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comp_in_comp_in_hetcode_e47e47bd

Read-only

Search PDB entries that contain a given chemical component hetcode. Returns structures where the component appears standalone or as part of a larger entity.

Instructions

This call returns a list of PDB entries that contain the given chemical component as defined in the PDB Chemical Component Dictionary. The list includes PDB entries where the component appears either as a standalone chemical component or as part of a larger entity.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
hetcodeYesHetcode for the compound title: Hetcode description: Hetcode for the compound

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.1.10

TDQS

B3.4/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered. The description adds genuine behavioral context beyond the annotations: the match is deliberately broad, covering the component both standalone and as part of a larger entity, which answers the key ambiguity an agent would have about exact vs. containment matching. It stops short of describing result size, ordering, or pagination.

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?

Two tight sentences with the core purpose front-loaded and the matching-scope qualifier second; no filler or redundant restatement of the title. Slightly verbose phrasing ('as defined in the PDB Chemical Component Dictionary') but it earns its place by defining the identifier source.

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

Completeness3/5

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

With one required parameter, no output schema, and annotations present, the description covers the essentials: what the tool returns and how the match is scoped. Because there is no output schema, it would ideally say what a returned 'PDB entry' looks like (IDs only vs. records) or whether the list is capped, which is a real gap.

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% for the single parameter, so the baseline is 3. The description does add a little meaning by tying the hetcode to the PDB Chemical Component Dictionary, but the schema already states 'Hetcode for the compound' and the description gives no format or case examples.

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?

Specific verb+resource: it returns PDB entries containing a given chemical component, and it clarifies the matching scope (standalone component or part of a larger entity). That scope statement meaningfully disambiguates from a plain 'entry lookup', but the description never names a sibling (e.g., ligand_sum_comp_sum_hetcode or similar_ligands_comp_similarity_hetcode) to help an agent choose between the component-related tools.

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 when-to-use guidance, no prerequisites, and no alternatives are mentioned despite several component/ligand siblings existing (similar_ligands, comp_intx, ligand_sum). The agent must infer from the return semantics alone that this is the 'which entries contain this hetcode' tool.

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