Chemical structure map
This view places 2909 records using chemical structure only: chiral Morgan count fingerprints and Tanimoto distance, projected to two dimensions with UMAP. Labels, antimicrobial classes, mechanisms, targets, and curation fields can color or filter the view, but they do not affect position.
Read local neighborhoods, not the axes or global spacing. UMAP preserves nearby structure better than map-wide distance. Current full-corpus trustworthiness@10 is 0.972 and 2D neighbor overlap@10 is 0.498. Multi-fragment structures are retained exactly as their records define them and are visibly marked.
Method and provenance
Model morgan-count-chiral-r2_0.90-r4_0.10+tanimoto+umap-precomputed-n15-d0.05-c2-rs42. The generator parses stored SMILES
first and falls back to standard InChI when RDKit rejects the stored
SMILES. This build used that fallback for
176 records and retained
189 multi-fragment records.
All 189 detected stereoisomer pairs have
nonzero model distance.
Distance is 90% radius-2 and 10% radius-4 chiral Morgan count-fingerprint
Tanimoto distance. Coordinates are generated with
UMAP(metric=precomputed, n_neighbors=15, min_dist=0.05,
random_state=42). A corpus or model-version change can move every
point.