As explained in
the metadata
section, you can attach custom metadata to almost every Atoms entity.
You can add metadatas to your joints is by adding new attributes on them. You can do it when exporting both a skeleton definition and an animation clip file (fbx or atomsclip).
Any attribute with a name starting with "atoms_" that you add to a joint in Maya will be added as a new metadata to that joint in your skeleton definition or animation clip.
For instance, if you were to add an attribute named atoms_testAttribute, an integer metadata named "testAttribute" will be added to your joint in the skeleton definition.
You would then be able to access it in python or C++ during the simulation and perform some specific action for that joint only.
You could also animate that attribute and export it in your animation clips.
