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radius_of_gyration

Read-onlyIdempotent

Compute radius of gyration for a molecular selection across trajectory frames, returning per-frame values and summary statistics.

Instructions

Radius of gyration (nm-scale, in VMD's Angstrom units) of a selection, computed for every frame. Returns a per-frame series plus min/max/mean.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoprotein
structureYes
trajectoryNo
mass_weightedNo
Behavior3/5

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

Annotations already provide readOnly, idempotent, non-destructive hints. Description adds output format details (per-frame series, min/max/mean) but does not disclose edge cases or limitations. Adequate but not exceptional beyond annotations.

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

Conciseness4/5

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

Two concise sentences with essential info. No fluff, but could be more structured (e.g., separating purpose from output).

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?

Missing parameter details and usage context. With 4 parameters and no output schema, the description is insufficient for correct invocation. Does not mention optionality or defaults.

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

Parameters1/5

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

Schema coverage is 0% and the description does not explain any parameters (selection, structure, trajectory, mass_weighted). Only mentions 'selection' vaguely. Fails to compensate for missing schema descriptions.

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 clearly states the tool computes radius of gyration per frame for a selection, with units (nm-scale in Angstroms) and output (per-frame series plus min/max/mean). This distinguishes it from sibling tools like rmsd or sasa.

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

Usage Guidelines2/5

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

No guidance on when to use this tool versus alternatives. Does not mention prerequisites or typical scenarios.

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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