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v0.2.0: The Structural Refinement & Benchmarking Milestone

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@elkins elkins released this 17 Jun 15:56
· 15 commits to main since this release
v0.2.0
9190579

Added

  • Benchmarking Suite: Validated diff-biophys against experimental NMR data for proteins 2KZV and GmR58A (Li et al. 2023).
  • Refinement Factories: New high-level APIs make_rdc_refinement_fns and make_ca_shift_loss to simplify experimental data integration.
  • Robust Backbone I/O: Direct support for loading PDB models and extracting N–CA–C coordinates into JAX arrays via biotite.
  • Edge Case Test Suite: Comprehensive tests for numerical singularities (CD), collinearity (Kabsch), and empty input handling.

Fixed

  • RDC Overfitting: Implemented fixed-tensor refinement (periodically updated) to prevent trivial Q-factor minimization.
  • NH Bond Reconstruction: Improved peptide-plane bisector method for more accurate NH vector orientations from backbone coordinates.
  • Test Coverage: Achieved 100% coverage across all core biophysical modules.
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