identify_cages
Detect clathrate cages via TRACE ring perception, assemble them, and classify by face counts to return cage-type counts and overall hydrate structure (sI/sII/sH).
Instructions
Identify clathrate cages (TRACE): ring perception -> cage assembly -> face-count typing.
Returns per-type cage counts (5^12, 5^12 6^2, 5^12 6^4, ...) and the overall structure (sI / sII / sH). Validated: sII -> 128x 5^12 + 64x 5^12 6^4; sI -> 16x 5^12 + 48x 5^12 6^2.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| box | No | Periodic box in nm (3/6/9 values); else from get_symmetry. | |
| rcut_nm | No | H-bond O-O cutoff in nm. | |
| angle_deg | No | H-bond donor angle cutoff in degrees. | |
| selection | No | Selection of the water system. | all |
| object_name | No | Object whose box to use. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||