The compass from bimsbbioinfo

for reduce method

hi,

Thank you for providing this interesting work! I have a question regarding the usage of the "reduce" method.. It seems that the developer only supports the Unix version, and I am using the Windows operating system which may not be compatible.

while I try to run the compass script without reduce method, the following warning info:

    print("***** WARNING: reduce is not installed      *****")
    print("***** WARNING: clashes and interaction fingerprinting may not work *****")
    print("***** WARNING: we highly recommend using reduce as in the paper for comparison *****")
    print("***** WARNING: Install instructions in README.md *****")

If I run the Compass method without using "reduce" method will it still function correctly? Will it affect the accuracy and precision of the predicted results of docking?

many thanks,

Best,

AttributeError: type object 'Molecule' has no attribute 'from_file'

hi,

please see the below error.

Traceback (most recent call last):
  File "c:\Users\lsy\anaconda3\envs\diffdock112\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "c:\Users\lsy\anaconda3\envs\diffdock112\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "d:\Cheminfo_Workshop\5_Docking_Lab\Compass-main\main_inference.py", line 327, in <module>
    main()
  File "d:\Cheminfo_Workshop\5_Docking_Lab\Compass-main\main_inference.py", line 324, in main
    recursive_docking_and_processing(args)
  File "d:\Cheminfo_Workshop\5_Docking_Lab\Compass-main\main_inference.py", line 87, in recursive_docking_and_processing
    binding_aff, clashes, strain, confidence_value = process_sdf_file(write_dir, sdf_file, args, protein_path_list, iteration, ligand_description)
  File "d:\Cheminfo_Workshop\5_Docking_Lab\Compass-main\main_inference.py", line 168, in process_sdf_file
    clashes, strain, inter_dict = posecheck_eval(protein_path, input_sdf_path)
  File "d:\Cheminfo_Workshop\5_Docking_Lab\Compass-main\compass.py", line 83, in posecheck_eval
    pc.load_protein_from_pdb(protein_file)
  File "d:\cheminfo_workshop\5_docking_lab\compass-main\posecheck\posecheck\posecheck.py", line 59, in load_protein_from_pdb
    self.protein = load_protein_from_pdb(pdb_path, reduce_path=self.reduce_path)
  File "d:\cheminfo_workshop\5_docking_lab\compass-main\posecheck\posecheck\utils\loading.py", line 85, in load_protein_from_pdb
    prot = plf.Molecule.from_file(tmp_path)
AttributeError: type object 'Molecule' has no attribute 'from_file'

I used the ProLIF version 2.0.3 as environment.yml depicted. however, the current version of ProLIF has remove the 'from_file" function from the Molecule class. May I know which right version of ProLIF you are using that still can allow for the proper usage of 'from_file" function?

many thanks,

Best,

bimsbbioinfo / compass Goto Github PK

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for reduce method

AttributeError: type object 'Molecule' has no attribute 'from_file'

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