Code

Alchemical Transfer Method#327

Code

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lohedges merged 96 commits intodevelOpenBioSim/biosimspace:develfrom feature_AToMOpenBioSim/biosimspace:feature_AToMCopy head branch name to clipboardOct 24, 2024

+8,967-33

Commits

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 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 23, 2024

• Testing for various analysis methods

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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

• 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 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

• 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

• 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 17, 2024

• 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 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 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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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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  dc9548a

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• Improve sectioning.

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  c1d8eb3

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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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