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View Code? Open in Web Editor NEWOfficial Implementation of Compass
Home Page: https://arxiv.org/abs/2406.06841
License: Other
Official Implementation of Compass
Home Page: https://arxiv.org/abs/2406.06841
License: Other
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,
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,
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