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Route-set chemical-idea diversity

RENKIN exposes diversity::template_disconnection_cds() as a deterministic diagnostic for a set of search::Route values. It is motivated by the Chemical Diversity Score described by Mrugalla et al., but it is intentionally a template-ID proxy, not the paper's atom-mapped formed-bond CDS.

Contract

  1. Each route becomes a set of its distinct stable template_id values.
  2. Duplicate sets are represented once.
  3. A strict superset of another set is treated as a route variation and omitted from the core set.
  4. The report applies all-to-all Jaccard-distance normalization to the remaining core sets. Zero or one core set returns 1.0.

The result is deterministic and invariant to route ordering, duplicate routes, and strict-superset variations. It measures diversity of recorded template families under RENKIN's current route representation. Two templates can encode the same formed bond, and one template can apply at different target bonds, so the value must not be labelled or benchmarked as exact atom-mapped CDS.

Exact atom-mapped CDS boundary

diversity::atom_mapped_formed_bond_cds() is available for atom-mapped Bridge RouteDocument values, such as SynPlanner exports. It derives formed-bond endpoint sets from mapped reaction evidence and returns None if any step is unmapped or malformed. It never falls back to the template-ID proxy and does not change the native Route JSON schema. Bond-order changes are not treated as newly formed bonds.

Provenance and licence boundary

  • Research motivation and the formed-bond CDS definition: F. Mrugalla et al., “Generating diversity and securing completeness in algorithmic retrosynthesis,” Journal of Cheminformatics 17, 72 (2025), https://doi.org/10.1186/s13321-025-00981-x, CC BY 4.0.
  • RENKIN's implementation was written independently in Rust. No paper text, figure, dataset, trained model, or upstream implementation source is included.
  • This diagnostic does not alter route search, candidate ranking, or stock membership.

This is a technical provenance record, not a freedom-to-operate opinion. Before a commercial deployment that depends materially on this metric, obtain a jurisdiction- and claim-specific patent review.