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Release 2024.4.0#282

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lohedges merged 124 commits intomainOpenBioSim/sire:mainfrom release_2024.4.0OpenBioSim/sire:release_2024.4.0Copy head branch name to clipboardFeb 5, 2025

Commits

Commits on Jul 10, 2024

• Initial update for angle restraints

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• Intial addition of alchemical dihedral restraints and angle restraints update

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Commits on Jul 16, 2024

• Update wrappers for angle and dihedral restraints classes

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• Added intial python code for implementing alchemical dihedral restraints

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• Added prototype code for adding alchemical dihedral restraints to OpenMM system

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• Fix conversion of dihedral restraints to OpenMM system

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Commits on Jul 17, 2024

• Added full end-to-end alchemical dihedral restraints implementation - bugs might still be lurking somewhere

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Commits on Jul 19, 2024

• Added full end-to-end alchemical angle restraints implementation, and also renamed the core alchemical angle/dihedral restraint c++ files

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• Add the missing corelib files for angle restraints

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Commits on Jul 20, 2024

• Merge branch 'OpenBioSim:devel' into feature_alchemical_restraints_contd

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Commits on Oct 23, 2024

• Update to the 2024.4.0.dev release. [ci skip]

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• Fix note formatting. [ci skip]

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• Fix tutorial section formatting. [ci skip]

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Commits on Oct 28, 2024

• Fix instantiation of QByteArray and counting of bytes. [closes #249]

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Commits on Oct 29, 2024

• Increase wait before terminating QThreads. [closes #251] [ci skip]

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• Update CHANGELOG. [ci skip]

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• Give thread a chance to finish and inform user. [ci skip]

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• Merge pull request #250 from OpenBioSim/fix_249

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• Expose missing timeout kwarg in dynamics.minimise(). [closes #253]

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• Add include_constrained_energies kwarg to map. [ref #255]

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• Add consistent minimisation settings. [closes #255]

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• Update CHANGELOG.

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Commits on Oct 30, 2024

• Merge pull request #254 from OpenBioSim/fix_253

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Commits on Nov 1, 2024

• Make Boresch restraints correction consistent with F=2kx

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• Update docs to make clear that F = 2kx for restraints

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Commits on Nov 8, 2024

• Don't always save frames and energies after dynamics.run() [ref #256]

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• Simplify test logic.

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• Fix thread safety issue in OpenMM minimiser. [closes #259]

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• Remove redundant include.

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Commits on Nov 11, 2024

• Update CHANGELOG.

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• Improve handling of OpenMM NaN errors at runtime.

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Commits on Nov 22, 2024

• Add support for REST2.

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Commits on Nov 26, 2024

• Allow per-lambda REST2 scaling factors.

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• Fix update of PeriodicTorsionForce parameters.

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• Fix calculation of molecule atom offset.

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Commits on Nov 28, 2024

• Add missing scale factor in exception.

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Commits on Nov 29, 2024

• Workaround for device change during minimisation. [ref #262]

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• Add minimisation step to QM/MM tutorials. [ref #262]

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• Fix QM-to-MM non-equilibrium work. [ref #262]

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Commits on Dec 2, 2024

• Update CHANGELOG. [ci skip]

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• Fix setting of RDKit bond orders. [ref #261]

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• Set bond stereo information. [ref #261]

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• Allow implicit hydrogens. [ref #261]

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• Assign sterochemistry from 3D coordinates. [ref #261] [ci skip]

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• XFail test since SDF stereochemistry is now preserved. [ref #261]

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• Update CHANGELOG.

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Commits on Dec 3, 2024

• Merge remote-tracking branch 'fjclark/bugfix-boresch-correction' into fix_262

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• Fix thread safety issue in OpenMM minimiser. [closes #259]

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• Update rest2_scale factor attribute when it changes.

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• Apply REST2 scale factor on instantiation.

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• Udpate lambda if REST2 scale factor changes.

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• Apply REST2 scaling factor in SOMMContext constructor.

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• Merge pull request #263 from OpenBioSim/fix_262

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Commits on Dec 4, 2024

• Add missing Sire-EMLE documentation updates. [ci skip]

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• Add REST2 related attributes to copy constructor.

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• Merge branch 'devel' into feature_repex

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• Make sure REST2 scale factor is reset after computing energies.

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• Only update lambda and REST2 scale factors if needed.

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Commits on Dec 9, 2024

• Fix update of triclinic box vectors. [closes #265]

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• Update CHANGELOG.

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Commits on Dec 13, 2024

• Merge pull request #266 from OpenBioSim/fix_265

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• Merge branch 'devel' into feature_repex

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Commits on Jan 6, 2025

• Try reducing the number of cores used to compile wrappers on Windows.

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• Revert change to number of cores used to compile wrappers. [ci skip]

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Commits on Jan 7, 2025

• Remove redundant optimised callback interface. [closes #269]

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• Merge pull request #271 from OpenBioSim/fix_269

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• Handle cis/trans double bond stereo value in SDF files. [closes #270]

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Commits on Jan 10, 2025

• Sync with upstream devel branch

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• Updated restraints tutorial to include angle and dihedral restraints, also slightly tidied up python API for these restraints

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• Add basic unit tests for the new restraints

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• Updated changelog and contributor pages for the PR

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Commits on Jan 13, 2025

• Add test for OpenMM REST2 modifications.

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• Update test to cover partial REST2 selection.

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• Typo.

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Commits on Jan 14, 2025

• Update alchemical dynamics docs with REST2 information.

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• Use reference platform for test.

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• Only need rest2_scale_factors when lambda_windows is not None.

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• Only loop until runtime is exceeded, not save interval.

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• Add test for dynamics save frequency modifications. [ref #256]

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• Merge branch 'devel' into feature_repex

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• Attempt to fix threading exception handling issue.

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• No need for inner while loop.

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• Remove early exit in set_lambda method.

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• Removed whitespace that was added and tidied up python restraints files [ci skip]

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• Added force names to custom OpenMM angle and torsion forces

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• Restore thread before throwing any exceptions.

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Commits on Jan 15, 2025

• Add test for non-perturbable REST2 atoms and fix partial selections.

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• Fix REST2 selection handling.

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• Update CHANGELOG.

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• Fix adjustment of block size based on sampling frequency.

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Commits on Jan 16, 2025

• Find force by name to avoid issues if ordering changes. [ci skip]

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• Use .num_frames() method for simplicity. [ci skip]

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• Add option to always save a frame when .run() exits.

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• Add option to always save the energy when .run() exits.

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Commits on Jan 17, 2025

• Null the SystemTrajectory pointer when deleting all frames. [ci skip]

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• Fix handling of positive formal charge when writing SDF. [closes #274]

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• Update CHANGELOG. [ci skip]

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Commits on Jan 20, 2025

• Merge branch 'fix_270' into feature_repex [ci skip]

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• Change hyperthetical->hypothetical

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• Update images to in line with actual outputs and remove redundant note

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• Subplots in code snippets in line with new plots [ci skip]

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Commits on Jan 21, 2025

• Reduce image sizes [ci skip]

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• Merge remote-tracking branch 'origin/Alchem_dynamics_docs_change' into feature_repex

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• Update CHANGELOG. [ci skip]

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• Removed redundant comments for restraints code [ci skip]

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• Merge remote-tracking branch 'akalpokas/feature_alchemical_restraints_2' into feature_repex

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• Merge pull request #273 from OpenBioSim/feature_repex

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Commits on Jan 24, 2025

• Exclude alchemical ions from the REST2 region.

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Commits on Jan 27, 2025

• Allow user to compute energies over subset of lambda windows. [ci skip]

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Commits on Jan 29, 2025

• Compute num_lambda_windows when lambda_windows is not None. [ci skip]

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• Clarify that all windows are used when None. [ci skip]

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• Merge pull request #277 from OpenBioSim/fix_rest2_alchemical_ions

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• Fix hasForceSpecificEquation

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• Update changelog [ci skip]

  

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Commits on Jan 30, 2025

• Merge branch 'devel' into bugfix-force-specific-equation [ci skip]

  

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• Merge pull request #280 from fjclark/bugfix-force-specific-equation

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Commits on Feb 3, 2025

• Add support for OpenMM MonteCarloMembraneBarostat.

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Commits on Feb 4, 2025

• Merge pull request #281 from OpenBioSim/feature_membrane_barostat

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• Merge branch 'main' into release_2024.4.0

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• Update CHANGELOG for the 2024.4.0 release.

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• Bump version.

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• Handle zero and NoneType for dynamics save frequencies. [closes #283]

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• Merge pull request #284 from OpenBioSim/fix_283

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• Merge branch 'devel' into release_2024.4.0

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