Atoms currently supports only cloth in Maya, although it can be visualized and rendered in Houdini too.
The cloth cache files are generated in a post process and you will need a cache sequence file as input.
Please have a look at this tutorial to know more.
Cloth tools
Cloth setup
The Cloth Setup tool allows you to tag variation meshes as "hidden". You can access the tool via the Atoms menu: Atoms > Tools > Cloth > Cloth Setup
Hidden meshes will be added to your variations, but won't be rendered or displayed in the viewport by the Atoms Proxy.
They will only used when generating cloth caches, you would usually tag nRigid meshes as hidden if they are not meshes used at render time.
The Cloth Setup UI lets you tag, untag and select all hidden meshes.
Constraints
Currently only the "Component", "Component to Component" and "Point to Surface" constraints are supported.
Once you have created your nCloth setup in your variation scene, the variation builder will take care of exporting it alongside your variations.