idpet 0.1.0

A Python package for analysis of conformational ensembles of intrinsically disordered proteins

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IDPEnsembleTools : an open-source library for analysis of conformational ensembles of disordered proteins

Overview

IDPensembleTools is a python package by which you can load and analyze multiple conformational ensembles in different formats such as (pdb, xtc,dcd,...)

Features

With IDPensembleTools, you can:

• Extract and visualize global features of structural ensembles such as (Rg, Asphericity, Prolateness, End to end distance,...)
• Extract and visualize local features of structural ensembles sucha as ( intera-atomic distances, phi-psi angles , alpha-helix content, ...)
• Performing dimensionality reduction methods (PCA, UMAP, t-SNE) on different extracted features of structural ensemble
• Comparing structural ensembles of disordered proteins using different similarity scores such as Kullback-Leibler (KL) and Jensen-Shannon (JS) divergence methods and visualize similarity matrix

For details, you can check our user-centric documentation , put the link to the documentation, is generated from our repository using Sphinx.

Installation

• Using pip: Using python package managment systme "pip" you can easily install IDPensembleTools (and its dependencies if needed), upgrade or uninstall with just one terminal command.

pip install idpet
pip install --upgrade idpet
pip uninstall idpet

• From source:

git clone https://github.com/hamidrgh/EnsembleTools.git
cd EnsembleTools
python setup.py install

Python Requirements and Dependencies

• Recommend specific version of Python
• Point to the dependencies (Numpy, Sklearn, pandas, matplotlib, mdtraj, ...)

Documentation

For details, you can check our user-centric documentation, is generated from our repository using Sphinx.

Citation

The link to the publication should be put here.

License

MIT License