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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). Returns the 0-based indices of the hits and of any structure RDKit could not read.

Input Schema

TableJSON 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

TableJSON 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
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and openWorldHint=false, covering the safety profile. The description adds useful behavioral context beyond annotations: the two-stage RDKit process (pattern-fingerprint screen, then atom matching) and the fact that unreadable structures are identified by index.

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?

Two sentences with no filler, and the core purpose is front-loaded. The return-value clause adds useful specificity without unnecessary length.

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 search tool with 100% schema coverage, annotations, and an output schema, the description sufficiently covers the core operation and return shape. It is slightly incomplete in ignoring the optional _files and _subject parameters, but those are schema-described and peripheral to the main search.

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 all four parameters are documented in the schema itself. The description adds little parameter-level detail beyond calling molecules a list of small molecules and smarts a substructure, 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 exactly what it does: identify small molecules containing a SMARTS substructure, and specifies the algorithm and what indices are returned. It does not differentiate from sibling tools such as screen_molecule_library or list_library, so an agent must infer the distinction from the name alone.

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 or when-not-to-use guidance is provided, and no alternative tool is named. The scenario is implied by the purpose statement, but there are no explicit conditions for choosing this tool over screen_molecule_library or other molecule tools.

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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