Currently the analysis code is monolithic, but debugging and experimentation could be made nicer by separating these pieces. There are 2 phases:
Compute BAR free energies for each transformation from foward and reverse works. This intermediate output could have a separate schema and be saved as JSON, for example.
Run DiffNet on the result of (1). User could have the option of running from stored JSON, or running the full pipeline including (1).
Currently the analysis code is monolithic, but debugging and experimentation could be made nicer by separating these pieces. There are 2 phases:
Compute BAR free energies for each transformation from foward and reverse works. This intermediate output could have a separate schema and be saved as JSON, for example.
Run DiffNet on the result of (1). User could have the option of running from stored JSON, or running the full pipeline including (1).