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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so safety is covered. The description adds that the design is scored 'against measured ligation data' and is 'high-fidelity', which tells the agent this is a data-driven optimisation rather than a heuristic. It says nothing about runtime cost, determinism, or the failure mode of an infeasible size.

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?

A single front-loaded sentence with no filler: core action first, then the optional pinning clause in parentheses. Every clause carries information, though the parenthetical could be read as a minor aside rather than a first-class mode.

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 an output schema present, return values need no explanation, and the eight parameters are fully documented in the schema, so the description only needs to establish purpose and the design conditions — which it does. What is missing is the search/optimisation cost profile and guidance for infeasible size or conflicting fixed junctions, which matter for a tool with a candidate-pool knob.

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 the schema already documents all eight parameters including enzyme/dataset/candidate_pool and the start_from no-worse-than guarantee. The description only restates the two headline semantics (size, pinned fixed junctions), adding little beyond the structured fields — baseline 3 is correct.

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 names a specific verb ('Design') and resource ('Golden Gate overhang set') and adds real scope: size-driven, scored against measured ligation data, with optional fixed junctions. It is distinguishable from neighbours like score_overhang_fidelity or check_golden_gate_parts, though it never explicitly names an alternative.

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?

Usage is only implied: an agent can infer this is the design step that precedes golden_gate_assemble, and the sentence 'optionally pinning junctions you cannot change (a fixed vector's own overhangs)' signals the pinned-junction case. There is no explicit when-to-use, when-not, or named alternative in the description itself; the useful routing hint ('Wire golden_gate_assemble.overhangs here') lives in the schema, not the description.

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