ENM Base class#22

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stratixs wants to merge 63 commits into

biotite-dev:masterfrom

stratixs:base-class

Commits on May 1, 2026

Update dependencies
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Commits on May 3, 2026

Add type information
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Commits on May 4, 2026

Add ENM base class
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Eigenvalues and -vectors as class attributes
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Moved shared nma calls into ENM base class
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Commits on May 8, 2026

Move adjacency calculation into ENM base class and Kirchhoff/Hessian
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Make ENM.eigen() be able to return number of zero eigenvalues
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Commits on May 9, 2026

Boost test coverage for GNM and ANM
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Make ForceField updatable
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Commits on May 10, 2026

Fix ForceField test
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Add benchmark dependency
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Commits on May 11, 2026

Fix inverse calculation
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Merge branch 'base-class' into perturbation
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Add covariance perturbation for GNM
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Commits on May 12, 2026

Fix covariance perturbation
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Commits on May 13, 2026

Restructure covariance perturbation
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Further covariance perturbation restructuring and optimization
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Commits on May 15, 2026

Initial ANM covariance perturbation
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Commits on May 17, 2026

Add cython setup for eigenvalue perturbation
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Sync changes with branches
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Use covariance matrix for msqf if available
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Commits on May 18, 2026

ANM msqf tests
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Add frequency perturbation
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Commits on May 21, 2026

Generalize modify_contact algorithm
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Merge branch eigen-perturbation into perturbation; update to covariance
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Commits on May 26, 2026

Rework modify_atom
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Merge branch 'perturbation' into base-class; upstream changes
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Merge branch 'base-class' into perturbation; mean square fluctuation
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Commits on May 30, 2026

revert changes to interaction calculation
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Make enm.eigen() return nb of zero eigenvalues instead of zero mask
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Commits on May 31, 2026

Streamline msqf calculation and use covariance if possible
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Commits on Jun 1, 2026

Merge branch 'base-class' into perturbation; eigen and msqf update
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Fix tests
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Interaction with higher precision and ForceField test with .cif file
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Remove duplicate test data
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Add msqf and bfactor one-rank perturbation
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Commits on Jun 2, 2026

Merge branch 'perturbation' into eigen-perturbation
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Commits on Jun 3, 2026

Add frequency perturbation
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Change functions names from '_pert' to _chng'
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Add msqf and bfactor algorithm for subsets
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Commits on Jun 4, 2026

Rework dcc calculation and add dcc one-rank update
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Function and variable renaming
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Docstring corrections
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Commits on Jun 5, 2026

Docstring overhaul
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Update README and advanced documentation
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github actions update
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Commits on Jun 6, 2026

Fix doc deploy env
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Fix githuib workflows
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Workflow fix
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Update test.yml
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Commits on Jun 7, 2026

Change build system to hatch
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Fix cython args and changes to deploy workflow
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Update deploy.yml
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Update deploy.yml
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Remove unnecessary hatch dev env and fix build-docs in deploy workflow
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Update deploy.yml
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Finalize deploy workflow
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Fix to modify_contact
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Merge branch 'eigen-perturbation' into perturbation; NMA perturbation,
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Commits on Jun 8, 2026

Merge branch 'perturbation' into base-class; numpy docstrings and hatch
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Prs test with cif
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fix deploy workflow
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Remove unused import
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