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


Keywords
ambermd, ambertools, interactive-analysis, molecular-dynamics, trajectory-analysis, visualization
License
GPL-3.0
Install
pip install pytraj==2.0.5

Documentation

Install | Features | How to get started? | Visualization

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pytraj website

PYTRAJ

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

Website: http://amber-md.github.io/pytraj

Features

  • support more than 80 types of data analyses (rmsd, radgyr, autoimage, pca, clustering,...)
  • read/write various file formats (.nc, .mdcrd, .dcd, .trr, .xtc, .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

Supported platforms: Linux, OSX

  • from AMBER suite distribution http://ambermd.org/.

  • from conda: conda install -c ambermd pytraj

  • from pip: pip install pytraj

  • from source code:

    git clone https://github.com/amber-md/pytraj
    cd pytraj
    
    python setup.py install
    
    # Note: openmp will be turned off in OSX.
    
    # AMBER user: overwrite pytraj in $AMBERHOME
    python setup.py install --prefix=$AMBERHOME
  • getting trouble? : check our webpage

How to get started?

Contributors and Acknowledgement

Please check here

Citation

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

something like:

"...used pytraj [1], a Python package binding to cpptraj program [2]"
  • [1] PYTRAJ: Interactive data analysis for molecular dynamics simulations. Hai Nguyen, Daniel R. Roe, Jason Swails, David A. Case. (2016)

  • [2] [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

Question/Suggestion?

nglview with pytraj in Jupyter notebook

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

pytraj website

License

GPL v3 (since pytraj is derived work of cpptraj)

But if you would like to reuse code snippets and pieces independent of cpptraj, I am (Hai) happy to license them (pieces of codes) under BSD-2 Clause or whatever you like. Just buzz us.