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cage_occupancy

Assign guest molecules to detected clathrate cages and compute occupancy for each cage.

Instructions

Compute clathrate cage occupancy: assign guest molecules to detected cages (one per cage).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
boxNoPeriodic box in nm (3/6/9 values); else from get_symmetry.
selectionNoSelection of the water system.all
object_nameNoObject whose box to use.
guest_selectionNoSelection containing guests (CO2/CH4). Defaults to `selection`.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

With no annotations provided, the description carries the full burden of disclosing behavior. It reveals the one-per-cage assignment rule but omits any side effects, requirements (e.g., prior cage detection), or constraints. It does not state whether the tool modifies state or what happens if cages are absent.

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?

The description is a single, direct sentence that front-loads the main action and includes the key behavioral detail. Every word contributes value, with no filler or repetition.

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

Completeness2/5

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

Despite having an output schema and well-documented parameters, the description does not place the tool within the broader workflow (e.g., dependence on identify_cages). It lacks edge-case behavior and preconditions, leaving the agent to guess how this tool integrates with siblings. For a specialized analysis tool, this is insufficient.

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?

The input schema documents all four parameters with descriptions, providing 100% coverage. The description adds minimal extra meaning about guest assignment but does not explain parameter roles or formats beyond what the schema already offers, so baseline 3 applies.

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 'Compute' and resource 'clathrate cage occupancy', clearly distinguishing it from sibling tools like identify_cages (detection) and mark_cages (visualization). It also states the core assignment logic (one guest per cage), making its purpose unmistakable.

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

Usage Guidelines3/5

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

The description implies usage after cage detection (since it references 'detected cages') but provides no explicit when-to-use or alternatives. There is no mention of prerequisites or when not to use this tool, leaving the workflow integration to be inferred.

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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