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app/.source-revision

@@ -1 +1 @@
-e00621c60857e6ce90e24f686d9cac9fd5287ab8
+2e4445e46d29dcea0ab2be13c8085a0457b3c700

app/services/rdkit_interactions.py

@@ -379,7 +379,9 @@ def calculate_interactions(protein_pdb: str, ligand_pdb: str, ligand_smiles: str
                     "donor_atom_index": did, "acceptor_atom_index": aid,
                     "donor_residue": _residue(donor), "acceptor_residue": _residue(acceptor_mol.GetAtomWithIdx(aid)),
                     "distance": round(distance, 3), "donor_h_acceptor_angle": round(best_angle, 2),
-                    "method": "RDKit donor/acceptor chemical features + explicit-H geometry",
+                    "method": "RDKit donor/acceptor chemical features + RDKit-generated-H geometry",
+                    "evidence_class": "Heuristic",
+                    "hydrogen_coordinates": "RDKit-generated with AddHs(addCoords=True); not experimentally observed",
                 })
 
     # Hydrophobic features are chemically classified by RDKit's BaseFeatures.
@@ -430,17 +432,23 @@ def calculate_interactions(protein_pdb: str, ligand_pdb: str, ligand_smiles: str
     }
     return {
         **categories,
-        "status": "COMPUTED",
+        "status": "DEGRADED" if protein_parse["residues_skipped"] else "COMPUTED",
         "engine": "RDKit",
         "engine_version": Chem.rdBase.rdkitVersion,
-        "method": "RDKit BaseFeatures chemical perception with explicit-coordinate geometry",
+        "method": "RDKit BaseFeatures chemical perception with coordinate geometry",
+        "hydrogen_coordinate_provenance": {
+            "source": "RDKit AddHs(addCoords=True) from prepared heavy-atom coordinates",
+            "experimental_hydrogen_coordinates": False,
+            "interpretation": "Hydrogen-bond angles involving generated hydrogens are model-dependent geometric candidates, not directly observed geometry.",
+        },
         "thresholds": dict(_THRESHOLDS),
         "counts": {key: len(value) for key, value in categories.items()},
         "limitations": [
             "Interaction classifications depend on the supplied protonation/tautomer state and prepared coordinates.",
             "RDKit feature perception is a computational model, not experimental evidence of binding.",
             "Only the provided receptor atoms and docked pose are evaluated; omitted waters, ions, cofactors, and alternate conformations are not inferred.",
-            "Residues listed in protein_parse.residues_skipped were excluded from chemical feature perception; a DEGRADED status must not be interpreted as complete receptor coverage.",\n            "Protein backbone amide N donors are excluded because the residue-wise parser does not reconstruct peptide connectivity; this can omit valid backbone hydrogen bonds.",
+            "Residues listed in protein_parse.residues_skipped were excluded from chemical feature perception; a DEGRADED status must not be interpreted as complete receptor coverage.",
+            "Protein backbone amide N donors are excluded because the residue-wise parser does not reconstruct peptide connectivity; this can omit valid backbone hydrogen bonds.",
             "Distances and angles are geometric screens, not interaction energies or binding-affinity measurements.",
         ],
     }