTACs\lib\site-packages\torch_geometric\nn\conv\gcn_conv.py", line 233, in forward size=None) File "D:\Anaconda3\envs\DeepPROTACs\lib\site-packages\torch_geometric\nn\conv\message_passing.py", line 415, in propagate decomposed_layers = 1 if self.explain else self.decomposed_layers File "D:\Anaconda3\envs\DeepPROTACs\lib\site-packages\torch\nn\modules\module.py", line 1270, in getattr type(self).name, name)) AttributeError: 'GCNConv' object has no attribute 'explain'

This is the complete error reporting interface.

Fenglei104 commented 10 months ago

Please see https://github.com/Fenglei104/DeepPROTACs/issues/9#issuecomment-1473532156 Thanks

Herbert0305 commented 10 months ago

Thank you for your answer, the above problem has been solved. Another problem is that I downloaded the protac,linker,warhead,e3_ligand file from protacdb, but the file did not indicate which linker,warhead and e3_ligand the protac is composed of. May I ask how do you deal with this problem?

Fenglei104 commented 9 months ago

Thank you for your answer, the above problem has been solved. Another problem is that I downloaded the protac,linker,warhead,e3_ligand file from protacdb, but the file did not indicate which linker,warhead and e3_ligand the protac is composed of. May I ask how do you deal with this problem?

Each page in PROTAC-DB contains the information. We collected them from the website.

Herbert0305 commented 6 months ago

Thank you for your answer. May I ask how you got the data in protacs_example.csv file? I downloaded the protacs.csv file in PROTACDB (it contains all the protac in PROTACDB), but a lot of data in the file was missing. For example, Degradation activity, Degradation Identification new 1, Degradation Identification and other data cannot be found. How did you get these data and fill them up? If possible, could you please share with me the method of obtaining and filling your data? Thank you. Also, I'd like to know how you tagged protac and generated label.pt.