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
stratixs
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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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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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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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c87dda2
Remove unused import
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38456cc