Rh-enamide¶

Rh-enamide is the first full bring-your-own-system case because it combines nine QM transition-state structures, a complete MM3 field, two custom OPT regions, a frozen base, QFUERZA initialization, objective evaluation, optimizer entry, and persistence.

Source and membership¶

Governing article: Donoghue, Helquist, Norrby, and Wiest, J. Chem. Theory Comput. 2008, 4, 1313–1323 (Zotero JXH5HHS6).
Authoritative membership: nine transition-state structures in the source sequence preserved by the loader.
Force field: one complete source MM3 file with the RhH3-E core and RH-PX OPT regions.

The inputs are tracked at examples/publication/rh-enamide, but wheel and sdist artifacts exclude the complete examples tree. Redistribution/licensing is not established; no broader rights statement is made.

Current claim¶

Row	Status	Substantiation
`repository-geometry-eigenmatrix-v1`, published or QFUERZA start	`partial_repository_reproduction`	Canonical Rh-enamide evidence and objective gaps

The repository profile includes all-nine bond, angle, and full-eigenmatrix targets. The article also used ESP charges and relative enthalpies; those are not silently approximated. Relative enthalpy remains typed but blocked until an MM backend exposes thermochemical enthalpy.

Run¶

python examples/publication/rh-enamide/run.py \
  --rh-enamide /path/to/q2mm/examples/publication/rh-enamide \
  --output-root /path/to/output \
  --bounded-ci

The JSON result reports citation/source status, exact order, active/frozen counts, QFUERZA audit, objectives/categories, execution policy, and saved paths. Remove --bounded-ci only when you intend to run the documented scientific optimizer. See the tutorial.