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Python API for cpptraj: a data analysis package for biomolecular simulation

Project description

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A Python front-end of [cpptraj program] ( (a data analysis package for biomolecular simulation):

* [Features](#features)
* [Install](#install)
* [How to get started?](#how-to-get-started)
* [Contributors and Acknowledgement](#contributors-and-acknowledgement)
* [Citation](#citation)
* [Question/Suggestion?](#questionsuggestion)
* [nglview with pytraj in Jupyter notebook](#nglview-with-pytraj-in-jupyter-notebook)
* [Demo: Interactive data exploration with Jupyter notebook](#demo-interactive-data-exploration-with-jupyter-notebook)
* [License](#license)


- support more than 80 types of data analyses (rmsd, radgyr, autoimage, pca, clustering,...)
- read/write various file formats (.nc, .dcd, .trr, .pdb, .mol2, ...)
- fast (core codes were written in C++ and Cython)
- support parallel calculation with trivial installation (openmp, multiprocessing, mpi, ...)
- interactive analysis with large trajectory data that does not fit to memory
- [>> many more with comprehensive tutorials] (


- from source:

git clone
cd pytraj

# linux
python ./ install

# osx: not well tested (yet)
python ./ install --disable-openmp

- from conda (develop version for linux, osx): `conda install -c pytraj-dev`

- from AMBER suite distribution []( AMBER16 will be available soon (around April 2016).

- getting trouble? : [check our webpage](

How to get started?

- examples:

import pytraj as pt
traj = pt.iterload("", "top.parm7")
pt.rmsd(traj, ref=0, mask='@CA')
pt.dssp(traj, ':2-16')
- check our website: [] (

Contributors and Acknowledgement

[Please check here](./contributors/)


If you would like to acknowledge our work, please cite both ``cpptraj`` and ``pytraj`` papers

- [PTRAJ and CPPTRAJ] ( Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe and Thomas E. Cheatham, III
Journal of Chemical Theory and Computation 2013 9 (7), 3084-3095

- PYTRAJ: Interactive data analysis for molecular dynamics simulations. Hai Nguyen, Daniel R. Roe, Jason Swails, David A. Case. (2016)

* code issue and stuff relating directly to `pytraj`, create [Issue](
* ask question about data analysis in general, send email to [AMBER Mailing List] (

[nglview]( with pytraj in Jupyter notebook

[![pytraj website](./examples/figures/nglview.png)](

Demo: Interactive data exploration with [Jupyter notebook] (

[![pytraj website](./examples/progress_bar.gif)](

BSD 2-Clause

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