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

Annotations already declare readOnly/destructive=false, so the safety profile is covered; the description adds genuinely useful behavioral context — mixed-format inputs still align because step identity is derived from the reaction and its parameters. It does not describe output shape, but an output schema exists, so that gap is minor.

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?

One front-loaded imperative sentence followed by a single supporting clause about cross-format behavior; nothing is redundant or padding. Appropriate size for a tool whose structured fields already carry the details.

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 annotations, 100% schema coverage, and an output schema, the description covers what an agent needs before calling: what is compared, in what order, and why formats don't matter. Slightly incomplete in not hinting what a failed/mismatched alignment means for interpreting results.

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% and the `key` enum is already fully explained in the schema, so the description is not required to carry parameter meaning. It reinforces the format-independence rationale that motivates `_files`/`_subject`, but adds no syntax or format detail beyond the schema.

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?

States a specific verb and resource — 'align two constructs' build procedures step by step, in order' — plus a plain-language gloss ('was this built the same way as that?'). That is clearly distinct from sequence-level siblings, though it never names an alternative such as compare_molecules or get_construction_history to draw the boundary explicitly.

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 implies the use case (did these two constructs follow the same build route), but there is no explicit when-to-use/when-not-to-use guidance and no routing to related tools. An agent must infer that this is a procedure comparison rather than a sequence comparison.

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