Add Residue Interaction Log Odds (RILO) and Packing Score by yusuf1759 · Pull Request #57 · aivant/peppr

yusuf1759 · 2025-09-18T05:19:53Z

Create ref-free version of PLIF scoring via residue-interaction log-odds
Make PLIF compatible with PPI
Create PPI version of RILO
Add packing and packing entropy score

OleinikovasV · 2025-10-09T15:19:31Z

src/peppr/logodds.py

What is the source of these values? Should we link in some documentations?

padix-key · 2025-10-16T08:53:03Z

src/peppr/logodds.py

@@ -0,0 +1,329 @@
+PLI_LOG_ODDS = {


Due to the large number of values, we should probably put them into a JSON file

padix-key · 2025-10-16T08:54:31Z

src/peppr/metric.py

+    References
+    ----------
+    .. [1] https://doi.org/10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H
+    .. [2] <link to notebook>


Which notebook should be linked here?

padix-key · 2025-10-16T09:04:22Z

src/peppr/metric.py

+    "RILOScore",
+    "RILOScore",
 ]


Suggested change

"RILOScore",

"RILOScore",

]

"RILOScore",

]

padix-key · 2025-10-16T09:07:12Z

src/peppr/metric.py

-
-
+from peppr.logodds import PLI_LOG_ODDS, PPI_LOG_ODDS, SCALING_FACTORS
+from peppr.packing import _compute_packing_entropy


This does not exist, right?

padix-key · 2025-10-16T09:08:55Z

src/peppr/metric.py

+        return False
+
+
+class iPackingEntropy(Metric):


Suggested change

class iPackingEntropy(Metric):

class InterfacePackingEntropy(Metric):

padix-key · 2025-10-16T09:09:57Z

src/peppr/metric.py

+    The metric is calculated by dividing the interface into small "shards" of residues
+    and evaluating the packing entropy for each shard.
+    The final score is the average packing entropy across all shards.


I think A formula would help here as well to explain the metric: https://sphinx-rtd-trial.readthedocs.io/en/latest/ext/math.html

padix-key · 2025-10-16T09:12:54Z

src/peppr/metric.py

+
+    References
+    ----------
+    .. [1] https://doi.org/10.1002/prot.22203


Are you sure this is the correct article? Admittedly I did not fully read it, but it does not comprise the term 'packing entropy' at all.

padix-key · 2025-10-16T09:14:37Z

src/peppr/metric.py

+
+    @property
+    def name(self) -> str:
+        return "RiloScore"


Suggested change

return "RiloScore"

return "RILO Score"

padix-key · 2025-10-16T09:18:51Z

src/peppr/metric.py

+import pandas as pd
 from peppr.bisyrmsd import bisy_rmsd
-from peppr.clashes import find_clashes
+from peppr.clashes import find_clashes, _find_interface_contacts


If you import this function from another module, it is not a private function anymore 😉

Suggested change

from peppr.clashes import find_clashes, _find_interface_contacts

from peppr.clashes import find_clashes, find_interface_contacts

padix-key · 2025-10-16T09:20:15Z

src/peppr/metric.py

+        ligand_interface_chain_resids =  [(a.chain_id, a.res_id) for a in combined_atoms[ligand_interface_chain_resids]]
+        packing_df = _compute_packing_entropy(
+            atoms_in=combined_atoms,
+            chains=["R", "L"],


We cannot rely on specific chain names here

padix-key · 2025-10-16T09:21:57Z

src/peppr/metric.py

+    The RILOScore is calculated by dividing the receptor-ligand interface
+    into small "shards" of residues and evaluating the interactions.


I think a Notes section with further details of the method would help here.

padix-key

I also left some comments below. I think the main part that is currently missing are tests. Furthermore, RILOScore seems a bit convoluted to at the moment, as it requires another metric, namely PLIFRecovery. Could you check, if it makes more sense to use the ContactMeasurement class directly? If the size of the code cannot be reasonably reduced, I would also suggest to put the logic into anther module.

yusuf1759 added 2 commits September 17, 2025 08:22

chore: add log-odds scores

a893d7f

chore: add packing scores scores

44c82a8

OleinikovasV reviewed Oct 9, 2025

View reviewed changes

padix-key reviewed Oct 16, 2025

View reviewed changes



		from peppr.logodds import PLI_LOG_ODDS, PPI_LOG_ODDS, SCALING_FACTORS
		from peppr.packing import _compute_packing_entropy

	class iPackingEntropy(Metric):
	class InterfacePackingEntropy(Metric):

	from peppr.clashes import find_clashes, _find_interface_contacts
	from peppr.clashes import find_clashes, find_interface_contacts

		The RILOScore is calculated by dividing the receptor-ligand interface
		into small "shards" of residues and evaluating the interactions.

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yusuf1759 commented Sep 18, 2025 •

edited

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