The Animation Retargeting in Atoms is possible thanks to the characterization of the Agent Types.
A characterization consists of tagging the joint chains of the skeleton by type, subtype, position and posing the rig in a reference pose.

Atoms will transfer the animation of the chains with the same tag set if any matching chain is found during the simulation .

You should always start this process from the scene that you used for exporting the agent type.
Before configuring the joint chains, users should pose the rig in the reference pose, normally the T-pose. Make sure that all the characterization files of your agents (sources and targets) are exported fitting the same reference pose: the more similar the reference poses, the better the retargeting is going to work.

All joints not belonging to a chain will not be considered during the retargeting process.

You have different tags that you can use, as explained below.

The tag type can have the following values:

• root, the skeleton root

• spine, any spine in your character

• clavicle, any clavicle joint, usually one joint only

• pelvis, the chains from the skeleton root to the first joint of the legs (only if you have joints in between)

• limb, the legs or arms

• effector, effector chain only transfer the rotations taking into account the offset from the reference pose.

Root and effector types transfer rotations between characters. 
Clavicle, pelvis, limb and spine also transfer rotations if the chain has less than two joints otherwise, they use an IK algorithm.

Other tags:

• subtype: only applies to limbs and effectors: arm, leg, foot, neck, head, thumb, index, etc.

• Horizontal: the position of the chain in terms of Right, Left or Centre.

• Vertical: the position of the chain in terms of Top, Bottom or Centre.

• Depth: then position of the chain in terms of Front, Back or Centre.

• Index: number to distinguish between different chains with the same configuration of the other tags (use 0 as default).

In case you have two chains with the same tag combination, and no chain with the same index is found on the source agent type, then the chain with the previous index is used.

From Atoms 4.0, you can set a pole vector for your chains. If no pole vector is provided an automatic pole vector will be evaluated automatically whenever possible. A pole vector should be provided by the user whenever the joints of any limb are on a straight line in bind pose or within an animation.

Please follow the Maya and Houdini tutorials to see how to use this UI.