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

Annotations already declare a safe read-only, closed-world operation. The description adds real behavioral context: it enumerates what the check reveals (site counts, flanking vs internal classification) and states the consequence of an internal site (must be domesticated before the reaction is trusted), which is beyond what annotations convey.

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?

Front-loaded with the core action and timing, then explains the diagnostic value. It is dense but every sentence earns its place; the em-dash clause is mildly rhetorical but still informative.

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?

For a 5-parameter tool with nested objects, an output schema, and annotations covering safety, the description gives enough to call it correctly and understand the result. It does not explicitly connect parameters to the diagnostic output, a minor gap given the output schema exists.

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 description coverage is 100%, so the schema itself documents parts, _files, enzyme, _subject, and include_subject. The description adds no parameter-level detail (e.g., enzyme default behavior or the include_subject toggle), so baseline 3 is appropriate.

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?

Specific verb+resource with clear scope: check parts for Type-IIS recognition sites, distinguishing deliberate flanking sites from internal mis-cut sites. It carves out a distinct role from siblings like golden_gate_assemble (which performs the assembly) and domesticate_part (which fixes internal sites).

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?

"Check parts BEFORE a Type-IIS assembly" gives explicit timing/context, and the domestication note implies the follow-up action when an internal site is found. It stops short of naming domesticate_part as the alternative tool explicitly.

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