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extract

Move selected atoms into a new object and remove them from the original structure, enabling focused analysis of specific molecular regions.

Instructions

Extracts a selection to a new object

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameYesName for the new object.
selectionNoAtoms to move into it. Unlike create, these are *removed* from the original object.all

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. The description simply says 'Extracts a selection to a new object' without explicitly stating that the selection is removed from the original object; this critical side effect is only clarified in the parameter description. The word 'extracts' hints at removal but is not explicit enough.

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 that immediately conveys the tool's purpose. It is appropriately sized and front-loaded with no unnecessary words.

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?

The tool has a simple two-parameter schema with full documentation and an output schema, so the basic usage is clear. However, the description lacks explicit disclosure of the removal side effect and offers no usage guidance, which is a gap given the lack of annotations. The schema compensates partially, but the description itself is thin.

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 input schema provides descriptions for both parameters with 100% coverage, so the baseline is 3. The main description adds no additional parameter semantics beyond what the schema already documents.

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 'Extracts a selection to a new object' clearly identifies the action (extract) and the resource (selection to a new object). It is specific enough to distinguish from siblings like 'create' because 'extract' implies removal, though it does not explicitly contrast with alternatives.

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 explicit guidance on when to use this tool versus alternatives such as 'create' or 'select'. The parameter description for 'selection' mentions 'Unlike create' but that is in the structured schema, not the main description, so the description itself lacks usage context.

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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