Prolif class implementation by talagayev · Pull Request #88 · OpenFreeEnergy/openfe_analysis

talagayev · 2026-02-18T11:36:07Z

First draft of the ProLIF implementation into OpenFE Analysis.

Changes made:

creation of ProLIFAnalysis class for calculation of interactions using ProLIF
Addition of first tests in test_prolif.py, which mainly look into if interactions were calculated sucessfully and protein/ligand conversion from MDAnalysis into ProLIF worked sucessfully.

Currently that is the first draft and PR is to see that the tests work etc.

Some notes:

Currently this is just calculating and returning the results in pd.DataFrame format, since that is easy to see if it worked. We can see what the best way is to present the results, be it 2D visualization of the interactions, dataframes or some other format.
As was mentioned by Irfan, the recognition and conversion of protein in MDAnalysis is sometimes tricky, which is the case here. So the code currently needs to guess bonds, which it does here:
universe.select_atoms("protein").guess_bonds(vdwradii=vdwradii)
But for the vdwradii it wants some values for Cl, Br etc. that we need to provide, so we need to see what defaults we select there.
For interactions we need to check what the default option should be, if default == all interactions or some interactions etc. and if the water-bridge interactions are default and if so, what water-bridge interaction order we make default. the current one is 3, which means it can be something like:
Ligand -- Water -- Water -- Water -- Protein
Same goes with ProLIFAnalysis.run() there we can also look into what the defaults have to be, how many cores and if the interactions should be atom based (Ligand with Protein atom) or residue based (Ligand with Protein residue).

This is the first draft, will be updated during further development :)

PS. A small thing I also noticed, since I tested it on different PCs with one being with Windows currently somehow python 3.14 has module loading Issues with rdkit and thus I had to downgrade there to python 3.13.

codecov · 2026-02-18T11:38:17Z

Codecov Report

❌ Patch coverage is 92.72727% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 97.31%. Comparing base (86b1a79) to head (6235484).

Files with missing lines	Patch %	Lines
src/openfe_analysis/prolif.py	90.27%	7 Missing ⚠️
src/openfe_analysis/utils/plotting.py	97.36%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #88      +/-   ##
==========================================
- Coverage   98.35%   97.31%   -1.04%     
==========================================
  Files          10       11       +1     
  Lines         487      597     +110     
==========================================
+ Hits          479      581     +102     
- Misses          8       16       +8

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IAlibay · 2026-02-18T11:41:30Z

+import prolif as plf
+
+
+class ProLIFAnalysis:


Can you subclass AnalysisBase here?

Yup should be doable, will look into it :)

Wanted to wait and see how RMSD will look like to use an identical structure and have this initial PR to have bulletpoints to discuss tomorrow during the meeting and also have an easier overview on what was changed etc. :)

We leave it as is for now and will change this when Prolif implements per frame analysis.

jthorton · 2026-02-19T11:39:47Z

I am not sure if this should be handled in the analysis class or in a protocol before running this class but there is an issue when doing this kind of analysis on trajectories from our hybrid topology protocol, where the connectivity of the end state ligands and identities of the atoms can get confused see this example on end stateB when looking at torsions. Should we add an option to provide and rdkit molecule for the ligand and use this to correct the ligand atom group automatically or should we have users fix this beforehand? This will be needed in the torsion analysis as well so a general function which could fix an atom group might be a good idea?

…FreeEnergy/openfe_analysis into prolif_class_implementation

hannahbaumann

Thanks @talagayev , this looks good! The main part I'm not sure about is the run function, maybe we can discuss that tomorrow!

into prolif_class_implementation

…FreeEnergy/openfe_analysis into prolif_class_implementation

talagayev · 2026-08-05T09:52:55Z

@hannahbaumann Code would be ready for another round of review :)

hannahbaumann · 2026-08-10T11:51:21Z

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hannahbaumann

Thanks @talagayev , this looks great! i finally got around to a full review, please let me know if you have any questions!

hannahbaumann · 2026-07-09T11:47:02Z

+        water_order: int = 3,
+        protein_cutoff: float = 12.0,
+        water_cutoff: float = 8.0,
+        interactions: Optional[Sequence[str] | str] = None,


Suggested change

interactions: Optional[Sequence[str] | str] = None,

interactions: Sequence[str] | Literal["all"] | None,

hannahbaumann · 2026-07-09T11:49:02Z

+        RDKit/ProLIF can detect donors/acceptors and bonded hydrogens.
+        """
+        # Protein: guess on the full protein so any pocket residue later has bonds
+        guess_ligand_bonds(self.universe.select_atoms("protein"))


Would it make sense to rename the function in utils to just guess_bonds or so? since the ligand part may be confusing for the protein and water.

hannahbaumann · 2026-07-09T11:51:06Z

+            else:
+                self.times = None
+        except Exception:
+            self.frames = None


Do we really need the try/except here? What happens if this was removed?

hannahbaumann · 2026-07-09T11:51:36Z

+        return self
+
+    @property
+    def ifp(self):


Maybe add type hint here of what the return would be.

hannahbaumann · 2026-08-13T09:19:09Z

+    analysis = ProLIFAnalysis(u, ligand_ag, interactions=["WaterBridge"])
+
+    assert analysis._parameters is not None
+    assert "WaterBridge" in analysis._parameters


Would it make sense to also test that there is a "WaterBridge" column in the interaction output?

hannahbaumann · 2026-08-13T09:33:16Z

+    calls = {}
+    traj = {0: None}
+
+    def ag(n):


Maybe you could also move some of these things that are repeated across different tests into fixtures?

hannahbaumann · 2026-08-13T09:37:43Z

+from openfe_analysis.prolif import ProLIFAnalysis
+from openfe_analysis.reader import FEReader
+
+


These tests look great! I think what might be missing is a testing of the start/stop/step in run, and to check the respective times, frames, n_frames when you slice the data like that.

Resolved the test_prolif.py conflict by keeping the refactored version (universe/ligand_ag fixtures, WaterBridge test renamed to *_warns_and_raises, with-water test removed, plotting tests moved to tests/utils/test_plotting.py). prolif.py, plotting.py and conft.py (Zenodo fix #125) auto-merged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

hannahbaumann · 2026-09-18T09:37:10Z

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…FreeEnergy/openfe_analysis into prolif_class_implementation

talagayev added 2 commits February 17, 2026 22:51

added prolif in environment.yml

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talagayev added 3 commits February 26, 2026 00:31

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talagayev and others added 8 commits April 16, 2026 00:41

Added 2D visualizationa and adressed comments

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talagayev requested review from hannahbaumann and jthorton April 22, 2026 09:52

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Comment thread src/openfe_analysis/prolif.py

hannahbaumann self-assigned this May 21, 2026

This was linked to issues May 21, 2026

prolif hook #22

Open

Protein-ligand contact analysis #6

Closed

talagayev and others added 2 commits May 27, 2026 23:59

Merge branch 'main' into prolif_class_implementation

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talagayev and others added 7 commits July 2, 2026 01:53

Merge branch 'main' of https://github.com/OpenFreeEnergy/openfe_analysis

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talagayev requested a review from hannahbaumann August 5, 2026 09:52

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hannahbaumann and others added 7 commits August 13, 2026 11:38

Merge branch 'main' into prolif_class_implementation

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…FreeEnergy/openfe_analysis into prolif_class_implementation

	interactions: Optional[Sequence[str] \| str] = None,
	interactions: Sequence[str] \| Literal["all"] \| None,

		from openfe_analysis.prolif import ProLIFAnalysis
		from openfe_analysis.reader import FEReader

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talagayev commented Feb 18, 2026

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