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Release 2024.3.0 #357

Merged
merged 148 commits into from
Oct 24, 2024
Merged

Release 2024.3.0 #357

merged 148 commits into from
Oct 24, 2024

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lohedges
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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]

@mb2055
Initial commit, still WIP
2516e40 
Begins to add support for serial AToM simulations in BioSimSpace OpenMM.
@mb2055
Added multi-simulation support
be8dc09
@mb2055
STILL WIP.
8e79065 
Several bug fixes, production simulations now run (contingent on minimisation and equilibration).
@mb2055
Removed redundant print statements
b874012
@mb2055
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
@mb2055
Added processrunner support
e6b63dd
@mb2055
Added fallback for systems with no carbon atoms, and exposed platform…
590089f 
… argument to BSS.FreeEnergy.AToM.relativeATM
@mb2055
More sensible default for distance restraint weight
dd83473
@mb2055
Adds support for annealing within AToM free energy protocols, aiming …
5c7cd18 
…to increase the stability of high lambda value calculations
@mb2055
Begins to add support for COM restraints
e360d60
@mb2055
Adds constants for COM restraint to atom protocol
9023a48
@mb2055
Adds CM restraint to atom utils and openmm processes
9ed4178
@mb2055
Re-factoring of annealing, removed the need for the anneal_options di…
5c87109 
…ctionary
@mb2055
Adds bespoke protocols for minimisation, equilibration and annealing …
d9224d1 
…of AToM systems.

Includes large amounts of re-factoring of ATM code.
@mb2055
Refactoring of AToM production, removing it from openmm process to it…
6dacf1d 
…s own process
@mb2055
Standardises units thorughout
b5c62a6
@mb2055
Bugfixes for production scripts
72ff6d8
@mb2055
Merge branch 'devel' into feature_AToM
b860627
@mb2055
Switches positional restraints in AToM processes to flat-bottom restr…
ea33d2d 
…aints in line with other methods
@mb2055
Added position restraint width argument that sets the width of the po…
0937c59 
…tential well used to positonally restrain atoms
@mb2055
A few bugfixes
973fee5
@mb2055
Adds energy trajectory reporting, achieved through the report_interva…
eeee0f0 
…l option
@mb2055
Changed default work directories to None
97e4136
@mb2055
Fixed bug with automatic ligand translation
3b35a86
@mb2055
Bugfixes for setting window-dependent variables from list
a0781cc
@mb2055
Switched to gallachio lab repo (wip)
4413b9e
@mb2055
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
@mb2055
Brings softcore constants of production in line with values used in G…
e28f10b 
…allachio lab repo
@mb2055
Merge remote-tracking branch 'origin/devel' into feature_AToM
43d5503
@mb2055
Updated and clarified unit checking for various parameters.
ddc56b1
lohedges and others added 23 commits October 7, 2024 13:25
@lohedges
Merge branch 'devel' into feature_AToM
fa894af
@mb2055
First draft of ATM tutorial
f2ec42d
@lohedges
Squash thermodynamic cycle image.
8ea5dec
@lohedges
Example input URLs now added and formatting tweaks.
aedf76c
@mb2055
Enhancements to the ATM tutorial.
22612af 
Also exposes AToMSetup to docs
@lohedges
Rotate perturbable and non-perturbable molecules independently.
0b9b29f 
[closes #354]
@lohedges
Remove redundant jupyter nb-extension commmands. [ci skip]
4095d96
@lohedges
Fix indexing of tutorials.
0e1933f
@lohedges
Fix sections.
d4e7ed0
@lohedges
Move API docs before examples.
dc9548a
@lohedges
Improve sectioning.
c1d8eb3
@lohedges
Switch from AToM to ATM.
24f8825
@lohedges
Merge remote-tracking branch 'origin/fix_354' into feature_AToM
f5b9429
@lohedges
Make class attributes private.
c2665ab
@lohedges
Blacken.
613c58c
@lohedges
Merge pull request #327 from OpenBioSim/feature_AToM
85e7f36 
Alchemical Transfer Method
@lohedges
Merge remote-tracking branch 'exscientia/devel' into sync_exscientia
38018a7
@lohedges
Guard test against missing OpenFF package.
58dba1c
@lohedges
Remove redundant variable.
e33f499
@lohedges
Test requires AMBER and OpenFF. [ci skip]
0365150
@lohedges
Merge pull request #356 from OpenBioSim/sync_exscientia
e84a422 
Synchronise with Exscientia remote
@lohedges
Update Sire version.
e446721
@lohedges
Update CHANGELOG for the 2024.3.0 release.
3435cdc
@lohedges lohedges merged commit aa83a91 into main Oct 24, 2024
5 checks passed
@lohedges lohedges deleted the release_2024.3.0 branch October 24, 2024 14:14
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5 participants
@lohedges @mb2055 @akalpokas @xiki-tempula @msuruzhon