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ENM Base class - #22

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stratixs wants to merge 63 commits into

biotite-dev:masterfrom

stratixs:base-class

Open

ENM Base class#22
stratixs wants to merge 63 commits into
biotite-dev:masterfrom
stratixs:base-class

Commits on May 1, 2026
- Update dependencies
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  af31ef6
Commits on May 3, 2026
- Add type information
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  68a6091
Commits on May 4, 2026
- Add ENM base class
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  1a4fc94
- Eigenvalues and -vectors as class attributes
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  561496c
- Moved shared nma calls into ENM base class
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  f68114f
Commits on May 8, 2026
- Move adjacency calculation into ENM base class and Kirchhoff/Hessian
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  4e6e697
- Make ENM.eigen() be able to return number of zero eigenvalues
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  cdb82a3
Commits on May 9, 2026
- Boost test coverage for GNM and ANM
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  ea615ae
- Make ForceField updatable
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  364f1a8
Commits on May 10, 2026
- Fix ForceField test
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  46a97f1
- Add benchmark dependency
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  aabd0c3
Commits on May 11, 2026
- Fix inverse calculation
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  8925369
- Merge branch 'base-class' into perturbation
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  53855aa
- Add covariance perturbation for GNM
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  7b5881f
Commits on May 12, 2026
- Fix covariance perturbation
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  24a2be6
Commits on May 13, 2026
- Restructure covariance perturbation
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  c4d4a00
- Further covariance perturbation restructuring and optimization
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  b658ad7
Commits on May 15, 2026
- Initial ANM covariance perturbation
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  460417e
Commits on May 17, 2026
- Add cython setup for eigenvalue perturbation
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  39d2795
- Sync changes with branches
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  c6ecc33
- Use covariance matrix for msqf if available
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  077f84c
Commits on May 18, 2026
- ANM msqf tests
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  fb18abf
- Add frequency perturbation
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  8c248d8
Commits on May 21, 2026
- Generalize modify_contact algorithm
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  bc36226
- Merge branch eigen-perturbation into perturbation; update to covariance
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  6c9c060
Commits on May 26, 2026
- Rework modify_atom
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  09dacde
- Merge branch 'perturbation' into base-class; upstream changes
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  16708de
- Merge branch 'base-class' into perturbation; mean square fluctuation
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  0a6d5b1
Commits on May 30, 2026
- revert changes to interaction calculation
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  01657f1
- Make enm.eigen() return nb of zero eigenvalues instead of zero mask
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  4443f9d
Commits on May 31, 2026
- Streamline msqf calculation and use covariance if possible
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  435ddb7
Commits on Jun 1, 2026
- Merge branch 'base-class' into perturbation; eigen and msqf update
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  2f060f2
- Fix tests
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  89ddfde
- Interaction with higher precision and ForceField test with .cif file
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  c5c0ea5
- Remove duplicate test data
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  fd55216
- Add msqf and bfactor one-rank perturbation
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  34db29e
Commits on Jun 2, 2026
- Merge branch 'perturbation' into eigen-perturbation
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  7330be5
Commits on Jun 3, 2026
- Add frequency perturbation
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  99616d8
- Change functions names from '_pert' to _chng'
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  eb30109
- Add msqf and bfactor algorithm for subsets
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  b341dfb
Commits on Jun 4, 2026
- Rework dcc calculation and add dcc one-rank update
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  9263a14
- Function and variable renaming
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  b6b0135
- Docstring corrections
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  1db6a98
Commits on Jun 5, 2026
- Docstring overhaul
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  872902b
- Update README and advanced documentation
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  5c28bee
- github actions update
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  7899877
Commits on Jun 6, 2026
- Fix doc deploy env
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  2d91503
- Fix githuib workflows
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  9b15662
- Workflow fix
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  3382454
- Update test.yml
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  80a508c
Commits on Jun 7, 2026
- Change build system to hatch
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  a2c3efa
- Fix cython args and changes to deploy workflow
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  b55a30e
- Update deploy.yml
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  8cd643a
- Update deploy.yml
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  committed
  46f5248
- Remove unnecessary hatch dev env and fix build-docs in deploy workflow
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  0d0661b
- Update deploy.yml
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  099b8c3
- Finalize deploy workflow
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  df81110
- Fix to modify_contact
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  a165ae0
- Merge branch 'eigen-perturbation' into perturbation; NMA perturbation,
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  committed
  18e5d2a
Commits on Jun 8, 2026
- Merge branch 'perturbation' into base-class; numpy docstrings and hatch
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  fcbd3b2
- Prs test with cif
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  c51e3d7
- fix deploy workflow
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  committed
  c87dda2
- Remove unused import
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  committed
  38456cc

Commits

Commits on May 1, 2026

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Commits on Jun 8, 2026