Release 2024.3.0 #357

lohedges · 2024-10-24T13:34:30Z

This is the PR for the 2024.3.0 release of BioSimSpace.

I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
I confirm that I have added a test for any new functionality in this pull request: [y]
I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y]
I confirm that I have permission to release this code under the GPL3 license: [y]

Begins to add support for serial AToM simulations in BioSimSpace OpenMM.

Several bug fixes, production simulations now run (contingent on minimisation and equilibration).

The introduction of this lever means that guesses have to be made regarding underlying details of the lambda schedule. Current assumptions are made using the base configs of both the Gallacchio lab and femto protocols

… argument to BSS.FreeEnergy.AToM.relativeATM

…to increase the stability of high lambda value calculations

…ctionary

…of AToM systems. Includes large amounts of re-factoring of ATM code.

…s own process

…aints in line with other methods

…tential well used to positonally restrain atoms

…l option

…protein. this is acheived by adding the ability to parse 'protein_index' as a list of ints. Required for the eralpha test system as it is truncated

…allachio lab repo

Also exposes AToMSetup to docs

[closes #354]

Alchemical Transfer Method

Synchronise with Exscientia remote

mb2055 added 30 commits January 3, 2024 16:58

Initial commit, still WIP

2516e40

Begins to add support for serial AToM simulations in BioSimSpace OpenMM.

Added multi-simulation support

be8dc09

STILL WIP.

8e79065

Several bug fixes, production simulations now run (contingent on minimisation and equilibration).

Removed redundant print statements

b874012

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

c0afe3c

The introduction of this lever means that guesses have to be made regarding underlying details of the lambda schedule. Current assumptions are made using the base configs of both the Gallacchio lab and femto protocols

Added processrunner support

e6b63dd

Added fallback for systems with no carbon atoms, and exposed platform…

590089f

… argument to BSS.FreeEnergy.AToM.relativeATM

More sensible default for distance restraint weight

dd83473

Adds support for annealing within AToM free energy protocols, aiming …

5c7cd18

…to increase the stability of high lambda value calculations

Begins to add support for COM restraints

e360d60

Adds constants for COM restraint to atom protocol

9023a48

Adds CM restraint to atom utils and openmm processes

9ed4178

Re-factoring of annealing, removed the need for the anneal_options di…

5c87109

…ctionary

Adds bespoke protocols for minimisation, equilibration and annealing …

d9224d1

…of AToM systems. Includes large amounts of re-factoring of ATM code.

Refactoring of AToM production, removing it from openmm process to it…

6dacf1d

…s own process

Standardises units thorughout

b5c62a6

Bugfixes for production scripts

72ff6d8

Merge branch 'devel' into feature_AToM

b860627

Switches positional restraints in AToM processes to flat-bottom restr…

ea33d2d

…aints in line with other methods

Added position restraint width argument that sets the width of the po…

0937c59

…tential well used to positonally restrain atoms

A few bugfixes

973fee5

Adds energy trajectory reporting, achieved through the report_interva…

eeee0f0

…l option

Changed default work directories to None

97e4136

Fixed bug with automatic ligand translation

3b35a86

Bugfixes for setting window-dependent variables from list

a0781cc

Switched to gallachio lab repo (wip)

4413b9e

adds support for pre-prepared systems with multiple molecules in the …

4397c5d

…protein. this is acheived by adding the ability to parse 'protein_index' as a list of ints. Required for the eralpha test system as it is truncated

Brings softcore constants of production in line with values used in G…

e28f10b

…allachio lab repo

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

43d5503

Updated and clarified unit checking for various parameters.

ddc56b1

lohedges and others added 23 commits October 7, 2024 13:25

Merge branch 'devel' into feature_AToM

fa894af

First draft of ATM tutorial

f2ec42d

Squash thermodynamic cycle image.

8ea5dec

Example input URLs now added and formatting tweaks.

aedf76c

Enhancements to the ATM tutorial.

22612af

Also exposes AToMSetup to docs

Rotate perturbable and non-perturbable molecules independently.

0b9b29f

[closes #354]

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

4095d96

Fix indexing of tutorials.

0e1933f

Fix sections.

d4e7ed0

Move API docs before examples.

dc9548a

Improve sectioning.

c1d8eb3

Switch from AToM to ATM.

24f8825

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

f5b9429

Make class attributes private.

c2665ab

Blacken.

613c58c

Merge pull request #327 from OpenBioSim/feature_AToM

85e7f36

Alchemical Transfer Method

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

38018a7

Guard test against missing OpenFF package.

58dba1c

Remove redundant variable.

e33f499

Test requires AMBER and OpenFF. [ci skip]

0365150

Merge pull request #356 from OpenBioSim/sync_exscientia

e84a422

Synchronise with Exscientia remote

Update Sire version.

e446721

Update CHANGELOG for the 2024.3.0 release.

3435cdc

lohedges temporarily deployed to biosimspace-build October 24, 2024 13:34 — with GitHub Actions Inactive

lohedges merged commit aa83a91 into main Oct 24, 2024
5 checks passed

lohedges deleted the release_2024.3.0 branch October 24, 2024 14:14

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Release 2024.3.0 #357

Release 2024.3.0 #357

lohedges commented Oct 24, 2024

Release 2024.3.0 #357

Release 2024.3.0 #357

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lohedges commented Oct 24, 2024