Since we're going to start running some complicated networks or adding forward and reverse transformations, this is the point where it is urgent to analyze all the edges and compute absolute free energies for individual compounds using the MLE from DiffNet. We should do that after transitioning to the new JSON data model (https://github.com/choderalab/covid-moonshot-infra/issues/32) since that will make managing compounds a lot easier, but it's critical we get the code example to do this before @hannahbrucemacdonald leaves since she's the expert on her https://github.com/openforcefield/arsenic code that implements this.
Since we're going to start running some complicated networks or adding forward and reverse transformations, this is the point where it is urgent to analyze all the edges and compute absolute free energies for individual compounds using the MLE from DiffNet. We should do that after transitioning to the new JSON data model (https://github.com/choderalab/covid-moonshot-infra/issues/32) since that will make managing compounds a lot easier, but it's critical we get the code example to do this before @hannahbrucemacdonald leaves since she's the expert on her https://github.com/openforcefield/arsenic code that implements this.