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Changelog

All notable changes to AlphaDynamics will be documented in this file.

v0.4.3 — 2026-05-09 (final Windows hotfix)

Fixed

  • Real source of charmap codec cant encode on Windows: -> in geometry.py:trajectory_to_pdb() REMARK header. The PDB file was opened without explicit encoding, so Windows used cp1252 (charmap) which doesnt support U+2192. Crash position 43 = exact location of arrow.
  • v0.4.2 only fixed CLI prints; geometry.py still wrote -> in the PDB header itself.
  • Now: open(out_pdb, "w", encoding="utf-8") + ASCII -> in REMARK.

Verified

  • cp1252 strict-encoding simulation now writes PDB without exception.

v0.4.2 — 2026-05-09 (Windows compatibility hotfix)

Fixed

  • Windows charmap (cp1252) crash on PDB generation. v0.4.1 used Unicode arrow (→) and Å in print statements, which crashed on default Windows console encoding (cp1252). Symptom: (3D PDB generation skipped: charmap codec cant encode character). Result: PDB never written.
  • Replaced Unicode arrows with ASCII -> in interactive output.
  • Replaced Å (Angstrom symbol) with A in unit labels.
  • Replaced Cα with Ca in user-facing prints.
  • Added sys.stdout.reconfigure(encoding="utf-8") on Windows for safety.

Notes

  • Same v0.4.1 functionality otherwise.
  • HTML/PNG plot files are unaffected (plotly/matplotlib write Unicode directly to file, no terminal encoding issue).

v0.4.1 — 2026-05-09 (same day patch)

Changed — auto-generate PDB

  • alphadynamics predict now automatically writes both .npz and .pdb by default. Previously you had to run alphadynamics rebuild separately. This was confusing UX.
  • Interactive prompt also auto-generates PDB after npz.
  • New flag --no-pdb to skip PDB generation if you only want torsions.
  • New flag --pdb-out to override PDB output path.
  • New flag --pdb-frames (default: 50) to subsample trajectory in PDB.

Notes

  • PDB uses ensemble member 0; subsampled to 50 frames for compact file size.
  • Diagnostics (Rg, end-to-end) printed automatically.
  • Link to live online viewer printed for convenience.

v0.4.0 — 2026-05-09

Added — 3D backbone reconstruction

  • New module alphadynamics.geometry: deterministic NeRF reconstruction (Parsons 2005) of backbone heavy atoms (N, Cα, C, O) from torsion trajectories with Engh-Huber 1991 standard bond geometry.
  • Functions: torsions_to_backbone(), trajectory_to_pdb(), radius_of_gyration(), end_to_end_distance(), trajectory_diagnostics().
  • New CLI subcommand alphadynamics rebuild: 
    alphadynamics rebuild rollout.npz -s KLVFFAE -o backbone.pdb --diagnostics
  • Output: multi-model PDB with backbone heavy atoms, openable in PyMOL / VMD / ChimeraX. Per-frame Rg and end-to-end distance diagnostics.
  • 13 new unit tests in tests/test_geometry.py.
  • README section "3D backbone reconstruction" with quickstart.

Notes

  • Backbone-only (no side chains, no hydrogens).
  • Torsion errors accumulate along the chain; for long peptides (N > ~50) end-to-end displacement may be substantial. Use as diagnostic visualization, not as high-resolution structure prediction.
  • Defaults: ω = 180° (all-trans). For cis-proline supply per-residue omega_deg array.
  • Terminal angles phi[0] and psi[-1] are undefined geometrically and are replaced with conventional defaults (-60° / +120°).

v0.3.9 — 2026-05-04

  • Robust checkpoint loader with AD-Init seeding
  • Scope warning for sequences > 20 aa

v0.3.0 → v0.3.8

  • Open-source release of sequence-only product
  • Interactive prompt mode
  • HTML Ramachandran plots (plotly)
  • Auto-update check on import
  • Pre-flight write checks

See git log for details on intermediate versions.