This directory contains third-party code vendored from:
https://github.com/Gervasiolab/OpenBPMD

Vendored file:
- openbpmd.py

Local modifications:
- CADDForge carries local changes to the vendored OpenBPMD script.
- Current local changes include configurable bias-deposition interval support
  and a changed default metadynamics hill height.
- Runtime minimization/equilibration coordinates use topology-bound NPZ archives
  and matching periodic vectors; analysis reads the original parameter topology.
- Native Amber Na+/Cl- names are excluded from solute equilibration restraints.
- Versioned runtime summaries retain protocol counts, software/source provenance,
  checksums and failure causes. Protocol step constants allow shortened generated
  scientific tests; production step counts retain their previous values.
- Optional CADDForge production telemetry observes completed metadynamics calls
  and phase boundaries. Integration calls, CSV/trajectory/bias output cadence,
  equilibration, scoring and scientific protocol settings are unchanged.

License:
- MIT License (see ../../../THIRD_PARTY_LICENSES/OpenBPMD-MIT.txt from repo root)

Correctness changes in CADDForge MD 0.15.0:
- Equilibration exports and DCD reporting preserve continuous engine positions;
  the discarded MDTraj imaging call and destructive DCD rewrite were removed.
- CV reference coordinates and solute/site connectivity are validated before
  production. The native joint ligand/anchor RMSD CV and zero-strength periodic
  centroid bond are retained; no per-step re-imaging or new forces are introduced.
- Element-based heavy-atom selections include names such as CH1/NH1 and shared
  protein-state recognition. Backbone fitting retains N/CA/C/O.
- cadd_md.openbpmd.scoring implements the native contact reference-distance rule,
  early-window normalization, first-frame exclusion, final-fifth aggregation and
  pooled population SD. It checks exact-frame engine CV agreement and writes
  checksum-bound completion records; incomplete/legacy caches are rejected.
- Runtime provenance records policy, source hashes, exact selections, frame steps,
  reference checksums, units and validation diagnostics. Custom overrides are
  explicitly unverified. No existing results are automatically rescored.
These are local modifications, not an upstream release. The original vendoring
revision was not recorded; no upstream commit identity is asserted. Upstream
comparison source: https://github.com/Gervasiolab/OpenBPMD/blob/main/openbpmd.py
The original MIT copyright, permission and disclaimer remain in the packaged
THIRD_PARTY_LICENSES/OpenBPMD-MIT.txt. Upstream authorship/version are retained.
