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[WIP] Restraints API#1043

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IAlibay wants to merge 52 commits intomainOpenFreeEnergy/openfe:mainfrom omm-restraintsOpenFreeEnergy/openfe:omm-restraintsCopy head branch name to clipboard

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Commits on Dec 4, 2024

• first pass at abstract classes

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Commits on Dec 5, 2024

• A start at restraints and forces

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Commits on Dec 6, 2024

• Add boresch restraint class

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• Fix units

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Commits on Dec 9, 2024

• Fix correction return in kj/mole

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• Add more restraint API bits

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• move some things around

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• Merge branch 'main' into omm-restraints

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Commits on Dec 11, 2024

• Some changes

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• Merge branch 'omm-restraints' of github.com:OpenFreeEnergy/openfe into omm-restraints

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Commits on Dec 12, 2024

• refactor restraints

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• add some angle checks

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• only construct with settings

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• Add more checks to utilities

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• host finding code

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• fix up weird black wrapping

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• remove old search file, add more changes to boresch search

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• Merge branch 'main' into omm-restraints

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• Remove duplicate methods

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• Apply suggestions from code review

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• Add some more docstring

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Commits on Dec 13, 2024

• Add minimized vectors on the collinear checks

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Commits on Dec 14, 2024

• add host atom finding routine

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• autoformatting

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• various fixes

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• docstring drive

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Commits on Dec 15, 2024

• Migrate to restraint_utils

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Commits on Dec 16, 2024

• base for restraint settings

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  c914b18

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• Fix up some things

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• Add restraint settings

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• Add missing settings imports

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Commits on Dec 17, 2024

• Settings and some tests for them

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• negative idxs test

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• addressing some mypy issues

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Commits on Dec 20, 2024

• Addressing reviews

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Commits on Jan 7, 2025

• Add a todo from last year

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Commits on Jan 20, 2025

• Merge branch 'main' into omm-restraints

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Commits on Jan 21, 2025

• Update to address review comments

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• Last review comment

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Commits on Jan 22, 2025

• Various fixes

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Commits on Jan 24, 2025

• Now with DSSP!

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• the big refactor

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• fix imports

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Commits on Jan 26, 2025

• Fix up secondary structure filtering & add chain selection

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• Add angle wrapping method

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• Add more tests

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• Add tests for heavy atom getter

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• Add extra test

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• Add some extra tests

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Commits on Jan 27, 2025

• Add collinearity tests & better explanation of code

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• Add tests and fix a few things

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• Angle variance tests

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