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Update Averaging over Groups of Molecules for Conformational Entropy #200

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Merged
skfegan merged 21 commits into from
Nov 27, 2025
Merged

Update Averaging over Groups of Molecules for Conformational Entropy #200

skfegan merged 21 commits into from
Nov 27, 2025

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@skfegan skfegan commented Nov 19, 2025

Summary

This pull request is to fix the averaging over groups of molecules for the conformational entropy.

Changes

  • Instead of calculating the histograms for each molecule. The histogram is generated once for each group with data from all the molecules in the group.
  • The functions for building the conformational states arrays are separated from levels.py into dihedral_tools.py
  • The functions for building new universes (new_U_select_atoms, new_U_select_frames, merge_forces) are separated from run.py into mda_universe_operations.py

Impact

  • The identification of peaks for dihedral conformations is properly averaged over molecules in the same group
  • Improved separation of concerns to make the code easier to change / maintain in the future

@skfegan skfegan requested a review from harryswift01 November 19, 2025 16:41
@harryswift01 harryswift01 changed the title 161 averaging multimer Update Averaging over Groups of Molecules for Conformational Entropy Nov 21, 2025
harryswift01 and others added 13 commits November 21, 2025 15:38
@harryswift01
Merge branch 'main' into 161-averaging-multimer
6140253
@skfegan
adding statement for case when there is no dihedral angle
1847d31
@skfegan
adding statement for case when there is no dihedral angle
8c1e23e
@harryswift01
remove duplicated args within arg_config_manager.py - force_file,…
725ac24 
… `file_format`, `kcal_force_units`
@harryswift01
fix test_process_united_atom_entropy within TestEntropyManager
35cdf0b
@harryswift01
Fix failing unit tests for DihedralAnalysis._get_dihedrals by:
e81a60f 
- Instantiating a DihedralAnalysis object before calling `_get_dihedrals`
- Correcting test expectations to match actual behavior:
  - united_atom level now asserts returned `.atoms` values
  - residue level tests now validate atom-group construction
  - residue tests with < 4 residues now expect empty list
@harryswift01
fix update_force_torque_matrices tests within TestLevelsManager
3a39c69
@harryswift01
fix test_main_entry_point_runs test within TestMain
2cb7a25
@harryswift01
fix unit tests for PR #200:
444701d 
- Ensured that all classes and functions are using instances correctly
- fix all unit and integration test
@harryswift01
add new unittest test_merge_forces and `test_merge_forces_kcal_conv…
ef08d5e 
…ersion` to atomically test `merge_foces`
@harryswift01
add new unittests for dihedral_tools.py
fd7eb37
@harryswift01
add new unittest test_run_entropy_workflow_with_forcefile
d3993be
@harryswift01
Merge remote-tracking branch 'origin/main' into 161-averaging-multimer
c7dbc0d
harryswift01
harryswift01 requested changes Nov 27, 2025
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Thanks for making all these updates @skfegan they look great! I’ve left a couple of minor comments just for clarity on my side, but nothing blocking. Once those are addressed, I’m happy to approve.

@harryswift01 harryswift01 self-requested a review November 27, 2025 11:41
harryswift01
harryswift01 approved these changes Nov 27, 2025
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This looks great now @skfegan, I'm happy to approve and merge this into main

@skfegan skfegan linked an issue Nov 27, 2025 that may be closed by this pull request
Issues with averaging for protein multimer #161
Closed
@skfegan skfegan merged commit e6b55e8 into main Nov 27, 2025
15 checks passed
@skfegan skfegan deleted the 161-averaging-multimer branch November 27, 2025 11:49
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Issues with averaging for protein multimer

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@skfegan @harryswift01