Skip to main content
This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!

Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis, VMD.

Project Description

Lightweight coordinate-only trajectory reader based on code from [GROMACS](http://www.gromacs.org/), [MDAnalysis](http://www.mdanalysis.org/) and [VMD](http://www.ks.uiuc.edu/Research/vmd/).

Used for coordinate retrieval in [MDSrv](https://github.com/arose/mdsrv) and [nglview](https://github.com/arose/nglview).

Should work with Python 2 and 3. If you experience problems, please file an [issue](https://github.com/arose/simpletraj/issues).

Installation

From PyPI:

pip install simpletraj

netCDF4

For reading .netcdf trajectory files the netCDF4 package is needed. As installing it can prove difficult, it is not a required package and must be installed separately.

If you use conda as your Python package manager:

conda install netcdf4

To install the NetCDF libraries and its Python package on debian/ubuntu:

sudo apt-get install libhdf5-serial-dev libnetcdf-dev pip install netCDF4

In case you get “ValueError: did not find HDF5 headers” try:

sudo su find / -name “libhdf5*.so*” # use what the above ‘find’ suggests to set ‘HDF5_DIR’ export HDF5_DIR=/usr/lib/i386-linux-gnu/hdf5/serial/ pip install netCDF4

Changelog

Version 0.4 and 0.5

  • FIX: Python 3 compatibility (iter/iteritems)

Version 0.3

  • FIX: DCD Python 2 compatibility

Version 0.2

  • ADD: package ready for PyPI
  • CODE: Python 3 compatibility
  • CODE: handle errors during offsets file reading/writing

Version 0.1

initial version (no release)

License

Generally GPL2, see the LICENSE file for details.

Release History

Release History

This version
History Node

0.5

History Node

0.4

History Node

0.3

History Node

0.2

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
simpletraj-0.5.tar.gz (87.7 kB) Copy SHA256 Checksum SHA256 Source Oct 5, 2016

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting