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pytraj

Python interface of cpptraj

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

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: acs.org
  • ✓
    Committers with academic emails
    2 of 18 committers (11.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.5%) to scientific vocabulary

Keywords

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

Keywords from Contributors

computational-chemistry drug-discovery mdanalysis molecular-dynamics-simulation molecular-simulation
Last synced: 6 months ago · JSON representation

Repository

Python interface of cpptraj

Basic Info
Statistics
  • Stars: 182
  • Watchers: 17
  • Forks: 38
  • Open Issues: 43
  • Releases: 22
Topics
ambermd ambertools interactive-analysis molecular-dynamics trajectory-analysis visualization
Created about 11 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

Install | Features | How to get started? | Visualization

Build status Coverage Status

pytraj website

PYTRAJ

A Python front-end of cpptraj program (a data analysis package for biomolecular simulation).

Website: http://amber-md.github.io/pytraj

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

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/.

  • from conda: conda install -c ambermd pytraj # Outdated versions, not support python 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  • from pip: pip install pytraj # Outdated versions, not support python 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

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

Contributors and Acknowledgement

Please check here

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: 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
  • ask question about data analysis in general, send email to AMBER Mailing List

nglview with pytraj in Jupyter notebook

Demo: Interactive data exploration with Jupyter notebook

pytraj website

License

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.

Owner

  • Name: Amber Molecular Dynamics
  • Login: Amber-MD
  • Kind: organization
  • Email: amber@ambermd.org

For experienced Amber users: development versions of some parts of AmberTools

GitHub Events

Total
  • Issues event: 6
  • Watch event: 9
  • Delete event: 13
  • Issue comment event: 16
  • Push event: 63
  • Pull request event: 19
  • Create event: 12
Last Year
  • Issues event: 6
  • Watch event: 9
  • Delete event: 13
  • Issue comment event: 16
  • Push event: 63
  • Pull request event: 19
  • Create event: 12

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 4,831
  • Total Committers: 18
  • Avg Commits per committer: 268.389
  • Development Distribution Score (DDS): 0.127
Past Year
  • Commits: 11
  • Committers: 4
  • Avg Commits per committer: 2.75
  • Development Distribution Score (DDS): 0.545
Top Committers
Name Email Commits
Hai Nguyen h****p@g****m 4,218
mdtools n****n@g****m 302
Hai Nguyen h****m 252
Jason Swails j****s@g****m 16
Daniel R. Roe d****e@g****m 14
c56pony n****r@g****m 8
c56pony 4****y 4
Jamie Smith s****9@u****u 3
Erik Cederstrand e****k@c****k 2
hichiaty h****y 2
Jamie Smith j****h@c****m 2
sastrys1 9****1 2
envirodug e****g 1
Cody c****y@q****m 1
Rocco Meli r****i@b****h 1
Ray Luo r****o@d****u 1
hongbo-zhu-cn h****n@g****m 1
Hai Nguyen h****t@H****l 1
Committer Domains (Top 20 + Academic)
dhcp-204146.bio.uci.edu: 1 bluemail.ch: 1 quantifiedcode.com: 1 crackofdawn.onmicrosoft.com: 1 cederstrand.dk: 1 usc.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 98
  • Total pull requests: 54
  • Average time to close issues: 6 months
  • Average time to close pull requests: 23 days
  • Total issue authors: 60
  • Total pull request authors: 6
  • Average comments per issue: 5.19
  • Average comments per pull request: 1.17
  • Merged pull requests: 35
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 12
  • Average time to close issues: 7 months
  • Average time to close pull requests: 11 days
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 1.4
  • Average comments per pull request: 0.33
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • hainm (17)
  • pindakaas42 (5)
  • tuckerburgin (4)
  • drroe (3)
  • TianmingQu (3)
  • d-beltran (2)
  • thepoole (2)
  • Manish315 (2)
  • ursulap (2)
  • krlitros87 (2)
  • khoroshyy (2)
  • markperri (2)
  • cloudella48 (2)
  • hmayes (2)
  • igordub (2)
Pull Request Authors
  • hainm (55)
  • drroe (12)
  • sastrys1 (3)
  • DrDomenicoMarson (2)
  • hichiaty (1)
  • hai-schrodinger (1)
Top Labels
Issue Labels
bug (8) new_options (3) improvement (2) doc (2) Tutorial (1) installation (1) help wanted (1) cpptraj_change (1)
Pull Request Labels
cpptraj_change (3) Tests (2)

Packages

  • Total packages: 3
  • Total downloads:
    • pypi 712 last-month
  • Total docker downloads: 371
  • Total dependent packages: 3
    (may contain duplicates)
  • Total dependent repositories: 20
    (may contain duplicates)
  • Total versions: 26
  • Total maintainers: 1
pypi.org: pytraj

Python API for cpptraj: a data analysis package for biomolecular simulation

  • Versions: 14
  • Dependent Packages: 3
  • Dependent Repositories: 20
  • Downloads: 712 Last month
  • Docker Downloads: 371
Rankings
Docker downloads count: 2.1%
Dependent packages count: 3.2%
Dependent repos count: 3.2%
Average: 4.8%
Stargazers count: 5.8%
Forks count: 6.4%
Downloads: 8.4%
Maintainers (1)
pycpptraj
Last synced: 6 months ago
proxy.golang.org: github.com/amber-md/pytraj
  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/Amber-MD/pytraj
  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago

Dependencies

environment.yml conda
  • cython
  • mock
  • netcdf4
  • numpy
  • parmed
  • pyflakes
  • pytest
conda-requirements.txt pypi
  • conda =4.3.25
  • hdf4 =4.2.12
  • libnetcdf =4.4.1
pip-requirements.txt pypi
  • cython ==0.29.16
  • mock ==2.0.0
  • numpy *
  • parmed *
  • pyflakes ==2.1.1
  • pytest *
setup.py pypi
  • numpy *
.github/workflows/python-package-conda.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite