Docking Contacts Analysis

From a docking experiment, look for the contacts between all the chains of the PDB input file(s) and if asked the interfaces between the chains.

Conda environment

A conda YAML environment file is provided: references/pymol_env.yml. The file contains all the dependencies to run the script. The conda environment is generated using the command:

# create the environment
conda env create -f references/pymol_env.yml

# activate the environment
conda activate pymol

Configuration file

A configuration file must be provided as the template in the repository.

Results

The outputs of the script are by pair of chains:

• a png file of the docking with the contacts.
• a png file of the docking interfaces if asked.
• a pymol session of the docking with the contacts (and the interfaces if asked).
• an updated pdb file.
• a heatmap of the contacts which format is set in the configuration file.
• a csv file of the contacts.
• a log file.