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 genuine behavioral insight beyond that: alignment is step-by-step and order-sensitive, and step identity is derived from the reaction and its parameters rather than assigned, which explains why cross-format builds match. It does not address return shape or failure modes, but the annotations lower the bar.

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?

Two sentences, front-loaded with the core action and scope, followed by the one non-obvious behavioral fact. No filler or restatement of the tool name.

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, the description need not explain return values, and annotations cover the safety profile. It conveys the alignment semantics and cross-format behavior an agent needs to call it correctly, though it could say more about how the required 'against' parameter interacts with the focused document.

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 already documents key, against, document, _files and _subject in detail, including the abstract vs processId distinction. The description adds no parameter-level information of its own, so the baseline of 3 applies.

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 gives a specific verb and resource ('Align two constructs' build procedures step by step, in order') and frames the question it answers, which is distinct from molecule-level siblings like compare_molecules. It stops short of explicitly naming an alternative or stating what it is not, so the differentiation from adjacent tools (get_construction_history, verify_construct) is left to inference.

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 rhetorical question 'was this built the same way as that?' implies the use case, and the format-independence note tells the agent this works across SnapGene/OpenCloning inputs. However, there is no explicit when-not guidance, no named alternative for related questions (e.g. history vs verification), and no prerequisites stated.

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