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align

Aligns one selection of atoms or residues to a target structure for structural comparison and superposition.

Instructions

Aligns one selection to another

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
mobileYes
targetNoall
optionsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

The description does not disclose any behavioral traits such as whether the alignment modifies the view, requires specific atom selections, or has side effects. No annotations are provided to supplement.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single concise sentence, but it lacks important details. It is front-loaded but under-specified, making it insufficient for effective tool invocation.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness1/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given three parameters and an existing output schema (not shown), the description fails to explain the tool's functionality, parameter roles, or return value. It is highly incomplete for a tool with this complexity.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters1/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The schema has 0% description coverage, and the description adds no information about the parameters 'mobile', 'target', or 'options'. The agent cannot infer their meanings or allowed values.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states the tool aligns one selection to another, which is a clear verb+resource. However, it lacks differentiation from sibling alignment tools like 'super' or 'fit', so it doesn't fully distinguish itself.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance on when to use this tool versus alternatives like 'super', 'fit', or 'intra_fit'. There is no context about prerequisites or when not to use it.

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

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