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similar_ligands_comp_similarity_hetcode_64e4dc75

Read-only

Identify chemical components similar to a PDB ligand hetcode, including stereoisomers, common scaffolds, and molecules with ≥60% PARITY similarity.

Instructions

Returns chemical components that are similar to the given chemical component. Results include stereoisomers, components sharing a common scaffold, and molecules with ≥60% PARITY score-based similarity.

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

A3.6/5.0
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 by structured data. The description adds real behavioral value by defining the similarity criteria returned: stereoisomers, common-scaffold components, and molecules with ≥60% PARITY similarity. It omits return format/ordering, and the idempotentHint=false is left unexplained.

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?

A single front-loaded sentence that names the operation first and then enumerates the result categories. No filler, no restatement of the title, and every clause carries information.

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?

For a read-only, single-parameter query, the description supplies the result semantics (which similarity categories are included) that the absent output schema cannot. It is nearly complete; only result ordering, limits, or pagination behavior are unaddressed.

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?

There is a single required parameter (hetcode) with 100% schema description coverage, so the schema already documents it. The description adds no format or syntax detail about the hetcode beyond referring to 'the given chemical component', matching the baseline 3 for schema-covered parameters.

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 ('Returns') and resource ('chemical components that are similar to the given chemical component'), making the operation immediately identifiable. It does not explicitly differentiate itself from sibling ligand tools such as ligand_sum_comp_sum_hetcode or comp_in_comp_in_hetcode, so it stops short of 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?

The description explains what results contain but never states when to use this tool versus the many sibling ligand/component tools, nor any prerequisites or exclusions. Usage is only weakly implied by the phrase 'similar to the given chemical component'.

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