Install | Features | How to get started? | Visualization
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
- 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)
Supported platforms: Linux, OSX
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from AMBER suite distribution http://ambermd.org/.
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from conda:
conda install -c ambermd pytraj -
from pip:
pip install pytraj -
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 $AMBERHOME python setup.py install --prefix=$AMBERHOME
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getting trouble? : check our webpage
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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)
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check our website: [http://amber-md.github.io/pytraj] (http://amber-md.github.io/pytraj)
If you would like to acknowledge our work, please cite both cpptraj and pytraj papers.
something like:
"...used pytraj [1], a Python package binding to cpptraj program [2]"
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[1] PYTRAJ: Interactive data analysis for molecular dynamics simulations. Hai Nguyen, Daniel R. Roe, Jason Swails, David A. Case. (2016)
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[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
- 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/)
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.