Steric clash checker

A tool to check steric clashes between predicted ligand pose and a target protein structure. It is build around the structure of the results provided by the blind-docking framework DiffDock.

Install

Easiest way is to run the tool inside a conda environment, for this you will need to have conda installed. To install the conda environment run the command below. It was tested on Apple Mac M1, for other platforms this might not work - refer to the version of the package in the clashCheckEnv.yml file.

git clone git@github.com:KoubaPetr/steric_clash_checker.git
cd steric_clash_checker/
conda create --name clashCheckEnv
conda activate clashCheckEnv

Example

python steric_clash_checker.py --dataset_folder_path data/user_predictions_testset --treshold 0.4 --log_to logs.txt --max_ranking 10

How to adapt to your data

1. Inside data/ create a directory YOUR_DIR for your dataset.

2. Inside YOUR_DIR create a directory TARGET_#NO for each target protein you are interested in.

3. Inside TARGET_#NO put the PDB file with the structure of your target protein and all the corresponding ligand poses in the .sdf format, for which you wish to check for the steric clashes.

4. Run:

   python steric_clash_checker.py --dataset_folder_path data/YOUR_DIR --treshold 0.4 --log_to logs.txt --max_ranking 10

By default, we use the treshold of 0.4 Angstrom to consider an atom pair as clashing, but you can specify your own value. See utils/ for a script which can help with the preparation of the dataset structure.