ProPrep 1.19.0

Added

• The Transformer Creator shows what the linked library expects. When it
  opens after an import it prints, for the residue the library fits, which
  heavy atoms share a name with the library unit, which exist only in the
  structure, which exist only in the library, and which differ only in
  case; a new lib command lists every library atom, and lib <chain> <resid> compares any residue. The site-match line after an import now
  reports the residue-name match and the atom-name overlap separately
  instead of calling a name match "100% of its atoms".

• The Force Field Parameterizer's import accepts a prep file in place of a
  library. Published parameter sets (the Bryce database, journal SI) often
  ship a residue as prep + frcmod; ProPrep's library, loader and
  transformers want an OFF library, so the wizard now converts the prep
  with tLEaP at import time, deposits the resulting library, and keeps the
  prep alongside it. The residue name is read from inside the prep, every
  residue of a multi-residue prep is saved, and a digit-leading residue
  name is refused with an explanation rather than failing inside tLEaP.

• Dihedral refinement is the same in every parameterizer and fits jointly.
  The small-molecule step sm-7 and the modified-amino-acid step 9 (both
  routes) share one engine: pick dihedrals from the parmchk2 penalty table,
  reuse any relaxed scan already run (the amino-acid linkage scan chosen at
  step 3, every scanned conformer, the de-novo sidechain scan), derive
  further scan inputs from the molecule's own optimization input at the
  optimized geometry, pause at a checkpoint until Gaussian has run, then fit
  every selected dihedral together in one paramfit run against a topology
  built from the current frcmod (after Seminario). Previously each dihedral
  was fitted alone against the topology built before any refinement, and
  the amino-acid routes could only refit the one torsion scanned at step 3.
  A refit is written under the residue's shared atom types and loaded after
  the protein force field, so before fitting, each scanned dihedral is
  checked against Amber's parameter files and residue libraries: a quad the
  force field defines explicitly, or that any standard residue contains, is
  shown but not refit; a quad covered only by a wildcard and absent from
  every standard residue, the usual covalent-linkage case, is refit.

• Undo. Typing undo at any prompt lists the answers recorded so far and
  rewinds the session to one of them, either asking that question again or
  replacing its answer and replaying what followed. ProPrep unwinds to the
  top, rebuilds its state, and replays the session log to that point in the
  same process, so the exit, relaunch, edit-the-log, replay cycle is no
  longer needed. The replaced tail is kept in a timestamped backup of the
  log. Requires session recording, which is on by default.

Changed

• The Structure Loader no longer says "cancel", which read as cancelling
  the structure just loaded. The source menu's last item is "Done (return
  to the Structure Loader menu)", the RCSB, AlphaFold, and AlphaFill method
  menus end in "Back to source selection", the search-refinement menu ends
  in "Back to results (no filter)", and a declined download says "Download
  skipped". The AlphaFold, AlphaFill, and UniProt entry prompts offer 'b'
  to go back, and the PDB search and UniProt structure pages offer 'back';
  the old 'c' and 'cancel' still work so recorded sessions replay. Menu
  numbers are unchanged.

Fixed

• ~/ProPrep/bin/proprep and ~/ProPrep/bin/proprep-web, launched by
  absolute path as INSTALL.md says, could not find tLEaP ("not found in
  PATH") and had no AMBERHOME. A console script never activates the
  environment it lives in, so the bundled AmberTools was invisible unless
  the user first sourced amber.sh. Both entry points now locate the
  Amber tree next to the running interpreter and set AMBERHOME and
  PATH themselves; an AMBERHOME that is already set and valid is kept.
  The ONIOM atom typer no longer falls back to a developer-machine path.

• CREST dihedral refinement handed tLEaP paramfit's output, which contains
  only the fitted terms; the final topology was built from an incomplete
  frcmod. The fitted terms are now spliced into the full frcmod.

• Re-running sm-7 in a new session found no refinement selection and
  skipped; the sm-5 choice is now persisted and sm-7 can also make it.
  Waiting for Gaussian no longer marks sm-7 completed.

• Replacing a fitted dihedral matched the reversed orientation by reversing
  the character string, so two-character types (c3-c3-os-c) never
  matched their reverse; multi-term dihedrals are now replaced whole.

• Scan angles were reported as 15-degree steps whatever step size was chosen.

• Resuming a de-novo modified-amino-acid run in a new session could not
  find the step-7 AC file when it had been given a custom residue name, so
  step 9 skipped the torsion refinement; a lone AC file in the run
  directory is now accepted.

• paramfit was allowed to fit dihedral periodicity as a continuous number
  and could return values such as 2.93; periodicity is now held at the
  parmchk2 value and only the barrier and phase are fitted.

• A modified amino acid parameterized against ff19SB changed every
  arginine and tyrosine in the protein. parmchk2 runs with -a Y, so the
  residue's frcmod carries a copy of each of its standard bonded terms,
  and tLEaP gives that file priority once it is loaded after the leaprc.
  The ff19SB path gave parmchk2 parm19.dat without frcmod.ff19SB, so the
  copies held the older single-term values for the guanidinium and
  hydroxyl torsions and replaced ff19SB's multi-term definitions system
  wide. parmchk2 now receives frcmod.ff19SB too, and a regression test
  loads a generated frcmod into an ff19SB peptide and checks that no
  parameter of any standard residue changes. ff14SB and ff99SB already
  passed their correction files and were unaffected.

• Seminario's "all" scope in the modified amino acid route refined the
  residue's standard bonded terms and wrote them under the shared atom
  types, which would have replaced the protein force field's values for
  every residue. The option stays listed, but choosing it now explains
  why only the by-analogy terms can be refined and asks again.

• An AlphaFold structure loaded from the AlphaFold Database did not appear
  in the Structure Viewer. The download is mmCIF, but the viewer told NGL
  every served file was PDB, so the model parsed as empty. The viewer now
  passes each file's format from its suffix (pdb, cif, mol2, ...), and
  structure names in the viewer and saved scenes drop whichever suffix the
  file has.

• Site templates in the Redox Site Detector now resolve bonds and custom
  boundary atoms by identity instead of position. A template recorded each
  bond as a row number in the residue table and each boundary atom as an
  index into the site's atom list, then replayed both as positions in every
  other site. Rows of same-type residues are ordered by a distance sort that
  is a near-tie, so the two Cys, two His, or two propionates swapped in
  about half the sites and produced 6 to 12 Å "bonds". Transformed HCO hemes
  also carry their grafted atoms in per-site order, so the boundary indices
  pointed at other atoms in 48 of 64 hemes of a multiheme structure, and at
  three sites the search then picked a neighbouring heme's His over the true
  one. Bonds now store residue names and bond the closest unused residue
  pair of those names; boundary atoms store residue name, ordinal, and atom
  name and fall back to the index only when the name is absent. The
  applied-bond log line now names both residues.

• The Homology Searcher no longer requires a loaded structure to run a
  BLAST search. The entry point checked for a structure before it ever
  reached the sequence-source prompt, so the "enter a sequence directly"
  and "load from FASTA" choices were unreachable without one, and since
  1.17 the menu greyed out the option to match. A structure is now
  optional: the prompt always lists the same three sources (typed, FASTA,
  loaded structure) so session replay is unaffected, and picking the
  structure source with nothing loaded explains and asks again. The
  MODELLER build still needs a template structure.

• Eleven bare except: clauses in the MD Manager, workflow editor, and
  restraint manager wrapped a prompt and would have swallowed the rewind
  signal (and a SystemExit); they now catch Exception.

Installers (SHA-256)

Self-contained installers with AmberTools, MODELLER and every dependency; no conda needed. See INSTALL.md.

a3600f71ce5e742fc32b25510dd4beb39073f40b912297218af4a8079e907269  ProPrep-1.19.0-Linux-x86_64.sh
0159220c6246537fb62629ba90f4c6d61f72761b154ffef5cad9ce457385c547  ProPrep-1.19.0-MacOSX-arm64.sh
cca1ada074edcd6ae17812521486698521a685922b241f8f753b3abf7f0830ac  ProPrep-1.19.0-MacOSX-x86_64.sh