prolintpy 0.9.0

Automated analyis and visualization of lipid-protein interactions.

prolintpy

A python package for the automated analysis and visualization of Protein-Lipid interactions.

prolintpy is a lightweight python library that is used by the ProLint webserver on the backend. 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.

Installation

Getting prolintpy is quite simple, especially if you have conda installed.

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

and then install prolintpy using pip:

python -m pip install prolint 

Installing from source

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

# create new environment
conda create --name prolint python=3.7
# install dependencies
conda install -c conda-forge numpy pandas==0.24.0 mdtraj scipy pyyaml colorcet bokeh==1.4.0 networkx nglview==2.7.7 matplotlib jupyterlab

After that, you clone this directory and install it, using:

git clone https://github.com/bisejdiu/prolint.git
cd prolint
python setup.py install

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.

Data Files

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