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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.

Project details


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