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ferchault / iago

Implicit Archiver for Generated Observables
MIT License
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Link gromacs toolchain #11

Open ferchault opened 7 years ago

ferchault commented 7 years ago

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:

  1. Understand the gromacs input requirements (guidance available).
  2. Write a python code to convert the file formats (using the MDAnalysis library).
  3. Write a wrapper for the various gromacs tools exposing their command line options in a python interface.
  4. Convert their output to the iago internal database structure.