Example: CASF2016 dataset/1a30
Input:1a30_ligand.sdf, 1a30_protein.pdb
Error:
CompletedProcess(args=['python', '../get_pocket/get_pocket.py', '--docking_result', '/gpfs/share/home/2100011892/CASF2016/CASF-2016/coreset/1a30/1a30_ligand.sdf', '--recptor_pdb', '/gpfs/share/home/2100011892/CASF2016/CASF-2016/coreset/1a30/1a30_protein.pdb', '--single_sdf_save_path', './results/tmp_sdfs/1a30', '--pocket_save_dir', './results/tmp_pockets/1a30'], returncode=0, stdout='sample is None 0\nnum compounds to get pocket 0\nwaiting for processing!\nall pocket done! check the outdir plz!\n', stderr='[16:53:52] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.\n[16:53:52] Explicit valence for atom # 6 C, 6, is greater than permitted\n[16:53:52] ERROR: Could not sanitize molecule ending on line 102\n[16:53:52] ERROR: Explicit valence for atom # 6 C, 6, is greater than permitted\n\n0it [00:00, ?it/s]\nget_pocket:: : 0it [00:00, ?it/s]\nget_pocket:: : 0it [00:00, ?it/s]\n')
And there is no result
Maybe you can reproduce this bug.