MolScope: A Transparent Representation-Aware Workflow Toolkit for Reproducible Medicinal-Chemistry Triage

Medicinal-chemistry review is often built from disconnected notebooks, spreadsheets, and slide decks that hide structure-normalization choices and blur the boundary between measured observations and heuristic prioritization. MolScope is an open-source Python workflow toolkit that converts molecular structure collections and optional assay joins into a canonical chemistry table, category-aware summaries, and decision-ready report and picklist artifacts. The workflow makes representation policy explicit, preserves evidence provenance, and packages outputs as portable HTML, Markdown, and CSV bundles. Using frozen example datasets, we show reproducible end-to-end execution, auditable handling of salts, tautomers, stereo ambiguity, charge state, and one bounded round-review example for comparative campaign support.