Installation and Quick Start

DynaBench package is compatible with all operating systems. The package requires Python with version 3.8 or higher, and Anaconda3 distributor.

System Dependencies

• python3 (3.8 or higher)

• Anaconda3

Python Dependencies

• ipywidgets

• ipykernel

• pdbfixer

• seaborn

• mdanalysis

• jsonpickle

• moviepy

• matplotlib

• pdb-tools

• freesasa

• nglview

Installation

We recommend you use git clone instead of download with .zip while installing the package. Downloading with .zip may cause problems in test pdbs Because test folders contain large files, there may be errors during cloning the repository. To avoid these possible error you can install GIT-LFS. To install git-lfs, please visit https://git-lfs.com/.

Clone the repository

git clone https://github.com/Atakanzsn/DynaBench.git

cd DynaBench

Create DynaBench environment

conda env create -f requirements.txt

conda activate DynaBench

Create IpyKernel for DynaBench

python -m ipykernel install --user --name dynabench

Build the DynaBench

python setup.py build
python setup.py install

Build FoldX for Energy Analysis

DynaBench uses FoldX for energy analysis. You should download FoldX by yourself. While running Residue-Based analysis, you should give FoldX executable path to the function.

Tests

Please run the jupyter notebooks in the tests folder to test the package. They will create folders with tests at the end. Check outputs with the folder without the tests at the end. Outputs should be identical.