Extracting and viewing the results
Docked ligands are stored in archives located in the /output-files folder (for example):
/VFVS/output-files/qvina02_rigid_receptor1/logs/1/0.tar.gz
In order to extract the docked poses and generate a file containing predicted affinities for each compound, one can use the following scripts:
The first script to execute is extract_poses_to_folder.py. It is meant to extract docking poses located in archives present in the current folder to a folder named /results. You can easily modify the path to the archive(s) you want to extract by editing the line 35 in the script:
Specify the path to your tar.gz file
tar_file_path = '0.tar.gz'
The second script, extract_scores.py, will generate a file named scores.csv, containing the names and binding affinities of all the previously extracted poses, located in the ./results folder. Please be aware that the script currently only extracts docking scores that have negative values.
The resulting file can be viewed in the linux terminal using for example vi or nano.
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