prolintpy 0.9.1

Automated analyis and visualization of lipid-protein interactions.

A python package for the automated analysis and visualization of lipid-protein interactions.

prolintpy is a lightweight python library that is used by the ProLint webserver on the backend to analyze Protein-Lipid interactions.. Use this tool if you want to customize analysis and visualization of lipid-protein interactions and want to scale-up your workflow beyond the capabilities of the ProLint webserver.

To get familiar with prolintpy please read the Documentation. You can also launch the binders: and test prolintpy without having to install it. We provide several tutorials in the form of these binders that you can complete in your browser. Please note, however, that these tutorials are still work in progres and we will improve them during the coming days. If you would like to download the tutorials they are located here: https://github.com/ProLint/tutorials

Installation

To install prolintpy simply execute:

python -m pip install prolintpy

This should work on most systems. On Windows and even WSL 1, MDTraj may present a problem to install. In that case, you may want to use conda to install MDTraj first:

# create new environment
conda create --name prolint python=3.7
conda install -c conda-forge mdtraj
python -m pip install prolintpy

Installing from source

If you want to install directly from the github repository then you can do that by typing:

git clone https://github.com/ProLint/prolintpy.git
cd prolintpy
python setup.py install

If you are using Windows, the same thing mentioned above applies.

Getting Started

Please follow the instructions provided in the documentation to get started. Note that, to use the visualization interface of prolintpy, you should use JupyterLab. At the top of your notebook file, make sure to call the output_notebook function:

from bokeh.io import output_notebook
output_notebook()

Additionally, if you want to use the show_contact_projection function, make sure that your installation of nglview is working properly. Follow the instruction provided there to ensure your installation is running correclty.

Input file requirements

Before you load the data to prolintpy make sure to first remove water & ions beads. Leave only membrane and protein beads in the system.