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Release 2024.3.0#357

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lohedges merged 148 commits intomainOpenBioSim/biosimspace:mainfrom release_2024.3.0OpenBioSim/biosimspace:release_2024.3.0Copy head branch name to clipboardOct 24, 2024

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Commits on Jan 3, 2024

• Initial commit, still WIP

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Commits on Jan 10, 2024

• Added multi-simulation support

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Commits on Jan 11, 2024

• STILL WIP.

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Commits on Jan 12, 2024

• Removed redundant print statements

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Commits on Jan 15, 2024

• Introduces the master lambda lever, set using a num_lambda argument.

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• Added processrunner support

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Commits on Feb 6, 2024

• Added fallback for systems with no carbon atoms, and exposed platform argument to BSS.FreeEnergy.AToM.relativeATM

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Commits on Feb 7, 2024

• More sensible default for distance restraint weight

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Commits on Feb 14, 2024

• Adds support for annealing within AToM free energy protocols, aiming to increase the stability of high lambda value calculations

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Commits on Feb 26, 2024

• Begins to add support for COM restraints

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• Adds constants for COM restraint to atom protocol

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Commits on Feb 27, 2024

• Adds CM restraint to atom utils and openmm processes

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Commits on Mar 5, 2024

• Re-factoring of annealing, removed the need for the anneal_options dictionary

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Commits on Mar 7, 2024

• Adds bespoke protocols for minimisation, equilibration and annealing of AToM systems.

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Commits on Mar 8, 2024

• Refactoring of AToM production, removing it from openmm process to its own process

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Commits on Mar 11, 2024

• Standardises units thorughout

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Commits on Mar 12, 2024

• Bugfixes for production scripts

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Commits on Mar 14, 2024

• Merge branch 'devel' into feature_AToM

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Commits on Mar 18, 2024

• Switches positional restraints in AToM processes to flat-bottom restraints in line with other methods

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Commits on Mar 19, 2024

• Added position restraint width argument that sets the width of the potential well used to positonally restrain atoms

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Commits on Apr 26, 2024

• A few bugfixes

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Commits on Apr 29, 2024

• Adds energy trajectory reporting, achieved through the report_interval option

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Commits on Apr 30, 2024

• Changed default work directories to None

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• Fixed bug with automatic ligand translation

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Commits on May 1, 2024

• Bugfixes for setting window-dependent variables from list

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Commits on May 10, 2024

• Switched to gallachio lab repo (wip)

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Commits on May 20, 2024

• adds support for pre-prepared systems with multiple molecules in the protein.

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Commits on May 21, 2024

• Brings softcore constants of production in line with values used in Gallachio lab repo

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• Merge remote-tracking branch 'origin/devel' into feature_AToM

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• Updated and clarified unit checking for various parameters.

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Commits on May 24, 2024

• Fixed issue with incorrect window index in python scripts

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Commits on May 28, 2024

• Added in-house analysis based on code from both the Gallachio lab repo and femto.

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• remove redundant print statement

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• fixed issue with setting protein index

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• Removes redundant print statement

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• Switched print statements to proper warnings

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Commits on Jun 3, 2024

• Remove redundant imports

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Commits on Jun 12, 2024

• WIP First stage of refactor, moves AToM make functionality to a new AToM class.

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Commits on Jun 17, 2024

• WIP AToM refactoring and testing

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Commits on Jun 24, 2024

• Continued refactor.

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• Deleted redundant functionality

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Commits on Jun 27, 2024

• fixed imports

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Commits on Jul 9, 2024

• Update Sire development requirement.

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• Fix formatting. [ci skip]

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Commits on Jul 10, 2024

• Update PFEP tutorial paper link

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• Merge branch 'OpenBioSim:devel' into feature_protein_FEP

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• Merge pull request #310 from akalpokas/feature_protein_FEP

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Commits on Jul 11, 2024

• Add support for merging ions. [closes #312]

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• Add unit test for ion merge.

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• Exclude sander.LES from allowed executables.

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Commits on Jul 12, 2024

• Continued refactor, includes single-point energy testing to ensure parity with Gallachio Lab code

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• Merge branch 'devel' into feature_AToM

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Commits on Jul 16, 2024

• WIP. Adds support for MBAR analysis, also updates openMM scripts to add on-the-fly saving of energy trajectories

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Commits on Jul 17, 2024

• Merge pull request #313 from OpenBioSim/fix_312

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Commits on Jul 23, 2024

• Testing for various analysis methods

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Commits on Jul 24, 2024

• Add missing extra_args kwarg. [closes #318]

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Commits on Jul 29, 2024

• Merge pull request #319 from OpenBioSim/fix_318

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• Typo. [ci skip]

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Commits on Jul 30, 2024

• Add AMBER to list of supported FEP engines. [ci skip] [closes #322]

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• Merge pull request #323 from OpenBioSim/fix_322

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Commits on Jul 31, 2024

• Cleaned up API documentation

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Commits on Aug 1, 2024

• Adds explanation of AToM functionality to FreeEnergy docs

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• Adds ignore_lower input to UWHAM analysis, allowing the first N samples to be ignored when calculating energies

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Commits on Aug 2, 2024

• Switch to using pip install. [ci skip]

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• Fixed docs for annealing and production protocols

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• Merge branch 'devel' into feature_AToM

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• Adds support for safely resarting simulaitons from checkpoints

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Commits on Aug 5, 2024

• Fixes for using BioSimSpace runner to run production, as well as fixes and tests for restarting from checkpoint!

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Commits on Aug 6, 2024

• Runner fix

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• Remove analysis methods used for testing

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Commits on Aug 7, 2024

• Alters UWHAM analysis to bring it more in line with GL code

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• Doc fixes

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Commits on Aug 8, 2024

• Switch to os.path for tests

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• Blacken

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• Switch to CPU platform for single point energy test, shortened length of simulations run in process tests

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• Remove debug print statement from analysis [ci skip]

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Commits on Aug 12, 2024

• Adds ignore_upper option to UWHAM analysis [ci skip]

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Commits on Aug 16, 2024

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

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• use the new sire

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

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Commits on Aug 20, 2024

• Makes atm file naming consistent, simplifies openmm protocol if statement, makes protocol setters and getters public

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Commits on Aug 21, 2024

• Merge pull request #53 from Exscientia/feat_sync

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• Fixing a box check in GMX (#54)

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• First stage of variable name standardisation, in this case the COM distance restraint

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• Next part of protocol renaming, this time for the alignment restraint and its corresponding constants

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• Next set of changes for protocol variable naming, this time the soft core parameters

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• Simplifies protocol check in atm_utils

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• Corrects spelling of Gallicchio

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• Make imports in ddg private

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• Change name of atm protocol test to bring in line with other test names

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• UWHAM analysis now returns energy in kcal/mol

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Commits on Aug 27, 2024

• Exclude lipids from heavy atom restraint for Gromacs Process (#55)

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• Changed Runtimerror to warning when UWHAM weights don't add to 1

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Commits on Sep 2, 2024

• Swaps the protein keywork with receptor when creating ATM systems (needed since some systems are host/guest)

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• Makes openMM import private [ci skip]

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Commits on Sep 5, 2024

• Fix the bug where AMBER Process will not use report interval (#56)

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Commits on Sep 6, 2024

• Relax constraint on single atom mappings. [closes #332]

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• Merge pull request #333 from OpenBioSim/fix_332

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Commits on Sep 12, 2024

• Fixing vacuum translations in GROMACS (#57)

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Commits on Sep 13, 2024

• Update underlying Sire object at each iteration. [closes #335]

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Commits on Sep 17, 2024

• Merge pull request #336 from OpenBioSim/fix_335

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• Updates view rigid cores with labelling and colour coding

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• Switches naming of ligand1 and ligand2 to ligand_bound and ligand_free

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Commits on Sep 18, 2024

• Formatting

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Commits on Sep 20, 2024

• Add method to remove the space property from a system.

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Commits on Sep 25, 2024

• Reference system needs to be converted to an end state. [closes #340]

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• Apply previous fix to Process.Namd.

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• Fix for running FreeEnergyMinimisation and FreeEnergyEquilibration with restraints using GROMACS

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• Apply same fix to Process.Amber.

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• Merge pull request #338 from OpenBioSim/feature_remove_space

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• Merge pull request #341 from OpenBioSim/fix_340

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• Merge pull request #342 from OpenBioSim/fix_339

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Commits on Sep 27, 2024

• Allow end-state connectivity property to differ. [closes #344]

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Commits on Sep 30, 2024

• Use direct RDKit conversion as intermediate for OpenFF.

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Commits on Oct 2, 2024

• Merge pull request #345 from OpenBioSim/fix_344

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• Merge pull request #349 from OpenBioSim/fix_348

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• Add missing copy of reference system.

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• Presever SMILES molecule properties when parameterising. [closes #331]

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• Update example mapping visualisation. [closes #350] [ci skip]

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Commits on Oct 4, 2024

• Formatting tweaks.

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• Make carbon atom search more robust.

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• Make variable name consistent.

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• Docstring formatting tweaks.

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• Refactor AToM code.

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Commits on Oct 7, 2024

• Merge pull request #352 from OpenBioSim/fix_330_2

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• Merge branch 'devel' into feature_AToM

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Commits on Oct 11, 2024

• First draft of ATM tutorial

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Commits on Oct 14, 2024

• Squash thermodynamic cycle image.

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• Example input URLs now added and formatting tweaks.

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Commits on Oct 21, 2024

• Enhancements to the ATM tutorial.

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Commits on Oct 22, 2024

• Rotate perturbable and non-perturbable molecules independently.

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• Remove redundant jupyter nb-extension commmands. [ci skip]

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Commits on Oct 24, 2024

• Fix indexing of tutorials.

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• Fix sections.

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• Move API docs before examples.

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• Improve sectioning.

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• Switch from AToM to ATM.

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• Merge remote-tracking branch 'origin/fix_354' into feature_AToM

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• Make class attributes private.

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• Blacken.

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• Merge pull request #327 from OpenBioSim/feature_AToM

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

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• Guard test against missing OpenFF package.

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• Remove redundant variable.

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• Test requires AMBER and OpenFF. [ci skip]

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• Merge pull request #356 from OpenBioSim/sync_exscientia

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• Update Sire version.

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• Update CHANGELOG for the 2024.3.0 release.

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