Skip to content

v0.4.0 — 3D backbone reconstruction (NeRF)

Choose a tag to compare

View all tags
@krisss0mecom krisss0mecom released this 09 May 18:11
· 5 commits to main since this release
v0.4.0
f6f729b

What's new

3D backbone reconstruction from torsion trajectories — convert AlphaDynamics rollout .npz to multi-model PDB you can open in PyMOL / VMD / ChimeraX.

pip install -U alphadynamics

alphadynamics predict --sequence KLVFFAE --output klvffae.npz
alphadynamics rebuild klvffae.npz -s KLVFFAE -o klvffae.pdb --diagnostics
pymol klvffae.pdb        # animate the trajectory

Or from Python:

from alphadynamics import predict_torsion_ensemble, trajectory_to_pdb
traj = predict_torsion_ensemble("KLVFFAE", n_ensemble=4, rollout_steps=200)
trajectory_to_pdb(traj[0], "KLVFFAE", "klvffae.pdb")

Implementation

  • New module alphadynamics.geometry — deterministic NeRF (Parsons 2005) backbone reconstruction 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.
  • 13 new unit tests, all passing.

Output: backbone heavy atoms (N, Cα, C, O) only. No side chains, no hydrogens. Suitable for visualizing dynamics; not for docking.

Diagnostic tool, not structure prediction

Torsion errors accumulate along the chain — for long peptides (N > ~50) end-to-end displacement may be substantial even for small per-residue errors. This is intrinsic to torsion-space reconstruction, not a flaw of the algorithm. Use as diagnostic visualization ("does the model produce a sensible chain or spaghetti?"), not as high-resolution structure.

Defaults

  • ω = 180° (all-trans peptide bond). For cis-proline, supply per-residue omega_deg array with appropriate 0°.
  • Terminal angles phi[0] and psi[-1] are undefined geometrically — replaced with conventional defaults (-60° / +120°).

References

  • Parsons et al. 2005, J. Comput. Chem. 26: 1063-1068 (NeRF algorithm)
  • Engh & Huber 1991, Acta Crystallogr. A 47: 392-400 (bond constants)

Links

Assets 2
Loading