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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

TableJSON Schema
NameRequiredDescriptionDefault
boxNoPeriodic box in nm (3/6/9 values); else from get_symmetry.
selectionNoSelection of the water system.all
cage_typesNoOnly draw these cage types (e.g. ['5^12','5^12 6^4']); default all.
edge_radiusNoCage edge (cylinder) radius in Angstrom.
object_nameNoObject whose box to use.
vertex_radiusNoCage vertex (sphere) radius in Angstrom.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full burden and discloses key behaviors: it builds a single CGO object named 'cages', the geometry (cylinders along edges, spheres at vertices), and the coloring by cage type. It does not mention whether the object overwrites an existing one, but the main side effect is clearly stated.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two dense, front-loaded sentences cover purpose, geometry, coloring, and the output object. No filler or redundant information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a visualization tool with complete parameter schemas and an output schema, the description is nearly sufficient. It explains the output artifact and how it will be used, but could explicitly state the prerequisite of prior cage detection (identify_cages). The gap is minor and mostly implied.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so all parameters are already documented in the schema. The description adds value by mapping cage types to colors, enriching the cage_types parameter, but does not elaborate on other parameters. Baseline 3 is appropriate.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('Draw') and resource ('each detected cage as a wireframe polyhedron'), clearly distinguishing it from sibling tools like identify_cages (detection) and cage_occupancy (analysis). It also specifies the visual elements and coloring scheme.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The phrase 'detected cage' implies a prerequisite of prior cage detection (likely via identify_cages), and 'for render_image' indicates it is a preparation step for rendering. While it does not explicitly name alternatives or exclusions, the context makes the intended usage clear.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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