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jean — Molecular Biology & Genomics

enumerate_reaction

Read-only

Run a reaction SMARTS over lists of reactants, every combination, with RDKit's reaction engine: one list per reactant template, in template order. Pick one of 94 library reactions (the 58 robust organic reactions of Hartenfeller et al. 2011 and 36 click-chemistry reactions, as AutoGrow4 encodes them) or pass your own SMARTS. Each product is sanitised; a product set is kept only when every product in it sanitises. Indices are 0-based.

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.
smartsNoyour own reaction SMARTS, reactants>>products. Only applies when template is custom.
_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.
templateNothe library reaction to run, or custom for your own SMARTS.83_Schotten_Baumann_amide
reactantsYesone list of SMILES or molfiles per reactant template, in template order.
max_combinationsNostop after this many reactant combinations.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
cappedYestrue when the run stopped at max_combinations
summaryYesthe run in words: products, combinations, and what was dropped or capped
productsYesevery product set as SMILES with the 0-based index of each reactant that made it

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.4/5.0
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, so safety is covered. The description adds non-obvious behavior beyond that: every product is sanitised, a product set is retained only if all its products sanitise, and indices are 0-based.

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?

Front-loaded with the core action, then the template choice, then the sanitisation rule and index convention. Dense but every sentence carries distinct operational information; the RDKit/AutoGrow4 attributions are slightly verbose but add provenance.

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

Completeness5/5

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

Given an output schema exists, return values need no explanation. For a combinatorial enumeration tool with nested arrays, the description covers the input structure, template options, sanitisation semantics and index base, leaving nothing essential unclear.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3, but the description adds real meaning: the reactants array maps one list per reactant template in template order (critical for a nested array), and the template parameter supports 'custom' paired with an own SMARTS string. It clarifies the index convention that the schema does not.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a precise verb and resource ('Run a reaction SMARTS over lists of reactants, every combination') and the engine used (RDKit). It is clearly distinguishable from related siblings like map_reaction_atoms or screen_molecule_library, which do not enumerate combinatorial reaction products.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explains how to use it – pick one of 94 library reactions or supply your own SMARTS, and supply one list per reactant template in template order. It gives clear operating context but does not name alternative tools or state when this tool should be avoided.

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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