SOAPify.HDF5er.HDF5erUtils
Simple submodule with support functions for SOAPify.HDF5er
Functions
|
Export a chunk of atom information in an h5py.Group |
|
Checks if the given group is a trajectory group |
|
Patch the non orthogonal box in the trajectory. |
- SOAPify.HDF5er.HDF5erUtils.exportChunk2HDF5(trajFolder, intervalStart, intervalEnd, boxes, coordinates)[source]
Export a chunk of atom information in an h5py.Group
- Parameters
trajFolder (h5py.Group) – the group in the hdf5 file
intervalStart (int) – the first frame to save within the group
intervalEnd (int) – the last frame to save within the group
boxes (list) – the list of the boxes, frame per frame (for each frame 6 floats representing the dimension and the angles of the box)
coordinates (list) – the list of the coordinates, frame per frame (for each frame a list that contains the coordinates of all atoms in that frame)
- SOAPify.HDF5er.HDF5erUtils.isTrajectoryGroup(trajGroup)[source]
Checks if the given group is a trajectory group
- Parameters
trajGroup (h5py.Group) – the group to check
- Returns
True if the group is a trajectory group, False otherwise
- Return type
- SOAPify.HDF5er.HDF5erUtils.patchBoxFromTopology(hdf5TrajFile, topologyFile)[source]
Patch the non orthogonal box in the trajectory.
This was a workaround for a __now solved__ bug in MDA, it can be used to change the box in a trajectory NOTE: this will only change the box, it will not modify the coordinates! NOTE: this function is not test covered and will be likely go deprecated soon