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
• 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

• 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)

• from source:

  git clone https://github.com/amber-md/pytraj
  cd pytraj
  
  # linux
  python ./setup.py install
  
  # osx: pytraj will use clang to compile cython extension.
  # if you want to change compiler, please check setup.py file
  python setup.py install --disable-openmp
  # Note: pytraj will install the most updated cpptraj. We recommend to have netcdf library.

• from conda (develop version for linux): conda install -c ambermd pytraj-dev

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

• getting trouble? : check our webpage

• examples:

  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)

Please check here

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)

• 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)

BSD 2-Clause