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dptech-corp / Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program
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How to get score when run unidock tooks? #89

Open smilenaderi opened 7 months ago

smilenaderi commented 7 months ago

When I use unidock tools I only get output ligand. How I can get score?

smilenaderi commented 7 months ago

@Hong-Rui

Hong-Rui commented 7 months ago

Hi, I've just add a module for doing this in branch feature/unidock-sdf-parsing https://github.com/dptech-corp/Uni-Dock/blob/feature/unidock-sdf-parsing/unidock_tools/unidock_tools/modules/ligand_prep/unidock_parsing_sdf.py

Temperally, you can use this docking pose analysis and scroing extraction functionality by something like this:

from unidock_tools.modules.ligand_prep.unidock_parsing_sdf import UniDockParsingSDF

unidock_parsing = UniDockParsingSDF(input_sdf_file_name_list,
                                    docked_sdf_file_name_list,
                                    n_cpu=12,
                                    working_dir_name='./')

unidock_parsing.run_unidock_parsing()

docking_pose_info_df_list = unidock_parsing.docking_pose_summary_info_df_list

@dp-yuanyn may integrate this and wrap it into a CLI later... And of course, some features like polar-hydrogen optimization algorithms might be added into this code later on...

Hope this helps.

dp-yuanyn commented 7 months ago

@smilenaderi Hi, if you use unidock tools, the docking score will be saved in output SDF file with property name docking_score, like this: result SDF img

smilenaderi commented 6 months ago

Thank you so much all. Perfect! It worked.

@Hong-Rui @dp-yuanyn Is there any guide on how to use Uni-mol in docker?