feat(steering): add FKC steered denoiser with RMSD/FNC CVs and examples#214
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Add Feynman-Kac Control (FKC) steering denoiser and supporting components: Source code: - steering/dpm_fkc.py: FKC steered denoiser with analytical Girsanov weights - steering/collective_variables.py: Add RMSD, FractionNativeContacts CVs - steering/potentials.py: Add LinearPotential - steering/utils.py: Add compute_sequence_alignment, kabsch_align - denoiser.py: Add GuidedScore dataclass for FKC pre-scaled scores - config/steering/cv_steer.yaml: FKC steering config example - toy_gmm.py: 1D Gaussian mixture model for toy examples Examples: - notebooks/fkc_steering.py: FKC steering toy demonstration - notebooks/gmm_umbrella_mbar.py: GMM umbrella sampling with MBAR analysis Tests: - test_integration.py: FKC integration, ODE consistency, cv_steer config tests - test_potentials.py: LinearPotential unit tests - test_utils.py: Sequence alignment tests - test_steering_numerically.py: Numerical validation on GMM Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
…e1/fkc-steering-v2
…ove toy_gmm, clean tests - Rename 'Feynman-Kac Control' to 'Feynman-Kac Corrector' everywhere - Clarify SMC (unbiased denoising) vs FKC (biased by reward) in README - Remove '(SMC only)' from ess_threshold docs (FKC uses it too) - Replace manual residue loop with topology.to_fasta() in RMSD CV - Remove decorative # === separator comment blocks - Move toy_gmm.py from src/bioemu/ to notebooks/ (not core library) - Remove trivial/redundant tests, tighten loose threshold (10.0 -> 1.0) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
…ack formatting Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
SummarySummary
Coveragesrc.bioemu - 89%
src.bioemu.colabfold_inline - 79.1%
src.bioemu.hpacker_setup - 69.2%
src.bioemu.steering - 79.5%
src.bioemu.training - 100%
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Add Feynman-Kac Control (FKC) steering denoiser and supporting components:
Source code:
Examples:
Tests: