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get_mappings_api_mappings__accession__get

Read-only

Maps PDB protein chains to UniProt, Pfam, InterPro, CATH, SCOP, GO, Ensembl, and HMMER using residue-level SIFTS data. Supports queries by PDB ID, UniProt accession, or domain accessions.

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, making safety clear. The description adds that it returns mapped residue segments and associated annotations, which is sufficient for a read-only query tool. No unexpected side effects are possible, and the behavior is well described.

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 is clear and front-loaded with the core purpose. It could be split into two sentences for readability, but it remains efficient, containing only relevant details without extraneous words.

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 the tool's complexity (multiple resources, bidirectional queries) and lack of output schema, the description adequately covers what the tool does and what it returns (mapped residue segments and annotations). No major gaps in expected information are present.

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% and the schema already lists acceptable accession types. The description restates many of these types (e.g., UniProt, Pfam) but adds little new meaning beyond what the schema provides, so baseline score of 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 tool provides unified SIFTS residue-level mappings between PDB chains and many sequence/domain resources. It lists specific resources (UniProt, Pfam, etc.) and distinguishes itself from siblings like get_uniprot_mapping by emphasizing 'unified' and broader scope.

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

Usage Guidelines4/5

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

The description mentions bidirectional query support (PDB-to-identifier and identifier-to-PDB), giving clear usage context. However, it does not explicitly state when to use this tool versus more specific sibling tools like get_uniprot_mapping, so some guidance is implicit rather than explicit.

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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