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wjgoarxiv

vmd-hydrate-mcp

by wjgoarxiv

radius_of_gyration

Calculate the radius of gyration of an atom selection in a trajectory frame to assess molecular compactness.

Instructions

Radius of gyration (Angstrom) of an atom selection at a frame.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pathYes
frameNo
topologyNo
selectionNoall
Behavior3/5

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

No annotations provided, so the description must carry the burden. It implies a read-only calculation, but does not explicitly state lack of side effects, permission requirements, or performance implications. Minimal transparency.

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?

The description is a single sentence, concise and front-loaded with the key output. However, it sacrifices detail for brevity.

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

Completeness1/5

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

With 4 parameters, no schema descriptions, no output schema, and no annotations, the description is severely incomplete. It fails to explain expected inputs, return value format, or behavioral details needed for correct usage.

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 description coverage is 0%, and the description adds no meaning beyond parameter names and types. Parameters like 'path', 'topology', and 'selection' are not explained, leaving the agent without guidance on valid input formats.

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

Purpose4/5

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

The description states the tool computes radius of gyration for an atom selection at a given frame, with Angstrom units. It is clear but uses a noun phrase rather than a verb, and does not explicitly distinguish from sibling tools like 'measure_geometry'.

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. The description does not mention prerequisites, limitations, or relation to sibling tools such as 'measure_geometry' or 'resolve_selection'.

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

Install Server

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