Amber-MD / pytraj

Install | Features | How to get started? | Visualization

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
• Install
• How to get started?
• Contributors and Acknowledgement
• Citation
• Question/Suggestion?
• nglview with pytraj in Jupyter notebook
• Demo: Interactive data exploration with Jupyter notebook
• License

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

• The best way is to install AmberTools via conda: conda install -c conda-forge ambertools compilers (https://ambermd.org/GetAmber.php)

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

• from conda: conda install -c ambermd pytraj # Outdated versions, not support python >= 3.9

• from pip: pip install pytraj # Outdated versions, not support python >= 3.9

• 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 $AMBERHOME
  # For expert user only
  python setup.py install --prefix=$AMBERHOME

• Getting trouble? : check our webpage

How to get started?

• examples:

  import pytraj as pt
  traj = pt.iterload("data.nc", "top.parm7")
  pt.rmsd(traj, mask='@CA', ref=0)
  pt.dssp(traj, mask=':2-16')
  pt.pca(traj, mask='!@H=', n_vecs=2)

• check our website: [http://amber-md.github.io/pytraj] (http://amber-md.github.io/pytraj)

Contributors and Acknowledgement

Please check here

Citation

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

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?

• code issue and stuff relating directly to pytraj, create Issue
• ask question about data analysis in general, send email to [AMBER Mailing List] (http://lists.ambermd.org/mailman/listinfo/amber)

nglview with pytraj in Jupyter notebook

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

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.