DOCK 3.8:How to install pydock3

pydock3 is a Python package wrapping the DOCK Fortran program that provides tools to help standardize and automate the computational methods employed in molecular docking.

Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.

Instructions

1. git clone the following repo: https://github.com/docking-org/pydock3 into a folder of your choice. Navigate to the folder first before cloning.

git clone https://github.com/docking-org/pydock3

2. Now that you have a new folder called pydock3, create a new conda environment to install packages into. Make sure it has python version>=3.8. Replace 'your_env_name' with your chosen environment name.

conda create -n your_env_name python=3.8

3. Activate the conda environment and install pydock3 onto it with pip. Do not cd into the pydock3 folder itself before running pip.

conda activate your_env_name

pip install -e pydock3

4. Check if it is installed by running the following in a folder of your choice. This will create a new folder named 'blastermaster_job' if successful.

pydock3 blastermaster - new

If the above runs without error, then it's installed. Navigate to Blastermaster (pydock3 script) for instructions on how to use this software.

Note: requires Python>=3.8