protein_prepwizard

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

With no annotations, the description carries the full burden. It discloses that the tool is long-running, returns a job_id, and the prepared structure is named <output_name>. It also lists the computational steps (Epik, Prime, minimization), but does not detail failure modes, authentication needs, or rate limits.

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 three sentences with no redundant information. The first sentence packs the core purpose and steps, the second lists input formats, and the third notes key behavioral traits (long-running, job_id). Information is front-loaded and efficiently presented.

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 complexity and lack of output schema or parameter descriptions, the description provides reasonable context: input formats, key operations, and return behavior. However, it omits prerequisites (e.g., valid structure, licensing) and expected execution time, which would be helpful.

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?

The schema has 0% description coverage, so the description must compensate. It maps to some parameters (fill_sidechains, fill_loops, epik_ph, minimize) but does not explain input_path or output_name. The description adds meaning but lacks detail on default values and parameter ranges.

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 prepares a protein structure for docking, listing specific steps (assign bond orders, add/optimize hydrogens, set protonation states, fill missing side chains/loops, minimize). It also specifies accepted input formats (.pdb/.mae/.cif), distinguishing it from sibling tools like fetch_pdb or convert_structure.

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 for docking preparation but does not explicitly state when to use this tool versus alternatives like ligprep or analyze_interactions. No exclusions or when-not-to-use guidance is provided, making the usage contextual but not prescriptive.

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