Get Compound 3D Structure

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

Annotations already declare readOnlyHint, idempotentHint, and openWorldHint. The description adds valuable behavioral context: it notes that not all compounds have 3D coordinates, that includeAlternateConformerIds adds an extra API call, and describes what each format returns.

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?

Four sentences, all essential: main purpose, format options with use cases, optional feature, and a caveat. No redundancy; front-loaded with the core action.

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?

Given the tool's simplicity and the presence of a complete input schema, output schema, and annotations, the description covers all necessary aspects: success and failure scenarios, format choices, and optional API overhead.

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?

Schema coverage is 100%, so baseline is 3. The description adds extra meaning: for format, it explains the difference between json (parsed atoms/bonds) and sdf (raw text for external tools); for includeAlternateConformerIds, it explains that it lists IDs and adds an API call. This exceeds the schema descriptions.

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 specifies 'Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID.' This clearly states the action and resource, and distinguishes it from sibling tools like pubchem_get_compound_details or pubchem_get_compound_image.

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?

The description indicates usage for obtaining 3D structures and provides a hint to use pubchem_search_compounds for name/SMILES resolution. However, it does not explicitly state when to use this tool over others or provide exclusion criteria.

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