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fragment

Loads a molecular fragment by its built-in name, such as benzene or alanine, into PyMOL for analysis and visualization.

Instructions

Loads a molecular fragment

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYesBuilt-in fragment name, e.g. "benzene", "ala", "formamide".

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations, the description carries full responsibility for behavioral disclosure. It only says 'Loads a molecular fragment' without indicating side effects, object creation, or the outcome of the load. This is insufficient for the agent 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.

Conciseness5/5

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

The description is a single, concise sentence with no filler or redundant information. It is appropriately sized for a simple tool with one well-documented parameter, earning a perfect score for conciseness.

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

Completeness3/5

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

Given the tool's simplicity (one parameter) and the presence of a rich output schema, the description is minimally viable. However, it lacks context about what happens after loading (e.g., object creation, display) and how it relates to sibling operations, leaving a clear gap in completeness.

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

Parameters3/5

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

The single parameter 'name' is fully described in the schema with a clear definition and examples ('benzene', 'ala', 'formamide'), giving 100% schema description coverage. The description adds no extra parameter meaning beyond what the schema already provides, so the baseline of 3 is appropriate.

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 clearly states the action ('loads') and resource ('molecular fragment'), giving a specific verb+resource. However, it does not explicitly differentiate from sibling tools like load_structure or fetch_structure, which also load molecular entities, so it lacks sibling differentiation.

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 provides no guidance on when to use this tool versus alternatives. There is no mention of when to choose 'fragment' over load_structure or fetch_structure, leaving the agent without context for tool selection.

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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