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get_mappings_api_mappings__accession__get

Read-only

Map protein structures to sequence and domain resources using a single accession. Retrieves residue-level mappings between PDB chains and UniProt, Pfam, InterPro, CATH, SCOP, GO, Ensembl, and HMMER.

Instructions

Provides unified SIFTS residue-level mappings between PDB protein chains (auth_asym_id or struct_asym_id) and all major sequence and domain resources, including UniProt, Pfam, InterPro, CATH, SCOP, GO, Ensembl, and HMMER. Supports both PDB-to-identifier and identifier-to-PDB queries, returning the mapped residue segments and associated annotations for each resource.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
accessionYesUniProt accession or 4-character PDB id code or Pfam domain accession or Interpro domain accession or CATH cathcode or SCOP sunid or GO accession. title: Accession description: UniProt accession or 4-character PDB id code or Pfam domain accession or Interpro domain accession or CATH cathcode or SCOP sunid or GO accession.
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false. The description adds that it returns mapped residue segments and annotations, and supports bidirectional queries, which enriches the behavioral context beyond what annotations provide.

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 two sentences, front-loaded with the main function, and efficiently conveys purpose, scope, and bidirectional capability without redundancy.

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 a single parameter and no output schema, the description adequately explains the input types (via schema) and the nature of the output (mapped residue segments and annotations). It is sufficiently complete for this tool's complexity.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema already describes the 'accession' parameter thoroughly with a list of accepted types (100% coverage). The tool description adds context about the mapping purpose and resources, but does not significantly expand on parameter semantics beyond the schema.

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 it provides unified SIFTS residue-level mappings between PDB chains and multiple sequence/domain resources, supporting bidirectional queries. This distinguishes it from sibling tools that focus on single-resource mappings.

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 lists supported resources and query directions but does not explicitly state when to use this tool over alternatives, nor when not to use it. Given many sibling tools with specific purposes, some guidance is missing.

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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