Dumping a Transformation to JSON#

If you’re trying to run a full campaign of simulations representing an alchemical network, we generally recommend saving objects using our storage tools, when avoids saving duplicate information to disk.

However, there are situations where it is reasonable to serialize a single Transformation. For example, this can be useful when trying to compare results run on different machines. This also provides a trivial way for a user to run edges in parallel, if they don’t want to use the more sophisticated techniques we have developed.

For these cases, we have made it very easy for a user to dump a transformation to JSON. Simply use the method Transformation.dump(). This can take a filename (pathlike) or an already-opened file object. For example:


Be aware this this is not designed to be space-efficient. That is, if you have the same object in memory used in two locations (for example, the same ProteinComponent is in both ChemicalSystems), then there will be a copy for each. This is particularly problematic if you are running an entire network of calculations; in that case, dumping transformation by transformation is not the most efficient way to prepare your simulations.

When you do dump a single transformation, it can be reloaded into memory with the Transformation.load() method:

transformation = Transformation.load("mytransformation.json")

Once you’ve saved to it JSON, you can also run this transformation with the openfe command line tool’s quickrun command, e.g.:

$ openfe quickrun mytransformation.json -d dir_for_files -o output.json