# PharmaDiff

PharmaDiff turns a 3D pharmacophore hypothesis into an atom-level subgraph and injects it as a condition into diffusion-based generation, producing 3D molecules that follow the prescribed spatial arrangement. Across 250 pharmacophore conditions drawn from the GEOM-Drugs test set it reaches a mean match score of 0.8964 and a perfect match rate of 0.6990, above PGMG, TransPharmer, REINVENT4, ShEPhERD and PhoreGen; its average docking scores on four targets also beat DiffSBDD, which needs the protein structure, though its PoseBusters pass rate is below ShEPhERD and PhoreGen.

PharmaDiff turns a 3D pharmacophore hypothesis into an atom-level subgraph and injects it as a condition into diffusion-based generation, producing 3D molecules that follow the prescribed spatial arrangement. Across 250 pharmacophore conditions drawn from the GEOM-Drugs test set it reaches a mean match score of 0.8964 and a perfect match rate of 0.6990, above PGMG, TransPharmer, REINVENT4, ShEPhERD and PhoreGen; its average docking scores on four targets also beat DiffSBDD, which needs the protein structure, though its PoseBusters pass rate is below ShEPhERD and PhoreGen.