AgnesHH / pycpptraj

Cpptraj API for Python: Data Analysis for Biomolecular Simulations

Welcom to pycpptraj!

Aim: Write cpptraj wrapper for Python user

• Short term goal: expose cpptraj library to Python
• Very long term goal: glue most of useful library in [AMBER] (http://ambermd.org/) by Python:
  • tleap --> pyleap
  • paramfit --> pyparamfit
  • reduce --> pyreduce
  • ParmedTools
  • (add many more)
• Why using pycpptraj:
  • It's fast
    • it's a wrapper of cpptraj (was written in C++ (by Daniel R. Roe))
    • it has interface with numpy. Data calculation are performed without copying to numpy array
    • (but it actually does not need numpy at all, just optional)
  • It has clean syntax
    • Python/Cython style with fancy indexing
  • It has been extensively testes
  • It's flexible:
    • you can write extension modules in either high (Python) or low (C/C++ or Cython) level

Status: pre-release version 0.1

Citing (optional):

• cpptraj : [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

• pycpptraj : (in preparation)

Install

• install libcpptraj: ./installs/libcpptraj.txt
• installs pycpptraj: ./installs/pycpptraj.txt

Usage:

• Make sure to export LD_LIBRARY_PATH before using

  • export LD_LIBRARY_PATH=$AMBERHOME/lib/:$LD_LIBRARY_PATH
  • or export LD_LIBRARY_PATH=$CPPTRAJHOME/lib:$LD_LIBRARY_PATH

• Check ./examples/

Version I am working on:

• Ambertools 14
• Development version of cpptraj on github
• Python 2.7.8 :: Anaconda 2.1.0 (64-bit)
• Cython 0.21 and 0.22pre and development version of Cython
  • Development version: https://github.com/cython/cython