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Jean — Molecular Biology & Genomics

canonical_tautomer

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A small molecule's tautomers and the canonical one, as RDKit's TautomerEnumerator finds and scores them: 37 hydrogen-shift transforms (after MolVS and Sitzmann 2010), scored by aromatic rings, twelve weighted groups and hydrogens on P, S, Se and Te, ties to the smaller SMILES.

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.
_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.
moleculeYesthe structure: SMILES or a molfile.
max_tautomersNostop the enumeration at this many tautomers.
max_transformsNostop after this many transform applications.

Output Schema

NameRequiredDescriptionDefault
summaryYesthe enumeration in words, with the cap when one was reached
canonicalYesRDKit's canonical tautomer, as canonical SMILES
tautomersYesevery tautomer enumerated, as canonical SMILES, sorted

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already cover the safety profile (readOnlyHint=true, destructiveHint=false, openWorldHint=false), so the description's job is to add context — and it does, disclosing the 37 hydrogen-shift transform set, the scoring criteria (aromatic rings, twelve weighted groups, hydrogens on P/S/Se/Te) and the deterministic tie-break to the smaller SMILES. That tells the agent the result is reproducible and how 'canonical' is decided. It does not mention cost or runtime behavior when enumeration is large, which is the main remaining gap.

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 dense sentence that front-loads the outcome ('tautomers and the canonical one') before the algorithmic detail. It is jargon-heavy but every clause carries real information; no filler or repetition.

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 an output schema present and annotations covering safety, the description supplies the algorithmic context an agent needs to trust and interpret the result. It stops short of describing truncation behavior when max_tautomers/max_transforms are reached, which matters for a tool whose defaults are 1000.

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 both tuning parameters (max_tautomers, max_transforms) and the molecule/_subject fields are already documented in the schema. The description adds nothing about what happens when a cap is hit or how molecule input format interacts with the enumeration, so 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?

The description names a specific resource (a small molecule's tautomers and the canonical one) and attributes the mechanism to RDKit's TautomerEnumerator, so an agent knows exactly what it returns. It never names a sibling such as enumerate_protonation_states or assess_small_molecule, so differentiation is left to the agent's inference from the subject matter.

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?

Usage is only implied: the tool canonically enumerates tautomers, which suggests it belongs in structure normalization/deduplication steps, but the description never states when to call it versus the nearby protonation-state or molecule-comparison tools. No prerequisites or exclusions are given.

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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