added flag to save json log file and improved trajectory preparation

Degiacomi-Lab / molearn

protein conformational spaces meet machine learning

https://degiacomi.org/software/molearn/

GNU General Public License v3.0

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Closed gwirn closed 2 months ago

gwirn commented 2 months ago

Moves the imaging (applying periodic boundary conditions) in front of saving the new topology. Furthermore, if imaging fails it tries a fallback solution by supplying an anchor molecule. Additionally it aligns all frames to the first frame of the trajectory.
Adds a flag to the Trainer class to be able to save the unformatted json strings to a log file.