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Release 2024.1.0#278

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Merged

lohedges merged 154 commits intomainOpenBioSim/biosimspace:mainfrom release_2024.1.0OpenBioSim/biosimspace:release_2024.1.0Copy head branch name to clipboardApr 15, 2024

+15,610-1,828

Commits

Commits on Dec 16, 2023

• Update Sire version. [ci skip]

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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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  0d03787

Commits on Jan 18, 2024

• Fix path to links file. [closes #231]

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  dc348b1

• Fix redirection of stderr for logger. [ref #232]

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Commits on Jan 23, 2024

• Merge branch 'fix_231' into fix_232

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  224428d

• Update copyright range.

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  c518ffe

Commits on Jan 24, 2024

• Match atoms by coordinates.

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Commits on Jan 26, 2024

• Merge pull request #233 from OpenBioSim/fix_232

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• Merge branch 'devel' into feature_atomcoordmatcher

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• Merge pull request #235 from OpenBioSim/feature_atomcoordmatcher

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  dff31eb

Commits on Feb 5, 2024

• Add _generate_binary_run_file staticmethod.

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  90855ee

• Allow use of a separate file as a reference for position restraints.

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  ddc5785

• Run pytest-black against Python 3.11.

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  62763b6

Commits on Feb 6, 2024

• Forgot to use selector for running pytest-black.

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  d18da44

• Also need to add source files to selector.

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  4998dd2

• Pin to pytest 7 until pytest-black is updated.

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  4175229

Commits on Feb 7, 2024

• Call staticmethod on class, not instance.

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  b7944d1

• Merge pull request #237 from OpenBioSim/fix_236

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  286a467

Commits on Feb 12, 2024

• Build Python 3.10 for macOS.

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  6ad3ac1

Commits on Feb 14, 2024

• Update support range. [ci skip]

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  bec58fb

Commits on Feb 19, 2024

• Remove redundant parmed import and references to parmed files.

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  5cc7dea

• Expose FreeEnergyMixin protocols. [closes #243]

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  1730723

• Remove shared properties when loading perturbable systems.

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  committed
  1cfa0bd

• Merge pull request #244 from OpenBioSim/fix_241-243

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  d94c19b

Commits on Feb 21, 2024

• Add support for using a reference system for position restraints.

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  7ab5c8d

Commits on Feb 22, 2024

• Add support for FEP with AMBER molecular dynamics engine.

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  committed
  5dc399a

• Fix funnel range used in correction calculation. [closes #246]

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  committed
  c8eba8d

• Change file extensions for interchange files to Sire defaults.

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  c2aaf0b

• Recover missing molecule0 and molecule1 properties. [closes #248]

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  50b5bb6

Commits on Feb 23, 2024

• Merge pull request #247 from OpenBioSim/fix_240_246

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

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Commits on Feb 26, 2024

• Improve error mesage when attempting to extract all dummy selection.

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  6e106dd

• Avoid setting all end-state properties when decoupling

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Commits on Feb 27, 2024

• Remove extra line to satisfy black

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  8c4e338

• Merge pull request #253 from fjclark/feature_somd_abfe_properties

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  848e90c

• Merge branch 'devel' into feature_amber_fep

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  24cbc65

Commits on Feb 29, 2024

• Merge pull request #251 from OpenBioSim/fix_250

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  6414428

• Merge branch 'devel' into feature_amber_fep

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  committed
  4f32f2d

• 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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  cb37485

Commits on Mar 8, 2024

• Only convert to end state if this isn't a FreeEnergy protocol.

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  234ca88

• Exclude standard free ions from AMBER restraint mask. [closes #258]

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  committed
  5adf455

• Add support for fractional exponents in __pow__ operator. [closes #259]

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  3a4a850

Commits on Mar 11, 2024

• Fix dimension mask for restraint force constants.

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  committed
  2d96b17

• Merge branch 'fix_256' into fix_258_259 [closes #257]

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  1f9699f

• Another dimension mask fix.

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  1ff16e9

• Handle addition or subtraction by a zero-valued integer or float.

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  committed
  33d5a15

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

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  3709cda

• Validate dimension mask in test, not unit string.

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  245aacb

• Switch to classmethods.

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  committed
  1126143

• Remove redundant offset variable.

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  de2a883

• Windows no longer pulls in requests by default.

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  0b429ef

• Use decimal representation to simplify __pow__ logic.

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  3f3e897

• This is a much simpler solution.

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  4e8bc6e

Commits on Mar 12, 2024

• Add custom _find_exe function for AMBER.

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  committed
  c9a7f0e

• Appears that igb=6 is only needed for pmemd.cuda.

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  committed
  004dbb3

• Remove invalid kwarg.

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  cdc962c

• Append process object for first lambda window.

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  committed
  5b68d72

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

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  baf0aef

Commits on Mar 13, 2024

• Add way of specifying extra command-line arguments for AMBER and GROMACS

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  34e2730

• Add **kwargs to all Process classes.

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  d01f254

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

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  18b95cb

• Don't use pmemd.cuda for vacuum FEP simulations.

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  4399905

Commits on Mar 14, 2024

• Add AMBER FEP analysis test.

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  committed
  777d459

• Add SOMD1 compatibility mode as an option for AMBER/GROMACS FEP.

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  31b34df

• Need to pass system to hasWater method.

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  b87d1ed

Commits on Mar 20, 2024

• Merge pull request #257 from OpenBioSim/fix_256

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  9a0e253

• Merge pull request #260 from OpenBioSim/fix_258_259

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  4480a5a

• Merge branch 'devel' into feature_amber_fep

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Commits on Mar 21, 2024

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

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• Use Langevin integrator for free-energy simulations.

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  3b52d29

Commits on Mar 22, 2024

• Pass explicit_dummies kwargs through to _generate_amber_fep_masks.

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  68bcc2c

• Remove redundant openff.Topology import.

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  6da2b9d

• Remove redundant openff.Topology import.

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  c10d28b

• Add support for using NAGL to generate AM1BCC charges.

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  40ecb82

Commits on Mar 25, 2024

• Add default _has_nagl flag.

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  9355e30

• Add support for clearing and disabling the file cache. [closes #265]

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  0a3bd90

• Allow user to choose to use NAGL to generate AM1-BCC charges.

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  committed
  0e2bb92

• Upgrade setup-miniconda action.

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  af9cced

• Manually add boltons.

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  04b423d

Commits on Mar 26, 2024

• Pin to boa version 0.16.

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  f987c2b

Commits on Mar 28, 2024

• Glob after converting files to a list.

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  46da6e7

• Add support for adding molecules from a SearchResult.

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  committed
  426e30a

• Merge branch 'feature_clear_cache' into feature_nagl

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  committed
  cac2302

• Need to exlude URLs from glob.

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  29aff16

• Convert all single string parameters to a list.

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  committed
  9b6cf96

• Need to use tishake=1 and an appropriate noshakemask in vacuum.

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  33bdd2d

• Use is_vacuum flag.

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  188fb68

Commits on Apr 8, 2024

• Merge pull request #264 from OpenBioSim/fix_gmx_integrator

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  authored
  25757a2

• Remove boa and packaging pins. [ci skip]

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  committed
  5d3ed74

• Merge pull request #266 from OpenBioSim/feature_clear_cache

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  ddc29de

• Filter base units list by type and base class. [closes #269]

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  committed
  e2919b5

• Make sure kwargs are supported in __init__.

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  committed
  7f11fbd

• Handle vaccum FEP simulations with pmemd and pmemd.cuda.

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  044ad4a

• Remove the parameters property before creating a partial molecule.

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  f1fb052

• Remove the parameters property when extracting a partial molecule.

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  committed
  185ccaa

Commits on Apr 9, 2024

• Merge pull request #267 from OpenBioSim/feature_nagl

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  27739b6

• Merge branch 'devel' into feature_amber_fep

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  committed
  2f0a0f9

• Add pmemd single-point energy tests.

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  698473b

• Update Python variants to match Sire.

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  8d781d4

• Fix Python variant platform excludes.

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  77d4524

• Upgrade versioneer.

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  f1d4223

• Remove duplicate __version__.

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  de627b9

• Blacken.

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  9e54237

• Use list rather than set so search strings are reproducible.

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  692849e

• Join protein and nucleic acid residue strings correctly.

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  81d8233

• Use try/except when matching by coordinates.

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  f44b35e

Commits on Apr 10, 2024

• Merge branch 'devel' into feature_amber_fep

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  de06ed7

• Exclude sander from free-energy simulations.

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  9b870cd

• Update to black 24.

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  11f59ff

• Merge branch 'fix_270' into feature_amber_fep

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  283c050

• Add AMBER as an example engine in hydration free-energy tutorial.

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  83fe05f

• Improve comment regarding single-point energy difference.

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  621b75a

• Use readMolecules to read NAMD output since MoleculeParser segfaults.

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  2ec7ee7

• Don't use SHAKE for minimisation. [ci skip]

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  844fb1d

• Figured out how to match vacuum energies.

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  6ded910

• Use correct file for reference system.

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  7294841

• Convert water topology of reference system so naming matches.

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  daad0e1

• Try debugging Windows error.

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  d33004c

• Remove debugging statements.

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  59323f5

• Use relative file names in OpenMM Python script.

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  3951502

Commits on Apr 12, 2024

• Switch to using os.path.join.

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  4d6f6a8

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

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  committed
  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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  fed23af

• 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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  861f5d3

• 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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  4dcf175

• Revert another copilot typo.

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  committed
  2c0b1e6

• Merge pull request #272 from OpenBioSim/feature_amber_fep

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  fdff786

• Merge branch 'devel' into final_fixes

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  23a3596

• Only run funnel metadynamics test locally.

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  5bd3545

• Port fileformat fix to sandpit.

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  1f7a46b

• Update test description.

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  c1cb363

• 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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  d8d5740

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

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  cfb4284

Commits on Apr 15, 2024

• Merge branch 'final_fixes' into sync_exscientia

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  77d6cfa

• 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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  d79961e

• Merge pull request #277 from OpenBioSim/sync_exscientia

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  3abcec4

• Merge branch 'main' into release_2024.1.0

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  cd2547b

• Update CHANGELONG for the 2024.1.0 release.

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  b7f68ba

• Update Sire version.

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  769ff19

• Typo. [ci skip]

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