Align

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

With no annotations, the description carries the full burden, but it does disclose meaningful behavior: this is a two-stage operation (sequence alignment followed by superposition) that transforms the mobile object's coordinates rather than merely computing a metric. It does not say whether the transform is applied permanently, what happens on partial sequence mismatch, or whether it fails when atom correspondence is ambiguous.

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 the action first, operands second, and the qualifier last — no filler. It is slightly under-informative for its brevity, but nothing is redundant.

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?

An output schema exists, so return-value explanation is not required, and only two well-described parameters are involved. Still, for a coordinate-transforming structural operation with zero annotations, the description should state whether the move is destructive/persistent and what preconditions (sequence correspondence) must hold.

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 both parameters are already documented ('Object/selection to move' and 'Reference object/selection'), which sets the baseline at 3. The description reinforces the directional relationship (mobile is moved onto target) but adds no syntax, selection-string format, or constraint 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?

The description names a specific compound action (sequence-align and then superpose) and the two operands (`mobile` onto `target`), so an agent knows exactly what operation is performed and on what. It falls short of 5 because it doesn't name the sibling it is contrasted with (e.g. `orient`) even though the parenthetical implies an alternative exists.

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 parenthetical '(use for different structures)' supplies a real selection condition versus same-structure superposition, which is more than nothing. However, no alternative tool is named, and there is no guidance on when this is inappropriate (e.g. identical structures, large sequence gaps).

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