Add correlated parameter perturbation to PerturbBundle#683
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Add correlated parameter perturbation to PerturbBundle#683everyday847 wants to merge 1 commit intoRosettaCommons:mainfrom
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Introduces <Correlation> sub-tags for PerturbBundle that specify Pearson correlation coefficients between bundle parameters. When present, correlated parameters are perturbed jointly via multivariate Gaussian sampling (Cholesky decomposition of the covariance matrix). Parameters not involved in correlations continue to be perturbed independently. Adds a Cholesky decomposition wrapper in numeric/linear_algebra/ backed by Eigen::LLT, exposing only vector1-based types.
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Nice -- this is a feature that had been on my wishlist for a long time.
…On Fri, May 1, 2026 at 12:16 PM Andy Watkins ***@***.***> wrote:
Introduces sub-tags for PerturbBundle that specify Pearson correlation
coefficients between bundle parameters. When present, correlated parameters
are perturbed jointly via multivariate Gaussian sampling (Cholesky
decomposition of the covariance matrix). Parameters not involved in
correlations continue to be perturbed independently.
Adds a Cholesky decomposition wrapper in numeric/linear_algebra/ backed by
Eigen::LLT, exposing only vector1-based types.
------------------------------
You can view, comment on, or merge this pull request online at:
#683
Commit Summary
- bb306f5
<bb306f5>
Add correlated parameter perturbation to PerturbBundle
File Changes
(7 files <https://github.com/RosettaCommons/rosetta/pull/683/files>)
- *M* source/src/numeric.src.settings
<https://github.com/RosettaCommons/rosetta/pull/683/files#diff-309e3689ece85463ad59432f4cd90eaf8af6d2c61f7074abed3ddd2566edffc8>
(1)
- *A* source/src/numeric/linear_algebra/cholesky_decomposition.cc
<https://github.com/RosettaCommons/rosetta/pull/683/files#diff-3b0af938815c3f8e97087b31ad343a7a9b1c9776244897edcfe2562729175ce5>
(69)
- *A* source/src/numeric/linear_algebra/cholesky_decomposition.hh
<https://github.com/RosettaCommons/rosetta/pull/683/files#diff-0c90fe074549e5a4ec8f5c50bff8b00dd0176d581e9d6a2f2c0f9d72fbe48802>
(38)
- *M* source/src/protocols/helical_bundle/PerturbBundle.cc
<https://github.com/RosettaCommons/rosetta/pull/683/files#diff-0991645d74e22310cfd667a3c3c8de7c0d9832a767245264ea3e05b525ea4d70>
(296)
- *M* source/src/protocols/helical_bundle/PerturbBundle.hh
<https://github.com/RosettaCommons/rosetta/pull/683/files#diff-38ad3b3d5c8ba693a8b89b524188d6b4c6e1293bfbc7bc2fd6a5ec27bc6bf0d7>
(42)
- *M* source/test/protocols.test.settings
<https://github.com/RosettaCommons/rosetta/pull/683/files#diff-9c214c7c7aa04f119433bca39c6fe25f202502f75d6fe0eda3991bed09c93052>
(1)
- *A*
source/test/protocols/helical_bundle/PerturbBundleCorrelatedTests.cxxtest.hh
<https://github.com/RosettaCommons/rosetta/pull/683/files#diff-4608d9c6c5fd199bb964c5fdfe23bbcd23ec5a1f4a7e1faa6b18c22d9bc89fb8>
(336)
Patch Links:
- https://github.com/RosettaCommons/rosetta/pull/683.patch
- https://github.com/RosettaCommons/rosetta/pull/683.diff
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Introduces sub-tags for PerturbBundle that specify Pearson correlation coefficients between bundle parameters. When present, correlated parameters are perturbed jointly via multivariate Gaussian sampling (Cholesky decomposition of the covariance matrix). Parameters not involved in correlations continue to be perturbed independently.
Adds a Cholesky decomposition wrapper in numeric/linear_algebra/ backed by Eigen::LLT, exposing only vector1-based types.