Jean — Molecular Biology & Genomics

decompose_r_groups

Read-only

RDKit's R-group decomposition of a list of small molecules on a core given as SMARTS (default RGroupDecomposition parameters): per matched structure its core and substituents R1, R2 …, and the structures the core does not match.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "molecules": "<molecules>",
      "core": "<core>"
    },
    "name": "decompose_r_groups"
  }
}

Input Schema

Name	Required	Description
`core`	Yes	the core, as SMARTS.
`_files`	No	The 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.
`_subject`	No	The 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.
`molecules`	Yes	the structures: one SMILES or molfile per entry.

Output Schema

Name	Required	Description
`rows`	Yes	per matched structure: its index and its groups (Core, R1, R2 …) as SMILES
`summary`	Yes	the decomposition in words, generated from this run
`unmatched`	Yes	input indices the core does not match

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A3.9/5.0

Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and a closed-world scope, so the safety profile is covered. The description adds real context beyond that: it states that default RGroupDecomposition parameters are used and, importantly, that non-matching structures are also returned rather than causing failure — a behaviour an agent could not infer from the schema.

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 with no filler, and the key scoping facts (list of molecules, SMARTS core, default parameters, unmatched structures included) come early. Slightly run-on with the parenthetical and trailing clause, but nothing is redundant.

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?

An output schema exists, so return shape need not be spelled out, yet the description still sketches the per-structure result (core plus R1, R2 …) and the unmatched bucket. Combined with annotations, this is enough for an agent to invoke the tool correctly; only failure/validation behaviour is left implicit.

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% and the schema already says core is SMARTS and molecules are one SMILES or molfile per entry, so the description mostly restates it. It does clarify that the core is a SMARTS pattern (not a molecule index) and that matching is per-structure, but adds no format or edge-case detail (e.g. what happens with unparsable SMILES).

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?

Names a specific chemistry operation (RDKit R-group decomposition) applied to a specific resource (a list of small molecules against a SMARTS core). This is unambiguous against neighbouring tools such as cluster_molecules, compare_molecules, or matched_molecular_pairs, which do different things.

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 implied: the agent can infer this is the tool for splitting molecules into a common core plus R1/R2 substituents. There is no explicit when-to-use statement, no alternative named for related tasks (e.g. matched_molecular_pairs, search_molecule_library), and no prerequisites such as required molecule validity or core-match expectations.

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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