Overview¶

Why bother using pytraj?¶

If you want to extend cpptraj’s functionanity to Python eco-system such as numpy, scipy, pandas, sklearn and many more. Check some examples here

What does pytraj offer?¶

• support many types of analysis

• support parallel processing

• able to handle many files at the same time

• able to handle very large trajectory

• simple (and fast) calculation:

  import pytraj as pt
  traj = pt.iterload('traj.nc', 'my_parm.top')
  pt.radgyr(traj)
  

• include many cpptraj features

  • automatic file detection by its content
  • smart autoimage function for PBC simulation.
  • ... (to be filled soon)

• able to be used in other langues, such as Julia

How to get started¶

• check installation
• learn in 5 minutes
• general concept
• check a list of things pytraj/cpptraj can do

Contributors¶

A list of contributors

Citations¶

if you find this project useful and would like to acknowledge our works, 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 (https://github.com/Amber-MD/pytraj), Hai Nguyen, Daniel R. Roe, Jason Swails, David A. Case (2015) (in preperation)

Contact¶

We always welcome your contribution, including (but not limited to) adding new code, bug report, suggestion about website, doc, ... or anything that comes up. Feel free to contact us. Even you do not like pytraj or some of its features, just tell us so we can make it better. Cheers.

• For bug reports, feature requests, code discussion ... please use the GitHub issue tracker
• For scientific discussion please send email to amber
• For things that directly related to cpptraj, please open issue here