generate_pseudo_atoms_def

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

With no annotations, the description carries the full burden. It explains the file's purpose and the required/optional keys for each atom entry, which adds behavioral context. However, it does not disclose side effects like file writing behavior, overwriting, or the `return_only` toggle.

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?

The description is well-structured and front-loaded with the core purpose. Every sentence adds value: the first identifies the output file and role, the second details required and optional atom fields. No redundant or vague phrasing.

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?

Despite explaining the atom item structure, the description omits important operational details: whether the tool writes to disk, how `return_only` changes behavior, what happens if `atoms` is missing required keys, and error conditions. For a generation tool with no output schema, these are significant 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?

Schema coverage is 0%, so the description must compensate. It does so for the `atoms` parameter by listing required and optional keys per item, adding substantial meaning beyond the bare schema. However, `work_dir` and `return_only` remain unexplained.

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 the tool's purpose: generating `pseudo_atoms.def`, the atom registry. It specifies the resource and the action ('Generate'). While it doesn't explicitly compare to sibling tools like `generate_molecule_def`, the unique role as atom registry is distinct enough.

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 implies usage: it is the tool for creating the registry that must include all atom types from various sources. It gives context about coverage requirements but does not explicitly state when to use this over alternatives 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.