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v0.4.1 — predict auto-generates PDB (UX fix)

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@krisss0mecom krisss0mecom released this 09 May 18:59
· 2 commits to main since this release
v0.4.1
0ccd956

What changed

alphadynamics predict now automatically generates both .npz and .pdb by default.

pip install -U alphadynamics

alphadynamics predict --sequence AAAY -o aaay.npz
# [predict] wrote aaay.npz
# [pdb] wrote aaay.pdb  (50 frames × 4 residues)
# [pdb] Rg = 3.36 ± 0.33 Å  |  end-to-end = 7.75 ± 1.66 Å
# [pdb] open in PyMOL/VMD/ChimeraX

pymol aaay.pdb     # animated 3D backbone trajectory

Why

v0.4.0 required a separate alphadynamics rebuild step after predict. Confusing UX. This patch makes the 3D pipeline one-command.

New flags (all optional)

  • --no-pdb — skip PDB generation (only .npz)
  • --pdb-out PATH — custom PDB output path (default: <output>.pdb)
  • --pdb-frames N — subsample to N frames in PDB (default: 50)

Interactive mode

alphadynamics (no args) → prompt → also auto-generates PDB after npz, prints diagnostics inline.

Backward compatibility

  • Default behavior changed (.pdb is now written unless --no-pdb)
  • All v0.4.0 functionality preserved (geometry module, rebuild subcommand still works for old .npz files)

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