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Jean — Molecular Biology & Genomics

search_molecule_library

Read-only

Which of a list of small molecules contain a SMARTS substructure, with RDKit's substructure library (pattern-fingerprint screen, then atom matching).

Input Schema

NameRequiredDescriptionDefault
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
smartsYesthe substructure, as SMARTS (a plain SMILES reads as one).
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
moleculesYesthe library: one SMILES or molfile per entry.

Output Schema

NameRequiredDescriptionDefault
hitsYes0-based indices of the molecules that contain the pattern, ascending
unreadYes0-based indices of the entries RDKit could not read, never searched
summaryYeshow many structures contain the pattern, of how many searched

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.6/5.0
Behavior3/5

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

Annotations already declare this as a read-only, non-destructive, closed-world operation. The description adds useful implementation context, namely a pattern-fingerprint screen followed by atom matching, but it does not discuss hit semantics, matching limitations, or performance characteristics.

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 a single, front-loaded sentence that states the question being answered and the underlying method. Every phrase contributes to understanding without unnecessary wording.

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?

The tool has an output schema, so the description does not need to explain return values. It is complete enough for a focused substructure search, though it lacks sibling routing and notes on matching behavior that would help an agent select it confidently.

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%, so the input schema already documents the parameters in detail. The description restates the key concepts of a molecule list and SMARTS substructure but does not add format rules or edge-case meaning beyond the schema.

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?

The description states a specific operation: identifying which small molecules contain a SMARTS substructure, using RDKit. It is clear about the resource and action, but it does not distinguish this tool from nearby siblings such as screen_molecule_library.

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 use case is implied by 'Which of a list of small molecules contain a SMARTS substructure,' but there is no explicit guidance on when to choose this tool over alternatives. No exclusions or sibling comparisons are provided.

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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