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Updating nonEQ branch with current main #74

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Updating nonEQ branch with current main #74

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9d96b61
update POPC Amber14sb parameters
David-Araripe Aug 18, 2025
ece21fc
change create_ddG_plot stylling
David-Araripe Aug 19, 2025
4d10c8d
update cog to use the correct logger and setup_logger
David-Araripe Aug 22, 2025
0f539d7
change potential pandas warning when writing dataframe
David-Araripe Aug 22, 2025
fd0d03b
update qprep_cli to neutralize out-of-sphere amino acids
David-Araripe Aug 22, 2025
4f3df65
improve logging, reduce verbosity
David-Araripe Aug 22, 2025
45a1612
fix but where ASP was always converted to ASH
David-Araripe Aug 23, 2025
8ffeed9
update qprep-cli for more consistent output naming, depending on the …
David-Araripe Aug 23, 2025
60f4c0a
capture all missing library errors from qprep
David-Araripe Aug 25, 2025
97de28c
more informative qprep error when ligands aren't present
David-Araripe Aug 25, 2025
712f945
isort
David-Araripe Aug 27, 2025
a477895
more informative error when generated topology doesn't contain the li…
David-Araripe Aug 27, 2025
e83ecab
Merge branch 'lipid21-params' of github.com:qusers/Q into lipid21-params
David-Araripe Aug 27, 2025
3b7f298
change typo
David-Araripe Aug 30, 2025
c8e81e8
max residue code length needs to be 3
David-Araripe Aug 30, 2025
1353622
add solution to convert popc molecules to Amber-like format within pr…
David-Araripe Aug 30, 2025
ebd9f31
avoid populating results json with nan
David-Araripe Sep 1, 2025
40bc1b6
change y axis to calc for consistency with the manuscript
David-Araripe Sep 10, 2025
a00ce4e
update readme with instructions and other clarity improvements
David-Araripe Sep 15, 2025
2fc0962
add nagl to macos environment
David-Araripe Sep 16, 2025
dfd6cf3
update tutorial
David-Araripe Sep 16, 2025
6a052a4
Merge pull request #41 from qusers/lipid21-params
jesperswillem Sep 17, 2025
f7860a5
Update README.md
jesperswillem Sep 19, 2025
7680d2b
Update README.md
jesperswillem Sep 19, 2025
b69651a
Update README.md
jesperswillem Sep 19, 2025
b3c3534
Update README.md
David-Araripe Oct 20, 2025
6617542
update tutorial files;
David-Araripe Nov 11, 2025
ccfdcf4
compile qprep during package installation and update install instruct…
David-Araripe Nov 13, 2025
feb2938
Delete benchmark-data-shevsea directory
jesperswillem Nov 17, 2025
1ea2b21
Merge pull request #52 from qusers/jesperswillem-patch-1
jesperswillem Nov 17, 2025
ca77b07
Update project.scripts order with a logical sequence of the commands …
David-Araripe Nov 18, 2025
d14b363
Update readme; reorder project scripts and add note about Q-GPU
David-Araripe Nov 18, 2025
c5fbced
add benchmarking section to the readme
David-Araripe Nov 18, 2025
9b2e1c1
add QligFEPv2 preprint citation to the #benchmarking section
David-Araripe Nov 18, 2025
a8ae384
update readme and move authors list to pyproject.toml
David-Araripe Nov 20, 2025
5b5dd3e
correct test commands
David-Araripe Nov 20, 2025
bb0fcb6
duplicated header
David-Araripe Nov 20, 2025
bcdc146
Bump up version
David-Araripe Nov 20, 2025
590bd5b
Merge pull request #53 from qusers/improve/readme
David-Araripe Nov 20, 2025
9aff904
Instructions for setting up on other HPC systems
David-Araripe Dec 3, 2025
7973d6c
make things clearer
David-Araripe Dec 3, 2025
23d55da
add section on compiling for local usage
David-Araripe Dec 3, 2025
0b7674f
fix markdown hyperlink
David-Araripe Dec 3, 2025
7ae4afd
adapt the part mentioning the benchmarks
David-Araripe Dec 3, 2025
5537117
remove the duplicated example statement
David-Araripe Dec 3, 2025
269525c
Merge pull request #66 from qusers/improve/readme-2
David-Araripe Dec 3, 2025
12efaa9
small fix on the tutorial & add figure with the perturbation mapping …
David-Araripe Dec 5, 2025
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5 changes: 3 additions & 2 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
recursive-include src/QligFEP/FF *
recursive-include src/QligFEP/INPUTS *
recursive-include src/QligFEP/resources *
recursive-include src/q6/ *.f90
recursive-include src/q6/ makefile
recursive-include src/q6 *.f90 *.F90
include src/q6/makefile
include src/q6/bin/q6/*
249 changes: 144 additions & 105 deletions README.md
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23 changes: 0 additions & 23 deletions benchmark-data-shevsea/QmapFEP/maps/CDK2_network.txt
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131 changes: 0 additions & 131 deletions benchmark-data-shevsea/benchmark/qligfep/inputfiles/1.BACE/CAT-13a.lib
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