Installation

We recommend installing pAPRika in a fresh conda environment if possible. There are three ways to install this package:

Installing from Conda

To install the latest release of paprika from conda, run:

conda install -c conda-forge paprika

In order to use all features of paprika, you must either have AmberTools (http://ambermd.org/AmberTools.php) in your $PATH or separately install AmberTools with the command below if it is not already installed in your environment:

conda install -c conda-forge ambertools=22

Optional dependencies

If you want to run simulations with Plumed-based restraints (needed for running APR in GROMACS) you can compile Plumed from source or install through conda:

conda install -c conda-forge plumed

Although GROMACS is available in conda (Bioconda), a version that is patched with Plumed is currently not available. Therefore, if you want to run GROMACS simulations in paprika you will need to compile from source manually (patched with Plumed).

Installing a stable version from source

To install the a stable version of paprika download the source code from Github. Then, unzip the files and change to the paprika directory:

tar -xvzf paprika-version.tgz
cd pAPRika-version/

Change the name field in devtools/conda-envs/test_env.yaml to be paprika and create the environment:

conda env create -f devtools/conda-envs/test_env.yaml

Activate the environment:

conda activate paprika

and install paprika in the environment:

pip install .

Installing latest from source

To install paprika with the latest features, clone the repository from the master branch on Github:

git clone https://github.com/GilsonLabUCSD/pAPRika.git

Change directory to the paprika folder, change the name field in devtools/conda-envs/test_env.yaml to paprika and create the conda environment:

conda env create -f devtools/conda-envs/test_env.yaml

Activate the environment:

conda activate paprika

and install paprika in the environment:

pip install .