Generate shape-based scoring results

shape_score.py is a script for scoring molecular docking poses. The main functions of this script include:

Reading original and docked SDF files
Calculating shape similarity scores
Sorting docking results
Saving processed results as PKL files
Logging failed target paths

The script logs detailed processing steps and outputs all failed target paths at the end of processing.

Environment Dependencies

You can install the required Python libraries using pip:

pip install rdkit easydict

Usage

Configuring Paths

Edit the following variables in the shape_score.py file to set your working directory and task name（here is just an example）:

base_path = '/home/megagatlingpea/workdir/delete_shape'
task = 'nabla510_finetune_293'

Ensure that the corresponding task directory exists under base_path, and each task directory contains an SDF subdirectory and original SDF files.

Running the Script

It's recommended to use the nohup command to run the script in the background, allowing it to continue executing even if the terminal is closed. Run the command as follows:

nohup python shape_score.py > process.log 2>&1 &

nohup: Ignores the hangup signal, allowing the script to run continuously in the background.
python process.py: Executes the script.
> process.log: Redirects standard output to the process.log file.
2>&1: Redirects standard error to standard output.
&: Puts the command in the background.

Viewing Logs

You can view the contents of the log file in real-time to monitor the script's execution:

tail -f process.log

Checking Failed Target Paths

The script records all failed target paths during processing and outputs them in the last line of the log file. You can use the eval function to read the failed list from the last line of the process.log file to easily see which paths failed processing.

with open('process.log', 'r') as f:
    lines = f.readlines()
    last_line = lines[-1]
    failed_targets = eval(last_line.split(':')[-1].strip())
    print("Failed target paths:")
for target in failed_targets:
    print(target)

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