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IMP Manual  develop.374319d7bb,2024/06/17
Serialization

Most IMP types can be serialized - that is, the internal state of an object, such as the values of its member variables, can be written to or read in from a file, string or stream. This allows for individual objects or an entire IMP run to be saved and later restored, or to be sent from one machine to another. In Python, the objects can be loaded or saved using the pickle module.

Serialization uses a compact binary format. However, it is not heavily optimized for size. If a smaller file size is desired, the Python pickle file can be compressed with a general-purpose compression tool such as gzip.

Note that IMP::Model is handled specially due to its large size. Objects that refer to the model (such as restraints or particles) will only include the ID of the model in the serialization stream, not the model itself. On deserialization these objects will be reassociated with the model by matching the ID. This requires that the model be deserialized before any of these other objects. To ensure this, pickle a tuple, list, or other ordered Python container containing the model before any other object.

Serialization relies on the excellent cereal library, which is required to build IMP.

To add serialization to a new class, simply add a suitable serialization function, as per the cereal docs. Most IMP classes define a serialize private method. The class will also need a default constructor (i.e. one that takes no arguments) if it does not already have one. If the class is visible to Python, make sure pickle support is enabled by using the IMP_SWIG_OBJECT_SERIALIZE or IMP_SWIG_VALUE_SERIALIZE macros in the SWIG interface.

If a class is polymorphic - i.e. it is a subclass that is referenced somewhere by a base class pointer, such as a Restraint subclass - then the serialization subsystem will need to store the name of the subclass in the serialized output and will need to know how to access derived class information. This is done by adding the IMP_OBJECT_SERIALIZE_DECL and IMP_OBJECT_SERIALIZE_IMPL macros to the .h file and .cpp file respectively. (These macros are used instead of cereal's CEREAL_REGISTER_TYPE macro.)

The serialization format is subject to change. It should not be considered portable between different machines (e.g. 32-bit and 64-bit, or Linux and Windows) or between different IMP versions, although this could be addressed in future if necessary.