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get_secondary_structure_api_pdb_entry_secondary_structure__p

Read-only

Retrieve secondary-structure annotations and per-residue structural predictions for a specified PDB entity, including helices, strands, disorder, and flexibility scores.

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).
Behavior4/5

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

Annotations already declare readOnlyHint=true, so the description's behavioral disclosure is limited to detailing the tool's output composition (helices, strands, predictions, scores, labels, source metadata). This adds value beyond annotations, though it omits potential constraints like rate limits or response size.

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 front-loads the main action, efficiently covering the tool's purpose and output. While slightly long, it contains no wasted words and earns its place.

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

Completeness5/5

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

Given the absence of an output schema, the description thoroughly describes the tool's return value: secondary-structure annotations, per-residue predictions, and associated metadata. For a simple fetch tool with two parameters, this is complete and actionable.

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 both parameters already described in the input schema. The description mentions 'PDB Entity ID' but adds no additional semantic context beyond what the schema provides, warranting the baseline score.

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 for a specified PDB Entity ID, explicitly listing helices, strands, and per-residue predictions. This specificity distinguishes it from sibling tools like get_annotations_api and get_domains_api.

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 for secondary structure data but lacks explicit guidance on when to use this tool over alternatives or when not to use it. No prerequisites or exclusions are mentioned, relying on the agent to infer from the tool's specific purpose.

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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