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[WIP] SepTop Protocol#1057

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hannahbaumann wants to merge 178 commits intoOpenFreeEnergy:mainOpenFreeEnergy/openfe:mainfrom hannahbaumann:start_septophannahbaumann/openfe_septop:start_septopCopy head branch name to clipboard

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Commits on Oct 23, 2024

• Initial commit SepTop settings

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Commits on Oct 24, 2024

• Initial SepTop protocol work

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• Some fixes

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• Implement a Setup unit and empty Run unit

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Commits on Oct 25, 2024

• Updating positions in the solvent and complex

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Commits on Nov 11, 2024

• Add some femto utils, setup alchemical system

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Commits on Nov 15, 2024

• Work on implementing restraints

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Commits on Nov 19, 2024

• Some more changes

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• Add some femto utils

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• Some fixes for the restraints

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• Create separate solvation settings for solvent and complex

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• Testing some things

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• Testing some things

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• Fix comp_resids_B

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• Fix restraints complex mdtraj

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• Update restraint selection

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Commits on Nov 20, 2024

• More edits Boresch restraints

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• Change type check restraints

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• Changes unitcell lengths

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• Small test unit cell

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Commits on Nov 21, 2024

• Update unit cell length

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• Update unit cell length2

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• small fix

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• More changes restraints

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• Print statements to help troubleshoot restraints

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• Update indices

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• Fix units

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• Update units

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• Small fixes

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Commits on Nov 22, 2024

• Change lambda settings

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Commits on Nov 26, 2024

• Serialize system

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• small fix

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• Only store system, topology

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• Start of run unit

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• Add run unit to create method

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• Add missing import

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Commits on Nov 27, 2024

• Write run unit

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• Remove unnecessary import

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• Remove verbose

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• Add states to run unit

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• Add simtype

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• Remove nocutoff

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• Small fixes

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• Change monotonic check

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• Put troubleshooting pdb files in the sharedbase path for now

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Commits on Nov 28, 2024

• Fix scaling restraints

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• Update boresch scaling

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• testing something

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Commits on Dec 2, 2024

• Test out not doing a preequ

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• Change min length solvent

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Commits on Dec 3, 2024

• Change phase detection

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• Adding print statements for debugging

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Commits on Dec 4, 2024

• Add print statements to help debug

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• Save prequ file

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• Run short equ

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• first pass at abstract classes

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• Update gather to separate setup and run results

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Commits on Dec 5, 2024

• Fix gather

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• A start at restraints and forces

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Commits on Dec 6, 2024

• Testing out using the openmmtools alchemical factory instead of femto

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• Add imports

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• Add boresch restraint class

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• Fix units

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Commits on Dec 9, 2024

• Adapt Lambda states

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• Add individual lambda restraints

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• Small FIx

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• Fix restraints sign

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• 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 10, 2024

• More tests and fixes

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• More updates

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Commits on Dec 11, 2024

• Merge branch 'main' into start_septop

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• Update compute location

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• Small fix

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• Adding some more docstrings

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• 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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• AlchemicalFactory changes

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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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• Add slow energy test

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• Move energy test to slow

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• Fix energy test

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• Fix off molecule

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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

• Merge branch 'main' into start_septop

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• base for restraint settings

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• Fix up some things

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• Subclass Parameterstate

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• Change AlchemicalRegion name

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• Update restraint lambda parameter

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• Update settings

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• Add restraint settings

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• Add missing settings imports

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• Change alchemical state def

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Commits on Dec 17, 2024

• Remove copy of AlchemicalFactory

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• Remove femto alchemy

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• Remove unnecessary file

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• Small fixes

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• 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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• Some fixes

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• Update tests

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Commits on Dec 18, 2024

• Merge branch 'main' into start_septop

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Commits on Dec 19, 2024

• Add tests protocol results

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• Merge branch 'main' into start_septop

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Commits on Dec 20, 2024

• Addressing reviews

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• debug failing test

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• Test restraints closer

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• Test restraints closer 2

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Commits on Jan 7, 2025

• Add a todo from last year

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Commits on Jan 8, 2025

• Merge branch 'main' into start_septop

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• Fix tests

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• Some mypy fixes

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• small fixes

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• More mypy fixes

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• Add gather test

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Commits on Jan 10, 2025

• Merge branch 'main' into start_septop

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• Some restaints updates

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Commits on Jan 13, 2025

• Dry run and make run function in the RunUnit

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• Delete commented out parts

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• Add test for user charges

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Commits on Jan 14, 2025

• Small test

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• Small fix

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• Add more tests

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• More tests

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• Add tests for cutoff and pressure

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Commits on Jan 15, 2025

• Merge branch 'main' into start_septop

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Commits on Jan 16, 2025

• Add tests for reference xml

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• Merge branch 'start_septop' of github.com:hannahbaumann/openfe_septop into start_septop

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• Test distance solvent restraint in dry run

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Commits on Jan 20, 2025

• Merge branch 'main' into omm-restraints

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• Add slow test for solvent 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 23, 2025

• Small changes

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• Merge branch 'main' into start_septop

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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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• Merge remote-tracking branch 'upstream/omm-restraints' into start_septop

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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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Commits on Jan 28, 2025

• Merge remote-tracking branch 'upstream/omm-restraints' into start_septop

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Commits on Jan 29, 2025

• First step towards using omm-restraints class

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• Small fixes

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• Fix type

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• Fix atom selection solvent restraints

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• Fix modeller positions

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Commits on Jan 31, 2025

• Use separate structures for getting Boresch restraints

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• Add equil traj output

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• Add traj output equil

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Commits on Feb 4, 2025

• Subclass MDOutputSettings for SepTop

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