Installation Guide

Instructions to install WatCon are as follows:

1. Clone the WatCon Repository

Clone the WatCon repository and change your working directory into WatCon

git clone https://github.com/kamerlinlab/WatCon.git

cd WatCon

2. Create a WatCon Conda Environment

conda env create -f WatCon.yaml

3. Add Modeller license

After you create the WatCon conda environment, you will receive this message:

Edit /anaconda3/envs/WatCon/lib/modeller-10.7/modlib/modeller/config.py
and replace XXXX with your Modeller license key
(or set the KEY_MODELLER environment variable before running 'conda install').

This message is prompted because certain features of WatCon are dependent on the Modeller package by the Sali Lab. This package requires a license which can be obtained here. Once you receive the license, simply edit the modeller config file with the license key.

Once completed, a WatCon environment should have been created so that you can freely use the code. With input files, call WatCon on the command line by

$ python -m WatCon.WatCon --input input.txt --name name_of_system

or simply import WatCon as a python package directly:

import WatCon.sequence_processing

sequence_processing.pdb_to_fastas('clean_pdbs/structure1.pdb', 'fasta', 'PTP1B')

Note

WatCon is compatible with Python versions >3.9 and <3.12. Attempting to use WatCon with Python versions outside of this range may result in unexpected behavior.