From Atoms 3.2 you can create your ragdoll setup files with the ragdoll builder.

The tool is accessible via the Atoms Menu: Atoms > Tools > Ragdoll builder

The first thing to do is to import an atoms skeleton as well as a skin geometry. The latter is optional, but it will give you a good sense of the mesh volume while you edit your rigid bodies.

You can use Q (Select), W (translate), E (Rotate) and R (Scale) shortcuts while using this window.

Select the joints that will need to be associated with a rigid body and press the shelf button .

Edit your rigid bodies so that they match the skin mesh volume, select the ones that will need to have a constraint then press the shelf button to create them.

You can copy-paste the dynamic attributes from the rigid body and constraints using the menu actions: Edit > Copy Attributes and Paste Dynamic Attributes. Alternatively, you can also use the CTRL+C and CTRL+V shortcuts.

To test your ragdoll within this tool, press the play button and see the result. While the simulation is playing, you can left-click and drag any rigid body to apply a force on your ragdoll.

Once you are happy with your setup, export it and use the file to configure the agent type in your host application.