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https://amber-md.github.io/pytraj/

Python interface of cpptraj
https://amber-md.github.io/pytraj/

ambermd ambertools interactive-analysis molecular-dynamics trajectory-analysis visualization

Last synced: 2 months ago
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Python interface of cpptraj

Host: GitHub
URL: https://amber-md.github.io/pytraj/
Owner: Amber-MD
Created: 2015-02-02T22:46:17.000Z (over 9 years ago)
Default Branch: master
Last Pushed: 2024-02-02T01:06:42.000Z (5 months ago)
Last Synced: 2024-04-17T06:02:53.096Z (2 months ago)
Topics: ambermd, ambertools, interactive-analysis, molecular-dynamics, trajectory-analysis, visualization
Language: Jupyter Notebook
Homepage: https://amber-md.github.io/pytraj
Size: 526 MB
Stars: 159
Watchers: 17
Forks: 38
Open Issues: 34
Metadata Files:
- Readme: README.md
- Changelog: changes.rst
- License: licenses/README

Lists

awesome-molecular-dynamics - PyTraj - A Python front-end of [CppTraj](https://github.com/Amber-MD/cpptraj). (Trajectory Analysis)

README

        [Install](#install) | [Features](#features) | [How to get started?](#how-to-get-started) | [Visualization](#nglview-with-pytraj-in-jupyter-notebook)

[![Build status](https://github.com/Amber-MD/pytraj/actions/workflows/python-package-conda.yml/badge.svg)](https://github.com/Amber-MD/pytraj/actions/workflows/python-package-conda.yml)

[![Coverage Status](https://coveralls.io/repos/Amber-MD/pytraj/badge.svg?branch=master&service=github)](https://coveralls.io/github/Amber-MD/pytraj?branch=master)

[![pytraj website](./examples/figures/pytraj.gif)](http://amber-md.github.io/pytraj/latest/index.html)

PYTRAJ 

------

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](#features)

* [Install](#install)

* [How to get started?](#how-to-get-started)

* [Contributors and Acknowledgement](#contributors-and-acknowledgement)

* [Citation](#citation)

* [Question/Suggestion?](#questionsuggestion)

* [nglview with pytraj in Jupyter notebook](#nglview-with-pytraj-in-jupyter-notebook)

* [Demo: Interactive data exploration with Jupyter notebook](#demo-interactive-data-exploration-with-jupyter-notebook)

* [License](#license)

Features

--------

- 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)

Install

-------

Supported platforms: Linux, OSX

- The best way is to install `AmberTools` via conda: `conda install -c conda-forge ambertools compilers` (https://ambermd.org/GetAmber.php)

- from AMBER suite distribution [http://ambermd.org/](http://ambermd.org/#AmberTools).

- from conda: `conda install -c ambermd pytraj` # Outdated versions, not support python >= 3.9

- from pip: `pip install pytraj` # Outdated versions, not support python >= 3.9

- from source code:

    ```bash

    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

    # For expert user only

    python setup.py install --prefix=$AMBERHOME

    ```

- Getting trouble? : [check our webpage](http://amber-md.github.io/pytraj/latest/installation.html)

How to get started?

------------------

- examples: 

    ```python

    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)

    ```

- check our website: [http://amber-md.github.io/pytraj] (http://amber-md.github.io/pytraj)

Contributors and Acknowledgement

--------------------------------

[Please check here](./contributors/)

Citation

--------

If you would like to acknowledge our work, please cite both ``cpptraj`` and ``pytraj``.

Something like: 

    "...used pytraj [1], a Python package binding to cpptraj program [2]"

- [1] PYTRAJ: Interactive data analysis for molecular dynamics simulations. Hai Nguyen, Daniel R. Roe, Jason Swails, David A. Case. (2016)

- [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 

Question/Suggestion?

--------------------

* code issue and stuff relating directly to `pytraj`, create [Issue](https://github.com/pytraj/pytraj/issues)

* ask question about data analysis in general, send email to [AMBER Mailing List] (http://lists.ambermd.org/mailman/listinfo/amber)

[nglview](https://github.com/arose/nglview) with pytraj in Jupyter notebook

---------------------------------------

Demo: Interactive data exploration with [Jupyter notebook] (http://jupyter.org/)

--------------------------------------------------------------------------------

[![pytraj website](./examples/figures/progress_bar.gif)](http://amber-md.github.io/pytraj/latest/index.html)

License

-------

GPL v3 (since pytraj is derived work of [cpptraj](https://github.com/Amber-MD/cpptraj/blob/master/LICENSE))

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.