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distance

Measure and display the distance between two molecular selections, creating a named distance object for analysis.

Instructions

Measures and draws a distance object between two selections.

Args: name: Name for the distance object (used to delete/recolor later). selection1: First selection. selection2: Second selection.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYes
selection1Yes
selection2Yes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations are provided, so the description carries full burden. It mentions that the distance object is drawn and that the name is used for later deletion/recoloring, which adds some behavioral context. However, it does not disclose side effects like modifying the scene or any requirements.

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

Conciseness4/5

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

The description is concise with a front-loaded summary sentence followed by an Args section. No extraneous text, and key information is presented efficiently.

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

Completeness4/5

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

All three required parameters are described with purpose. With an output schema present, return value details are not needed. For a simple measurement tool, the description is complete and sufficient.

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

Parameters4/5

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

Schema description coverage is 0%, but the description provides meaningful explanations for all three parameters: name for identification/deletion, selection1 and selection2 as the two selections. This adds value beyond the schema's type-only definitions.

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

Purpose5/5

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

The description clearly states the verb (measures and draws) and the resource (distance object between two selections). This distinguishes it from sibling tools like dihedral or angle, which measure other geometric properties.

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?

The description does not provide explicit guidance on when to use this tool versus alternatives. It merely assumes the user wants to measure a distance, without explaining context or exclusions.

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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