For analysing atomistic trajectories, the gromacs code has well-tested and fast C++ implementations. We should leverage this by converting our trajectory data to their format (there are open-source libraries for that) and then feed it to their toolchain. Finally, the output (plain-text) has to be parsed back for storage in the database.
Steps:
Understand the gromacs input requirements (guidance available).
Write a python code to convert the file formats (using the MDAnalysis library).
Write a wrapper for the various gromacs tools exposing their command line options in a python interface.
Convert their output to the iago internal database structure.
For analysing atomistic trajectories, the gromacs code has well-tested and fast C++ implementations. We should leverage this by converting our trajectory data to their format (there are open-source libraries for that) and then feed it to their toolchain. Finally, the output (plain-text) has to be parsed back for storage in the database.
Steps: