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intra_fit

Aligns all states of a molecular object to the reference state for structural comparison and trajectory analysis.

Instructions

Fits all states within an object

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior1/5

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

No annotations are provided, and the description gives no behavioral details (e.g., whether modifications are made, side effects, or prerequisites). The description is insufficient to understand the tool's behavior.

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

Conciseness2/5

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

The description is very short (7 words), which is concise but under-specified. It lacks necessary information to be useful.

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 the low parameter count and absence of annotations, the description should provide more context about the tool's purpose, behavior, and expected input. It fails to do so, making it incomplete.

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 input schema has one parameter 'selection' with no description in the schema. The tool description does not explain what the 'selection' parameter expects, leaving it undefined. Schema description coverage is 0%.

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

Purpose2/5

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

The description states 'Fits all states within an object', providing a verb and resource. However, 'fits' is ambiguous (structural fitting? alignment?) and does not distinguish from sibling tools like 'intra_rms', 'align', or 'super'.

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

Usage Guidelines1/5

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 vs alternatives. No context or conditions are mentioned.

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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