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geometry_build

Generate molecular geometry from a SMILES string, producing coordinate files in PDB or XYZ format for computational chemistry.

Instructions

Generates a geometry for the input SMILES

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
formatYesOutput file format (default: pdb)
smilesYesSMILES
output_fileYesURI to coordinate output file (must be within root path)

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
messageYes
successYes
Behavior2/5

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

No annotations are provided, so the description must carry the full burden. It fails to disclose that the tool writes to an output file, any destructive behavior, computational cost, or authorization needs. The description is too brief.

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 a single sentence with no wasted words. It is front-loaded with the core function. However, it could be slightly expanded without losing conciseness.

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

Completeness2/5

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

Given no annotations and required output file, the description does not mention output format restrictions, file path constraints (although schema says 'must be within root path'), or any side effects. An output schema exists, so return values are covered, but behavioral context is lacking.

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 description coverage is 100%, so the schema itself documents all parameters. The description adds minimal extra meaning beyond 'for the input SMILES'. Baseline 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 verb 'generates' and the resource 'geometry' for a SMILES input. It distinguishes from sibling tools like geometry_optimize (optimizes existing geometry) and SMILES tools (query/manipulate SMILES strings), though 'geometry' could be more explicitly '3D molecular geometry'.

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 this tool versus alternatives like geometry_optimize or SMILES tools. There is no mention of prerequisites, such as needing a valid SMILES or that geometry_optimize might follow.

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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