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PaddlePaddle / PaddleHelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
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Error while processing the refined set #152

Open VirtualChemist opened 3 years ago

VirtualChemist commented 3 years ago

Hi, When i executed the following command for python code under the following path (https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/drug_target_interaction/sign)

python preprocess_pdbbind.py --data_path_refined refined-set --dataset_name pdbbind2016 --output_path out --cutoff 5

the command ended with following error.

Traceback (most recent call last): File "preprocess_pdbbind.py", line 362, in process_dataset(args.data_path_core, args.data_path_refined, args.dataset_name, args.output_path, args.cutoff) File "preprocess_pdbbind.py", line 308, in process_dataset processed_dict[name] = gen_feature(path, name, featurizer) File "preprocess_pdbbind.py", line 80, in gen_feature assert x == 8 AssertionError

Looking for your support.

Thanks

agave233 commented 3 years ago

In fact, this assert-statement is used to ensure we have removed HOH in the mol2 file, which is not necessary for the data in your case. You can just delete this line to run the code.