- 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
- It's fast
-
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 libcpptraj: ./installs/libcpptraj.txt
- installs pycpptraj: ./installs/pycpptraj.txt
-
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/
- 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