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some errors occur while doing shape search

Open MachineGUN001 opened this issue 1 year ago • 0 comments

hi,

previously I can run the vsflow well after preparing the 3D shape database.

the command line I used for shape screening: !python ../vsflow shape -smi {query_smi} -d ../data/lib_53188_3d.vsdb -o ../results/shapesmi_20230705A -np 20 -t 2000 -s pharmacophore --pymol

after runing about 1hour, some errors occur and no screening data including smi, or sdf were generated.

those errors I have not seen before and detailed info of errors are below :

Finished shape screening in 3224.48202 seconds
Filtering and sorting results...
CPU times: total: 1 s
Wall time: 54min 55s
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 116, in spawn_main
    exitcode = _main(fd, parent_sentinel)
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 125, in _main
    prepare(preparation_data)
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 236, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 287, in _fixup_main_from_path
    main_content = runpy.run_path(main_path,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 288, in run_path
    return _run_module_code(code, init_globals, run_name,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 97, in _run_module_code
    _run_code(code, mod_globals, init_globals,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vsflow", line 3, in <module>
    from vslib import run
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vslib\run.py", line 27, in <module>
    config = pickle.load(open(f"{home}/.vsflow/.config", "rb"))
EOFError: Ran out of input
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 116, in spawn_main
    exitcode = _main(fd, parent_sentinel)
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 125, in _main
    prepare(preparation_data)
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 236, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 287, in _fixup_main_from_path
    main_content = runpy.run_path(main_path,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 288, in run_path
    return _run_module_code(code, init_globals, run_name,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 97, in _run_module_code
    _run_code(code, mod_globals, init_globals,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vsflow", line 3, in <module>
    from vslib import run
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vslib\run.py", line 27, in <module>
    config = pickle.load(open(f"{home}/.vsflow/.config", "rb"))
EOFError: Ran out of input
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 116, in spawn_main
    exitcode = _main(fd, parent_sentinel)
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 125, in _main
    prepare(preparation_data)
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 236, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\multiprocessing\spawn.py", line 287, in _fixup_main_from_path
    main_content = runpy.run_path(main_path,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 288, in run_path
    return _run_module_code(code, init_globals, run_name,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 97, in _run_module_code
    _run_code(code, mod_globals, init_globals,
  File "c:\Users\lsy\anaconda3\envs\aisynth\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vsflow", line 3, in <module>
    from vslib import run
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vslib\run.py", line 27, in <module>
    config = pickle.load(open(f"{home}/.vsflow/.config", "rb"))
EOFError: Ran out of input
Traceback (most recent call last):
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vsflow", line 6, in <module>
    run.main()
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vslib\run.py", line 1560, in main
    args.func(args)
  File "d:\Cheminfo_Workshop\9_VirtualScreening\VSFlow-master\vslib\run.py", line 965, in shape
    props = copy.deepcopy(mols[feat[4]]["props"])
KeyError: 'props'

could you please provide some suggesions how to fix the tissues? it did confuse me for a long time. many many thanks,

Best, Sh-Y

MachineGUN001 avatar Jul 06 '23 16:07 MachineGUN001