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symexp

Generate symmetry-related copies of a selection using crystal symmetry, producing neighboring molecules within a specified cutoff distance.

Instructions

Generates symmetry-related copies

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
segiNoOptional segment identifier for the new objects.
cutoffNoDistance in Angstrom out to which to generate mates.20
prefixYesPrefix for the generated symmetry-mate objects.
obj_nameYesObject holding the crystal symmetry. Separate from the selection below: cmd.symexp needs both.
selectionYesSelection whose crystallographic neighbours to build.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior1/5

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

With no annotations, the description must disclose behavioral traits, but it only states the action without noting that it creates new objects with a prefix, requires a symmetry object, or that it is non-destructive. The lack of side-effect information is a significant gap.

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 a single short sentence, which is efficient but under-specified for a tool with 5 parameters. It omits critical behavioral and usage context, so it is not appropriately sized; it is too sparse.

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?

For a tool with 5 parameters, no annotations, and a dependency on crystal symmetry context, the one-sentence description is inadequate. It fails to explain the interaction between obj_name and selection, the effect of cutoff, or the prefix naming convention.

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?

Schema coverage is 100%, with each parameter having a description (e.g., 'Distance in Angstrom out to which to generate mates'). The description adds no additional parameter semantics, but the schema is sufficient, so baseline 3 applies.

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 uses the specific verb 'generates' with the resource 'symmetry-related copies', which conveys the core action. It is distinguishable from generic copy tools by the 'symmetry-related' qualifier, though it lacks explicit mention of crystallographic context.

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 is provided on when to use symexp versus alternative tools. There is no mention of prerequisites or contextual instructions, such as needing an existing symmetry object or the relationship between obj_name and 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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