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doms_ent_doms_id_entity_id_17aad3ce

Read-only

Retrieve sequence and structural domain annotations (CATH, SCOP, Pfam, InterPro) for a PDB entity using PDB ID and entity ID, including boundaries, identifiers, names, and chain metadata.

Instructions

Returns sequence and structural domain annotations for a specified PDB Entity ID, including domain boundaries, identifiers, and names from CATH, SCOP 1.75, Pfam and InterPro domain resources, along with metadata such as the entity’s Best Chain ID.

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).

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.1.10

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and idempotentHint=false, so the safety profile is covered. The description adds no behavioural detail such as pagination, response size, or coverage caveats; its only real contribution is enumerating the returned domain resources, which is return-value content rather than behaviour.

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?

A single front-loaded sentence with the verb and resource first, followed by source list and metadata. It is a little list-heavy at the tail (Best Chain ID), but nothing is redundant enough to waste the agent's reading budget.

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?

With no output schema, the description carries the burden of describing returns and does so concretely (domain boundaries, identifiers, names, source databases, Best Chain ID metadata). Both parameters are documented in the schema and the operation is read-only, so little is missing beyond guidance on failure/empty cases.

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% and the schema already specifies the 4-character PDB id and the numeric entity id pattern. The description only references 'a specified PDB Entity ID' and adds no format, range, or cross-parameter constraints beyond the schema, so the baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Returns sequence and structural domain annotations') and enumerates the exact source databases (CATH, SCOP 1.75, Pfam, InterPro), which distinguishes it from generic neighbours like annot_ent_annot. It stops short of explicitly naming which sibling to use instead, so it earns a 4 rather than a 5.

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?

There is no statement of when to use this tool, when not to, or which sibling covers the adjacent case (e.g. annot_ent_annot for general annotations, sec_struct for secondary structure). The 'for a specified PDB Entity ID' clause only restates the required input, not usage context.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.