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get_secondary_structure_api_pdb_entry_secondary_structure__p

Read-only

Retrieve secondary-structure annotations and per-residue structural predictions (disorder, folding, flexibility) for a PDB entity, including helices, strands, scores, and source metadata.

Instructions

Returns secondary-structure annotations for a specified PDB Entity ID, including helices and strands, plus per-residue structural predictions from external tools (e.g., disorder, folding propensity, flexibility), each with associated scores, labels, and source metadata.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
entity_idYesEntity id (molecule number in mmcif-speak). type: string pattern: ^[0-9]+$ title: Entity Id description: Entity id (molecule number in mmcif-speak).
Behavior3/5

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

Annotations already indicate readOnlyHint=true; the description adds that results include scores, labels, and source metadata, but does not disclose other behavioral traits.

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 that packs relevant details without unnecessary words, though it could be slightly more concise.

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

Completeness4/5

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

Given no output schema, the description adequately explains what is returned (helices, strands, predictions, scores, labels, source metadata), covering the main aspects.

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%, so the parameters are well-documented. The description does not add additional parameter-level insights beyond what the schema provides.

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 tool returns secondary-structure annotations (helices, strands) and per-residue predictions, distinguishing it from sibling tools like get_domains which return domain information.

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 vs alternatives, nor any exclusion criteria or prerequisites.

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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