feat: steering to avoid chain breaks and clashes#171

Merged

nw13slx merged 71 commits intomainfrom

luwinkler/cli_steering

Jan 21, 2026

Commits on Jul 21, 2025

feat: add TODO for fk steering implementation in heun_denoiser
ludwigwinkler
committed

Commits on Jul 22, 2025

Merge branch 'main' into luwinkler/fk_steering
ludwigwinkler
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gitignore test outputs and test case for steering
ludwigwinkler
committed
Merge branch 'luwinkler/fk_steering' of os.github.com:microsoft/bioemu into luwinkler/fk_steering
ludwigwinkler
committed

Commits on Jul 25, 2025

first prototype
ludwigwinkler
committed

Commits on Jul 28, 2025

feat: implement Kabsch alignment and enhance steering functionality with FK sampling
ludwigwinkler
committed

Commits on Aug 3, 2025

feat: add wandb to .gitignore to exclude Weights and Biases files
ludwigwinkler
committed

Commits on Aug 19, 2025

Refactor steering module and add new steering run script
ludwigwinkler
committed

Commits on Aug 22, 2025

Add BioEMU development rules and enhance load_md script
ludwigwinkler
committed

Commits on Aug 29, 2025

Commits on Sep 1, 2025

Commits on Sep 3, 2025

Enhance steering capabilities and update documentation
ludwigwinkler
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Refine steering documentation and enhance configuration handling
ludwigwinkler
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Update README to refine steering section and enhance CLI usage instructions
ludwigwinkler
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Update README to include Python API example for steering and remove Hydra configuration section
ludwigwinkler
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Commits on Sep 10, 2025

Update .gitignore to exclude documentation files
ludwigwinkler
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Commits on Sep 30, 2025

Refactor steering configuration and enhance disulfide bridge potential
ludwigwinkler
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Add guidance steering capabilities and update experiment scripts
ludwigwinkler
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Enhance guidance steering implementation and update experiment configurations
ludwigwinkler
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Commits on Oct 1, 2025

Enhance guidance steering comparison and update configurations
ludwigwinkler
committed

Commits on Oct 17, 2025

Modify final resampling step in denoiser.py
YuuuXie
authored

Commits on Oct 20, 2025

fix x0 type
YuuuXie
authored

Commits on Nov 4, 2025

Add physicality steering comparison notebook and update configurations
ludwigwinkler
committed
Merge branch 'luwinkler/cli_steering' of github.com:microsoft/bioemu into luwinkler/cli_steering
ludwigwinkler
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Update README.md

ludwigwinkler
and
sarahnlewis
authored
Update README.md

ludwigwinkler
and
sarahnlewis
authored
Update README.md

ludwigwinkler
and
sarahnlewis
authored
refs for readme on steering and smc
ludwigwinkler
committed
Merge branch 'luwinkler/cli_steering' of github.com:microsoft/bioemu into luwinkler/cli_steering
ludwigwinkler
committed
Update notebooks/README_hydra_run.md

ludwigwinkler
and
sarahnlewis
authored
some renaming files and typos
ludwigwinkler
committed
Merge branch 'luwinkler/cli_steering' of github.com:microsoft/bioemu into luwinkler/cli_steering
ludwigwinkler
committed
Remove unused guidance images: deleted `guidance_steering_comparison.png` and `guidance_visualization_display.png` to clean up the repository.
ludwigwinkler
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Remove profiler module: deleted `src/bioemu/profiler.py` as it is no longer needed
ludwigwinkler
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Remove unused steering scratch pad: deleted `src/steering_scratch_pad.py` as it is no longer needed.
ludwigwinkler
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Remove unused denoiser configuration: deleted `src/bioemu/config/denoiser/em.yaml` as it is no longer needed.
ludwigwinkler
committed
Remove unused guidance steering configuration: deleted `src/bioemu/config/steering/guidance_steering.yaml` as it is no longer needed.
ludwigwinkler
committed
Merge branch 'main' into luwinkler/cli_steering
ludwigwinkler
authored

Commits on Dec 3, 2025

Commits on Dec 8, 2025

cleaned up notebooks and configs
ludwigwinkler
committed

Commits on Dec 16, 2025

Commits on Jan 12, 2026

Refactor steering parameters and update configuration for consistency across codebase
ludwigwinkler
committed
Add disulfide bridge steering potential and example scripts for comparison
ludwigwinkler
committed
Merge branch 'main' into luwinkler/cli_steering
ludwigwinkler
authored
Add type hints to log_physicality and potential_loss_fn functions for improved clarity
ludwigwinkler
committed
Refactor logging in log_physicality function and add logger initialization
ludwigwinkler
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ReadMe update and typo fix
ludwigwinkler
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reverted back to no return sample() function
ludwigwinkler
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Remove sample result validation from steering tests for cleaner output
ludwigwinkler
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Update steering section in README to clarify the use of steering particles
ludwigwinkler
committed

Commits on Jan 20, 2026