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added 3 commits
February 3, 2026 13:31
…ameters and metrics This commit modifies the disulfide bridge steering example and related classes to incorporate additional input parameters for atom positions and distances. The steering potential now supports both Cα-Cα and Cβ-Cβ distance metrics, improving flexibility in steering configurations. Additionally, the example script is updated to reflect these changes, ensuring accurate distance calculations and visualizations.
- Remove batch_frames_to_atom37 and _batch_adjust_oxygen_pos from convert_chemgraph.py - Simplify log_physicality in steering.py to remove C-N distance calculations - Remove test_batch_frames_to_atom37_correctness_and_performance test - Keep get_atom37_from_frames and _adjust_oxygen_pos for PDB output functionality
SummarySummary
Coveragesrc.bioemu - 88.2%
src.bioemu.colabfold_setup -
src.bioemu.hpacker_setup - 58.8%
src.bioemu.openfold.np - 44%
src.bioemu.openfold.utils - 50.1%
src.bioemu.training - 100%
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sarahnlewis
approved these changes
Feb 5, 2026
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Due to the insufficient power of the current steering algorithm, we should forego the Disulfide potentials which requires more capable steering. This also does not necessitate the reconstruction of the backbone atoms, obviating a series of batched transformations for atom37 reconstructions as steering is done exclusively on the Ca positions.