mark_cages
Visualize detected water cages as wireframe polyhedra with color-coded cage types, using cylinders and spheres for edges and vertices, and output a renderable CGO object.
Instructions
Draw each detected cage as a wireframe polyhedron — cylinders along the O-O ring edges
plus spheres at the water-oxygen vertices, colored by cage type (5^12=cyan, 5^12 6^2=violet,
5^12 6^4=red, ...). Builds a single CGO object named cages for render_image.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| box | No | Periodic box in nm (3/6/9 values); else from get_symmetry. | |
| selection | No | Selection of the water system. | all |
| cage_types | No | Only draw these cage types (e.g. ['5^12','5^12 6^4']); default all. | |
| edge_radius | No | Cage edge (cylinder) radius in Angstrom. | |
| object_name | No | Object whose box to use. | |
| vertex_radius | No | Cage vertex (sphere) radius in Angstrom. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||