Installation

PELE Platform is shipped as a Conda package that can be installed using conda-forge and nostrumbiodiscovery channels from Anaconda.

Requirements

• Miniconda3 or Conda package

• Schrödinger Suite (2017-1 or later)

• PELE++ code (optional, only required to run PELE but not to run PELE Plotter or the Analysis package)

OS support

Currently, the platform only supports Linux and MacOS operating systems.

Conda installation

The most straightforward way to install the Platform is with Conda. The preferable installation strategy is to generate a new Conda environment to hold the source code and its dependencies. In order to generate a Conda environment and install the Platform, please, follow the steps below:

# Create a new conda environment from scratch:
conda create -n pele_platform

# Activate the new conda environment:
conda activate pele_platform

# Install Python 3.8:
conda install -c conda-forge python=3.8

# Install PELE Platform 1.6.4
conda install -c nostrumbiodiscovery -c conda-forge pele_platform=1.6.4

# Export environment variables
export PELE=/path/to/PELE-1.X/
export SCHRODINGER=/path/to/schoringer/20XX/
export PELE_LICENSE=/path/to/pele/licenses/

For more information on setting up your environment and licenses, see Environment Variables

Singularity

We have several ways available to run pele_platform from Singularity containers. This method is ideal for running pele_platform and PELE software on HPC systems.

If you are interested in learning more about it, please contact it@nostrumbiodiscovery.com.

Test installation

git clone https://github.com/nostrumbiodiscovery/pele_platform.git

cd pele_platform/tests

conda activate pele_platform

python -m pele_platform.main ../pele_platform/Examples/induced_fit/input_fast.yaml