count_atoms

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

Annotations already declare idempotentHint, readOnlyHint, and destructiveHint=false. The description adds no further behavioral context beyond stating it counts atoms, which is obvious.

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

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

One sentence with inline code examples is concise, but could benefit from structured formatting for clarity.

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

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

With 3 parameters and no output schema, the description fails to explain the return value (expected integer count) and the purpose of 'trajectory' parameter, leaving important gaps.

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

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

Only the 'selection' parameter is addressed with examples; the 'structure' and 'trajectory' parameters are left unexplained despite schema coverage being 0%. The description does not compensate for the lack of schema documentation.

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

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

The description clearly states 'Count atoms matching a VMD atom-selection expression', using a specific verb and resource. It is distinct from sibling tools like contacts, distance, and rmsd which measure other properties.

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

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

Examples of valid selections are provided, which imply usage but there is no explicit guidance on when to use this tool vs alternatives like contacts or rmsd.

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