deepmodeling / deepmodeling/Uni-Mol
demo.sh doesn't make pkl file
- Dominant language
- Python
- Stars
- 1.2k
- Forks
- 181
- PR merge metrics
- No merged PRs in 30d
Description
sh demo.sh
Namespace(model_dir='checkpoint_best.pt', input_protein='../example_data/protein.pdb', input_ligand='../example_data/ligand.sdf', input_batch_file='input_batch.csv', input_docking_grid='../example_data/docking_grid.json', output_ligand_name='ligand_predict', output_ligand_dir='predict_sdf', mode='single', batch_size=4, nthreads=8, conf_size=10, cluster=True, use_current_ligand_conf=False, steric_clash_fix=True)
Start preprocessing data...
Number of ligands: 1
1it [00:01, 1.89s/it]
Total num: 1, Success: 1, Failed: 0
Done!
Error: mkl-service + Intel(R) MKL: MKL_THREADING_LAYER=INTEL is incompatible with libgomp.so.1 library.
Try to import numpy first or set the threading layer accordingly. Set MKL_SERVICE_FORCE_INTEL to force it.
Traceback (most recent call last):
File "/home/sangmin/apps/docking/Uni-Mol/unimol_docking_v2/interface/demo.py", line 189, in
main_cli()
File "/home/sangmin/apps/docking/Uni-Mol/unimol_docking_v2/interface/demo.py", line 185, in main_cli
main(args)
File "/home/sangmin/apps/docking/Uni-Mol/unimol_docking_v2/interface/demo.py", line 24, in main
output_ligand) = clf.predict_sdf(
^^^^^^^^^^^^^^^^
File "/home/sangmin/apps/docking/Uni-Mol/unimol_docking_v2/interface/predictor/unimol_predictor.py", line 82, in predict_sdf
output_sdf = self.postprocess(output_pkl,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sangmin/apps/docking/Uni-Mol/unimol_docking_v2/interface/predictor/unimol_predictor.py", line 66, in postprocess
mol_list, smi_list, coords_predict_list, holo_coords_list, holo_center_coords_list, prmsd_score_list = postprocessor.postprocess_data_pre(output_pkl, output_lmdb)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sangmin/apps/docking/Uni-Mol/unimol_docking_v2/interface/predictor/processor.py", line 331, in postprocess_data_pre
predict = pd.read_pickle(predict_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sangmin/anaconda3/envs/PLBA/lib/python3.11/site-packages/pandas/io/pickle.py", line 189, in read_pickle
with get_handle(
^^^^^^^^^^^
File "/home/sangmin/anaconda3/envs/PLBA/lib/python3.11/site-packages/pandas/io/common.py", line 872, in get_handle
handle = open(handle, ioargs.mode)
^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/sangmin/apps/docking/Uni-Mol/unimol_docking_v2/interface/predict_sdf/ligand_predict.pkl'
how to solve this problem?
Contributor guide
No contributing guide indexed for this repository
Assessment
This issue has not been assessed yet.