Tools · Cheminformatics & Structure

Reaction Atom Mapper

Atom-map reaction SMILES, check element, mass, and charge balance, report stereocenter changes, and extract reaction templates.

Updated October 1, 2026

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The Reaction Atom Mapper checks reactions before you rely on them. It works out which reactant atom becomes which product atom (atom mapping), confirms the reaction is balanced, reports what happens to stereocenters, and can extract reusable reaction templates. Use it to clean a reaction dataset, or to check reactions from Reaction Enumeration or Retrosynthesis. It validates reactions only: it doesn't predict products or plan routes. It runs on CPU.

How it works

Mapping with RXNMapper, a transformer model that maps atoms without hand-written rules, with a confidence score per reaction. Set min_confidence to flag low-confidence mappings.
Roles: molecules are sorted into reactants, reagents, and products.
Balance: element, mass, and formal-charge differences between products and reactants (hydrogens included only with balance_hydrogens), and product atoms that map to nothing.
Stereochemistry: each tetrahedral center is created, destroyed, inverted, retained, or undetermined; double bonds that gain or lose E/Z are reported.
Templates (extract_templates): retro and forward templates extracted with RDChiral, up to max_templates.

Inputs

1 to 10,000 reactions, as a reaction_smiles list (reactants>reagents>products) with optional reaction_ids, or as a table. Tables can hold reaction SMILES in a column, or separate reactant, reagent, and product columns, so the provenance table from Reaction Enumeration and the routes table from Retrosynthesis work without changes.

Outputs

File	Contents
`mapped.csv`	One row per reaction: status (`mapped`, `low_confidence`, or `rejected`), the mapped SMILES, confidence, the balance differences, and stereo changes
`diagnostics.csv`	Every problem found, as `error`, `warning`, or `info`, with a code such as `parse_error`, `unbalanced_elements`, or `stereo_change`
`templates.csv`	Extracted templates (when you asked for them)
`reaction_map_audit.json`	Model and software versions

Reactions that can't be parsed are listed as rejected; the job carries on.

Run it from the API

Submit with Submit a job and the job_type below. Price it first with Estimate job reservation cost: submitting reserves that amount from your wallet, and the charge settles at the actual runtime.