deepmedchem 0.3.0b4

Enamine REAL now defaults to the filtered 2026-09-06.2 release in production: approximately 93.41B source reagent combinations, with a 95% interval of 93.19–93.63B. These are estimated combinations, not unique molecular graphs.

• Exact SMILES/SMARTS substructure search is enabled, with all 326 route partitions indexed and final products verified against the original query.
• Sampling, similarity, selections, runs, and substructure share the historical topology policy and exact Ro5/Veber product limits. Price estimates remain available.
• The CLI marks estimated counts with ~ and labels result summaries as source combinations.
• README, live examples, and notebook documentation reflect production. Substructure examples allow an HTTP timeout margin above the server budget, and documentation links point to the current guide.

Install or upgrade:

python -m pip install --upgrade --pre deepmedchem==0.3.0b4

The existing database="enamine" alias and Python search methods continue to work. Complex substructure queries remain bounded by the requested timeout and can return partial results.

Validation: production acceptance checked all 300 returned products independently, with eight positive substructure cases and a bounded empty-result case. CLI/export/documented examples passed. Core, processing, backend and SDK suites passed (335 tests total), along with the SDK/backend contract and documentation build. SDK CI passed on Python 3.9–3.13.