Code

Sync with Exscientia remote#277

Code

Merged

lohedges merged 45 commits intodevelOpenBioSim/biosimspace:develfrom sync_exscientiaOpenBioSim/biosimspace:sync_exscientiaCopy head branch name to clipboardApr 15, 2024

+1,418-710

Commits

Commits on Jan 5, 2024

• Merge remote-tracking branch 'upstream/main' into feat_2023.5.1

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Commits on Jan 9, 2024

• Merge pull request #33 from Exscientia/feat_2023.5.1

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Commits on Jan 26, 2024

• Backport fixes from PR #233. [ci skip]

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• Merge pull request #234 from OpenBioSim/backport_233

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Commits on Feb 7, 2024

• Backport fix from PR #237. [ci skip]

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Commits on Feb 8, 2024

• Merge pull request #239 from OpenBioSim/backport_237

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Commits on Feb 19, 2024

• Backport fixes from PR #244. [ci skip]

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Commits on Feb 20, 2024

• Merge pull request #245 from OpenBioSim/backport_244

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Commits on Feb 23, 2024

• Backport fixes from PR #247. [ci skip]

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• Merge pull request #249 from OpenBioSim/backport_247

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• Merge remote-tracking branch 'OpenBioSim/main' into feat_meain

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Commits on Feb 29, 2024

• Backport fixes from PR #251 and #253. [ci skip]

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• Merge pull request #254 from OpenBioSim/backport_251_253

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• Merge remote-tracking branch 'OpenBioSim/main' into feat_meain

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• Merge pull request #35 from Exscientia/feat_meain

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Commits on Mar 4, 2024

• Only write couple molecule when the decoupled mol is not perturbable (#36)

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Commits on Mar 5, 2024

• Langevin integrator for Free Energy calculations (#37)

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Commits on Mar 11, 2024

• Allow Gromacs to write dihedral_restraints in the presence of restraint-lambdas (#38)

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Commits on Mar 12, 2024

• Implement the Schrödinger's derivation of the analytical correction for Boresch restraint (#40)

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Commits on Mar 13, 2024

• Have the position restraint deals with the alchemical ion (#39)

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Commits on Mar 21, 2024

• Merge remote-tracking branch 'obs/main' into feat_main (#41)

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Commits on Apr 12, 2024

• Switch to using os.path.join.

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• Preserve fileformat property when creating a system from a molecule.

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  bd60625

• Make sure base protocol returns None for getRestraint.

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  a42aa2e

• Add missing thermostat_time_constant to metadynamics protocol.

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  65115b2

• Add temperature control to Metadynamics and Steering protocols.

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  557bbac

• Refactor fixtures.

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• Add local test for metadynamics simulations.

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  75ab3bd

• Use NAMD specific system in tests so we validate parsing too.

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• Make fixtures module specific.

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  b36da43

• Add tests for steered MD and funnel metadynamics.

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  631f1a4

• Revert copilot update to interchange file extensions.

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• Revert another copilot typo.

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• Merge branch 'devel' into final_fixes

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• Only run funnel metadynamics test locally.

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  5bd3545

• Port fileformat fix to sandpit.

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• Update test description.

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• Merge remote-tracking branch 'exscientia/devel' into sync_exscientia

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  dac5521

• Fix duplicate tests and add missing guards.

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  a1ec8af

• Remove references to redundant "future" branch. [ci skip]

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• Remove references to mamba since libmamba is now default solver.

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Commits on Apr 15, 2024

• Merge branch 'final_fixes' into sync_exscientia

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• Synchronise files untouched by Exs with core.

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  fc3897d

• Add missing skipif decorator.

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  958eaf6

• Guard test against missing GROMACS package.

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