Add BoreschRestraintAnalysis class by hannahbaumann · Pull Request #123 · OpenFreeEnergy/openfe_analysis

hannahbaumann · 2026-07-07T11:51:40Z

No description provided.

review-notebook-app · 2026-07-07T11:51:45Z

Check out this pull request on

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

codecov · 2026-07-07T11:54:17Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.35%. Comparing base (ff29d21) to head (4235567).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #123      +/-   ##
==========================================
+ Coverage   98.26%   98.35%   +0.09%     
==========================================
  Files           9       10       +1     
  Lines         461      487      +26     
==========================================
+ Hits          453      479      +26     
  Misses          8        8

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

jthorton · 2026-07-15T13:33:04Z

+        if len(atomgroup) != 6:
+            raise ValueError(
+                f"atomgroup must contain exactly 6 atoms (3 host + 3 guest), got {len(atomgroup)}."
+            )


Does it make sense to check that there are no bonds between the H and G atoms or that they are in different residues?

[personal take] I could go either way, but I personally wouldn't bother (i.e. flexibility is always good).

jthorton · 2026-07-15T14:03:06Z

@@ -0,0 +1,393 @@
+{


This could also be used in ABFEs as well, can we make the intro more generic to absolute calculations and then narrow the scope to septop for this example?

Reply via ReviewNB

Wrote this more general now.

jthorton · 2026-07-15T14:03:06Z

@@ -0,0 +1,393 @@
+{


typo: includea -> includes
Analysis unit -> Analysis Unit ?
match on - > match outputs["repeat_id"]

Reply via ReviewNB

Fixed this!

jthorton · 2026-07-15T14:03:06Z

@@ -0,0 +1,393 @@
+{


Is this only plotting the first and last frame? It makes the plots look strange and quite different from what we would expect in practice, so it might be best to plot more frames to avoid confusing users when they run this analysis. I think we should highlight what the interacting lambda is in the text for each case, as it swaps going from A to B.

Reply via ReviewNB

This was from a very short simulation, I didn't have one at hand with more frames, will update that after running some more simulations!

Added a traj from a full simulation.

Nice this looks much better, would it be worth swapping the labels to interacting/non-interacting and using a consistent colour between the plots to make it clear what the lambda values correspond to or is there a way to make it clear the interacting state changes between the ligand A and B plots?

I updated this, since technically, the user could also plot more lambda windows, I added something that in that case it would go back to lambda_* in the label.

Nice that is much nicer to me! How does it look with y-axis labels or is it too crowded?

Good point! I added the units as ylabels, since the titles already have the type, I thought the unit would be enough.

jthorton · 2026-07-15T14:03:06Z

@@ -0,0 +1,393 @@
+{


For the future, maybe we should be adding some shaded region for the std of the reference value to indicate what a reasonable fluctuation is.

Reply via ReviewNB

IAlibay

Only just reviewing the analysis class itself, it looks great! So I'll approve on my end.

That being said, I agree with Josh's comments on the notebook (didn't read too deeply into the notebook details though).

IAlibay · 2026-07-16T11:24:05Z

+    Notes
+    -----
+    Bond length is reported in Angstrom; angles and dihedrals are reported
+    in radians, matching the units returned by MDAnalysis's


Something to think about doing (not here) is to make the final results united.

jthorton · 2026-08-12T08:22:41Z

@@ -0,0 +1,440 @@
+{


Add a reference/link to read more about Boresch restraints?

Reply via ReviewNB

Added a reference to the original paper.

jthorton

This is great thanks @hannahbaumann !

Add BoreschRestraintAnalysis class

4227a6c

This was linked to issues Jul 7, 2026

Make analysis class for Boresch restraint analysis #121

Closed

Analysis for Boresch-style restraint stability #117

Closed

hannahbaumann and others added 4 commits July 7, 2026 14:01

add tests

4c56f09

Merge branch 'main' into boresch_analysis

6086cd5

Merge branch 'main' into boresch_analysis

8e00c67

Update notebook

2187f23

hannahbaumann requested review from IAlibay and jthorton July 14, 2026 12:00

jthorton reviewed Jul 15, 2026

View reviewed changes

IAlibay approved these changes Jul 16, 2026

View reviewed changes

hannahbaumann added 2 commits July 31, 2026 16:03

Address review comments

f0c9806

Update with full complex traj data

59c4035

hannahbaumann requested a review from jthorton August 11, 2026 08:24

Update lambda labels

a3e7ab2

jthorton reviewed Aug 12, 2026

View reviewed changes

address review comments

4235567

jthorton approved these changes Aug 12, 2026

View reviewed changes

hannahbaumann requested a review from jthorton August 12, 2026 11:14

hannahbaumann merged commit 86b1a79 into main Aug 12, 2026
9 checks passed

hannahbaumann deleted the boresch_analysis branch August 12, 2026 11:16

Uh oh!

Conversation

hannahbaumann commented Jul 7, 2026

Uh oh!

review-notebook-app Bot commented Jul 7, 2026

Uh oh!

codecov Bot commented Jul 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

jthorton Jul 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

jthorton Jul 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

jthorton Jul 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

jthorton Jul 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

IAlibay left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

jthorton Aug 12, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

jthorton left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

codecov Bot commented Jul 7, 2026 •

edited

Loading

jthorton Jul 15, 2026 •

edited

Loading

jthorton Jul 15, 2026 •

edited

Loading

jthorton Jul 15, 2026 •

edited

Loading

jthorton Jul 15, 2026 •

edited

Loading

jthorton Aug 12, 2026 •

edited

Loading