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.
1 maintainer
Metadata
1 maintainer
Release files for simpletraj 0.5
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