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get_pdb_structure

Retrieve detailed information about a protein structure by providing its PDB ID. Access structural data for bioinformatics and drug discovery analysis.

Instructions

Get detailed information about a PDB structure by PDB ID.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYesPDB ID (e.g., '1TUP', '6VXX')
Behavior2/5

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

No annotations are provided, so the description carries full burden. It merely states 'get detailed information' without specifying what information is returned (e.g., metadata, coordinates) or any behavioral traits like rate limits or authentication. The description is too vague for an agent to fully understand tool 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, front-loaded sentence with no extraneous words. Every part serves a purpose.

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?

The description is minimal for a data retrieval tool. It does not explain what 'detailed information' includes, nor does it address possible outcomes or response format. The lack of output schema makes this gap significant, as the agent has no prior on return structure.

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% (one parameter with clear description and examples). The tool description adds nothing beyond the schema, so baseline 3 is appropriate.

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 'get', the resource 'PDB structure', and the identifier method 'by PDB ID'. It effectively distinguishes from sibling tools like 'search_pdb_structures' which would be used for searching rather than direct retrieval.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage when a PDB ID is known, but provides no explicit guidance on when to use this tool versus alternatives like 'search_pdb_structures' or 'get_alphafold_structure'. No exclusions or conditions are mentioned.

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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