super

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

Annotations already declare destructiveHint=true and readOnlyHint=false, so the safety profile is covered. The description adds nothing beyond that: it never states that atom coordinates are transformed in place, that the target selection stays fixed, or how the result is reported. For a destructive coordinate-mutating operation, one sentence restating the name's meaning is thin.

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 no filler or redundancy. It is efficient, though the extreme brevity comes at the cost of substance rather than being a structural flaw.

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 values need not be described, but the tool is a destructive in-place coordinate transformation with three parameters including a free-form 'options' passthrough, and the description explains none of the operational behavior or constraints. Given the complexity and the crowded alignment sibling set, the definition is not complete enough for confident selection.

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 schema itself explains that 'mobile' is the selection to move and 'target' is the one that stays put, so the description need not repeat this. Its phrase 'one selection onto another' aligns with that mapping but adds no semantics beyond the schema. Baseline 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: 'superimposes one selection onto another,' which is a real structural superposition rather than a tautology on the opaque name 'super'. It does not, however, distinguish this operation from close siblings like align, rms_cur, or intra_fit, so the agent must infer the difference from name alone.

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 when-to-use guidance at all: no statement that this performs a sequence-dependent structural superposition, no comparison to align or rms_cur, and no prerequisites such as both selections containing matching atom counts. The agent is left to guess among several alignment-family siblings.

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