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Align CodeEntropy with entropy methods used in 2019 paper - #267

Merged

jkalayan merged 23 commits into

mainfrom

UArovib-fix

Feb 5, 2026

Merged

Align CodeEntropy with entropy methods used in 2019 paper#267
jkalayan merged 23 commits into
mainfrom
UArovib-fix

Commits on Jan 27, 2026
- add modified UA-rovib, modified RES-rovib and dimensions in universe ops
  jkalayan
  committed
  5d65da5
Commits on Jan 30, 2026
- add combined FTmatrices, match UA bonded axes to Jon's code, comment out Sconf calcs for speedier testing
  jkalayan
  committed
  993f827
- add arg to choose between axes schemes
  jkalayan
  committed
  316f8d4
Commits on Feb 2, 2026
- Merge remote-tracking branch 'origin/main' into UArovib-fix
  jkalayan
  committed
  612b5d0
- uncomment Sconf calcs
  jkalayan
  committed
  e4a41f4
- match main line space
  jkalayan
  committed
  3a8295b
- remove redundant axes methods
  jkalayan
  committed
  8a6ecdd
- fix unit tests within `test_entropy.py` in relation to changes within PR #267
  harryswift01
  committed
  5d076f1
- fix unit tests within `test_levels.py` in relation to changes within PR #267
  harryswift01
  committed
  59c9399
- fix unit tests within `test_mda_universe_operations.py` in relation to changes within PR #267
  harryswift01
  committed
  9bcaa37
Commits on Feb 3, 2026
Commits on Feb 4, 2026
- unwrap/make whole molecules for MOI, COM and PA calcs
  jkalayan
  committed
  5340484
- Merge branch 'UArovib-fix' of https://github.com/CCPBioSim/CodeEntropy into UArovib-fix
  jkalayan
  committed
  ae5da4a
- remove unused calcs
  jkalayan
  committed
  0f4d218
- update docs
  jkalayan
  committed
  63183fd
- Merge remote-tracking branch 'origin/main' into UArovib-fix
  harryswift01
  committed
  8190c8a
- fix unit tests within `test_axes.py` in relation to PR #267
  harryswift01
  committed
  7209969
- fix unit tests within `test_levels.py` in relation to PR #267
  harryswift01
  committed
  1278269
- fix sorting bug in `get_vanilla_axes` moment of inertia
  harryswift01
  committed
  658e276
- reduce tolerance within `test_conformational_entropy_calculation`
  harryswift01
  committed
  d4f5924

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Align CodeEntropy with entropy methods used in 2019 paper - #267

Align CodeEntropy with entropy methods used in 2019 paper#267
jkalayan merged 23 commits into
mainfrom
UArovib-fix

Commits on Jan 27, 2026

add modified UA-rovib, modified RES-rovib and dimensions in universe ops

Commits on Jan 30, 2026

add combined FTmatrices, match UA bonded axes to Jon's code, comment out Sconf calcs for speedier testing

add arg to choose between axes schemes

Commits on Feb 2, 2026

Merge remote-tracking branch 'origin/main' into UArovib-fix

uncomment Sconf calcs

match main line space

remove redundant axes methods

fix unit tests within `test_entropy.py` in relation to changes within PR #267

fix unit tests within `test_levels.py` in relation to changes within PR #267

fix unit tests within `test_mda_universe_operations.py` in relation to changes within PR #267

Commits on Feb 3, 2026

include additional unit tests within `test_entropy.py` in relation to changes within PR #267

include additional unit tests within `test_levels.py` in relation to changes within PR #267

introduce new unit tests within `test_axes.py` in relation to changes within PR #267

relax tolerance for `forcetorqueTRANS` and `forcetorqueROT` vibrational entropy test

Commits on Feb 4, 2026

unwrap/make whole molecules for MOI, COM and PA calcs

Merge branch 'UArovib-fix' of https://github.com/CCPBioSim/CodeEntropy into UArovib-fix

remove unused calcs

update docs

Merge remote-tracking branch 'origin/main' into UArovib-fix

fix unit tests within `test_axes.py` in relation to PR #267

fix unit tests within `test_levels.py` in relation to PR #267

fix sorting bug in `get_vanilla_axes` moment of inertia

reduce tolerance within `test_conformational_entropy_calculation`