Comments (4)
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.
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@smilenaderi Hi, if you use unidock tools, the docking score will be saved in output SDF file with property name docking_score, like this:
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from uni-dock.
Thank you so much all. Perfect! It worked.
@Hong-Rui @dp-yuanyn
Is there any guide on how to use Uni-mol in docker?
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Related Issues (20)
- 1.1.1 source release contains version string 1.1.0 HOT 1
- Error in vina score HOT 2
- typo in examples HOT 1
- missing installation instruction in unidock_tools
- How to dock
- WARNING: Could not find any conformations
- run unidock, report segmentation fault while using file index
- OOM using ad4 scoring function
- CUDA Runtime Error when using ad4 maps HOT 4
- Fail on screening test case mmp13 on version v1.1.x HOT 2
- Unidock pipeline fails to read ligand index HOT 1
- target_compile_features no known features for CXX compiler HOT 6
- Unknown order of ligands in the output HOT 2
- in ligand index, unable to find mol file, only first without others. HOT 1
- Seed doesn't seem to be working properly. HOT 3
- Cuda runtime error =
- Segmentation Fault (Core Dumped)
- v1.1.2 randomly changes its output without any valid cause HOT 1
- cmake -B build -D FETCH_BOOST=ON does not fetch boost HOT 6
- Compiling error on CUDA 11
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