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IDPEnsembleTools : an open-source library for analysis of conformational ensembles of disordered proteins
IDPensembleTools is a python package by which you can load and analyze multiple conformational ensembles in different formats such as (pdb, xtc,dcd,...)
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.
- 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- Recommend specific version of Python
- Point to the dependencies (Numpy, Sklearn, pandas, matplotlib, mdtraj, ...)
For details, you can check our user-centric documentation, is generated from our repository using Sphinx.
The link to the publication should be put here.
MIT License
