Lightweight coordinate-only trajectory reader based on code from GROMACS, MDAnalysis and VMD.
Used for coordinate retrieval in MDSrv and nglview.
Should work with Python 2 and 3. If you experience problems, please file an issue.
From PyPI:
pip install simpletraj
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
- FIX: Python 3 compatibility (iter/iteritems)
- FIX: DCD Python 2 compatibility
- ADD: package ready for PyPI
- CODE: Python 3 compatibility
- CODE: handle errors during offsets file reading/writing
initial version (no release)
Generally GPL2, see the LICENSE file for details.