Skip to content

Latest commit

 

History

History
48 lines (39 loc) · 2.14 KB

README.md

File metadata and controls

48 lines (39 loc) · 2.14 KB
Raw

Environment setup

Install via Docker

With a Linux Debian server, it is highly recommended to set up the environment via docker, since all you need to do is a simple make command.

cd ./docker
make

Note

  • The make will automatically build the docker image and run the container, inside which your host home directory will be mounted to ${HOME}/home. The docker image supports running any command inside a tmux session.
  • If make exits with error messages with pip, try make again in case of any network connection timeout.
  • Once make succeeds, note that exiting from container wound't stop it, nor the tmux sessions running within. To enter an existing container, simply run make again. If you need to stop this container, run make kill.
  • For customized environment setup, please refer to files docker/Dockerfile, docker/asset/requirements.txt and docker/asset/apt_packages.txt.
  • If your bash does not highlight properly, try sh -c "$(wget https://raw.github.com/ohmyzsh/ohmyzsh/master/tools/install.sh -O -)" to reinstall zsh template.
  • PoseCheck should be manually installed. See instructions below.

Install via Conda

You can also build your own environment through conda env create -f environment.yml. Here the main packages are listed:

Package Version
CUDA 11.6
NumPy 1.23.1
Python 3.9
PyTorch 1.12.0
PyTorch Geometric 2.1.0
RDKit 2023.9.5

For evaluation, you will need to install vina (affinity), posecheck (clash, strain energy, and key interactions), and spyrmsd (rmsd).

# for vina docking
pip install meeko==0.1.dev3 scipy pdb2pqr vina==1.2.2 
python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3

# for posecheck evaluation
git clone https://github.com/cch1999/posecheck.git
cd posecheck
git checkout 57a1938  # the calculation of strain energy used in our paper
pip install -e .
pip install -r requirements.txt
conda install -c mx reduce

# for spyrmsd
conda install spyrmsd -c conda-forge