ProPrep 1.15.0

Added

• Modified amino acid parameterization gained a from-structure route (Route B):
  a structure analyzer, a redesigned ten-step workflow with an explicit
  conformer-selection step, consistent residue naming, and resume resilience
  at every step. Torsional sampling is shared with Route A, which now
  auto-generates its sidechain scan rather than requiring one to be specified.
• Route B can optionally run a relaxed dihedral scan as a sampling mode and
  refit the scanned torsion with paramfit, so a rotatable bond that GAFF
  describes poorly can be corrected without leaving the workflow.
• Conjugate naming checks the force-field library for an existing residue of
  the same name before writing, and offers to reuse it instead of silently
  producing a second definition.
• The MD wizard offers the mdin keywords its own help text already referred
  to, adds baro_stochastic and ninterface, and completes four features
  that were previously only half-exposed. Coverage was swept against the full
  Amber manual by parameter index.
• Batch replay checks up front that every run supplies each variable the
  template needs, and fails loudly on divergence rather than blocking on
  stdin. The summary now distinguishes runs that failed from runs never
  attempted, and writes a retry list naming the runs still owed.
• The web shell tees each session to a plain-text transcript.
• The structure viewer can measure dihedrals, supports per-representation
  opacity, and defaults to an orthographic camera.
• The membrane builder offers solvate-only directly from the lipid menu.
• Force-field preparation deposits finished parameters from every
  parameterizer's final step, so the deposited library no longer depends on
  which route produced the parameters.
• An in-place updater, update_proprep_in_ambertools.sh, refreshes ProPrep
  inside an existing conda AmberTools environment without a full reinstall.
• Workspace inventory gained compact --abbrev output that collapses
  duplicate labels.

Changed

• The MD manager treats the restraint manager as authoritative for imported
  mdin files, so restraints defined on import are no longer overwritten by
  the file's own restraint block.
• Heme transformers require their match criteria to be met exactly and clamp
  the bond credit awarded, so a partially matching site is no longer claimed
  by a transformer that does not fit it.
• The Seminario refinement scope reads "by-analogy" rather than "flagged",
  which describes what the option actually does.
• The membrane builder's "Advanced" geometry menu is now "Specialized
  Geometry".
• Component-type display names in the PDB filter come from a single source,
  so the triage table and the filter menu can no longer disagree.
• Checklist step numbers and section headings remain legible on light
  terminal backgrounds.
• The viewer's measurement pick marker is a fixed radius rather than scaling
  with the structure.

Fixed

• Heme HMO (ferric) and HMR (ferrous) parameter sets had lost the trans
  pyrrole N-Fe-N angles; both are restored.
• The generated mdin carried an inverted comment for ntmin, and several MD
  wizard parameter descriptions were inaccurate. The help text was audited
  against the Amber manual across all 89 parameters and the advisory fields,
  which could not be kept correct, were dropped.
• Force-field parameter analysis no longer crashes on string-valued
  *_structure keys.
• Route B step 9 recovers the antechamber AC file on resume, and step 10
  reconstructs RedoxSite objects before syncing, so a resumed run no longer
  fails where a continuous one succeeds.
• The protonation summary surfaces desolvation, and the viewer no longer
  renders a stale structure after an edit.
• The installer no longer defaults past the orphan purge when run through
  curl | bash, self-heals on the update path, and forces a standalone
  ProPrep to win the ambertools-dac file clobber.
• Workspace inventory covers aliased receivers, wrappers, and comments, and
  excludes legacy metallo files that cannot be imported.