super

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

With no annotations provided, the description carries the full burden of behavioral disclosure, but it only restates the operation. It does not disclose whether the command modifies coordinates, whether the operation is reversible, or what side effects may occur, which is important for a structural alignment tool.

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?

The description is a single sentence front-loaded with the action verb and no filler. It is concise and effective, though it borders on being too terse for the complex domain.

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 full schema coverage and an output schema present, the description plus schema provides a minimally viable understanding of the tool's behavior. However, given the complex structural biology context and the many sibling tools, it lacks alternative differentiation and important behavioral context such as side effects or prerequisites.

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?

The input schema covers all three parameters with meaningful descriptions, so the baseline is 3. The tool description itself adds no additional parameter semantics beyond what the schema already provides.

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 uses a specific verb ('superimposes') and identifies the resource ('one selection onto another'), making the core function immediately clear. However, it does not differentiate this tool from sibling tools like 'align' or 'intra_fit', which also involve structural superposition.

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?

There is no guidance on when to use this tool versus alternative alignment/superposition tools in the sibling list. The schema's parameter descriptions ('Selection to move', 'this one stays put') clarify parameter roles but do not provide usage context or exclusion criteria.

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