Skip to main content

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

Project description

[![Build Status](https://travis-ci.org/Amber-MD/pytraj.svg?branch=master)](https://travis-ci.org/Amber-MD/pytraj)
[![Binstar Badge](https://binstar.org/ambermd/pytraj-dev/badges/version.svg)](https://binstar.org/ambermd/pytraj-dev/)
[![Coverage Status](https://coveralls.io/repos/Amber-MD/pytraj/badge.svg?branch=master&service=github)](https://coveralls.io/github/Amber-MD/pytraj?branch=master)
[![Binder](http://mybinder.org/images/logo.svg)](http://mybinder.org/repo/hainm/notebook-pytraj)

PYTRAJ
------
A Python front-end of [cpptraj program] (https://github.com/Amber-MD/cpptraj) (a data analysis package for biomolecular simulation): http://amber-md.github.io/pytraj

* [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)


Features
--------

- 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] (http://amber-md.github.io/pytraj)


Install
-------

- from source:

```bash
git clone https://github.com/amber-md/pytraj
cd pytraj

# linux
python ./setup.py install

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

- from conda (develop version for linux, osx): `conda install -c https://conda.anaconda.org/ambermd pytraj-dev`

- from AMBER suite distribution [http://ambermd.org/](http://ambermd.org/). AMBER16 will be available soon (around April 2016).

- getting trouble? : [check our webpage](http://amber-md.github.io/pytraj/latest/installation.html)


How to get started?
------------------

- examples:

```python
import pytraj as pt
traj = pt.iterload("data.nc", "top.parm7")
pt.rmsd(traj, ref=0, mask='@CA')
pt.dssp(traj, ':2-16')
```
- check our website: [http://amber-md.github.io/pytraj] (http://amber-md.github.io/pytraj)

Contributors and Acknowledgement
--------------------------------

[Please check here](./contributors/)

Citation
--------

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

- [PTRAJ and CPPTRAJ] (http://pubs.acs.org/doi/abs/10.1021/ct400341p): 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)

Question/Suggestion?
--------------------
* code issue and stuff relating directly to `pytraj`, create [Issue](https://github.com/pytraj/pytraj/issues)
* ask question about data analysis in general, send email to [AMBER Mailing List] (http://lists.ambermd.org/mailman/listinfo/amber)

[nglview](https://github.com/arose/nglview) with pytraj in Jupyter notebook
---------------------------------------

[![pytraj website](./examples/figures/nglview.png)](http://amber-md.github.io/pytraj/latest/index.html)

Demo: Interactive data exploration with [Jupyter notebook] (http://jupyter.org/)
--------------------------------------------------------------------------------

[![pytraj website](./examples/progress_bar.gif)](http://amber-md.github.io/pytraj/latest/index.html)


License
-------
BSD 2-Clause

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pytraj, version 1.0.1
Filename, size File type Python version Upload date Hashes
Filename, size pytraj-1.0.1.tar.gz (29.5 MB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page