From ca664e4d539d8d3fb9057108bc65c5439697b762 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 26 Jul 2023 13:46:18 +0200
Subject: [PATCH] feat: SCHWED-5954 report type of isomorphism
---
modules/mol/alg/pymod/ligand_scoring.py | 13 +++++++++++--
modules/mol/alg/tests/test_ligand_scoring.py | 6 +++---
2 files changed, 14 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 2a462b78d..41e906649 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -1466,7 +1466,11 @@ class LigandScorer:
"target ligand (different stoichiometry)")
# Could not be assigned to any ligand - must be different
- return ("identity", "Ligand was not found in the target (by isomorphism)")
+ if self.substructure_match:
+ iso = "subgraph isomorphism"
+ else:
+ iso = "full graph isomorphism"
+ return ("identity", "Ligand was not found in the target (by %s)" % iso)
def _find_unassigned_target_ligand_reason(self, ligand, assignment="lddt_pli", check=True):
# Is this a target ligand?
@@ -1519,8 +1523,13 @@ class LigandScorer:
# Could have been assigned but was assigned to a different ligand
return ("stoichiometry", "Ligand was assigned to an other "
"model ligand (different stoichiometry)")
+
# Could not be assigned to any ligand - must be different
- return ("identity", "Ligand was not found in the model (by isomorphism)")
+ if self.substructure_match:
+ iso = "subgraph isomorphism"
+ else:
+ iso = "full graph isomorphism"
+ return ("identity", "Ligand was not found in the model (by %s)" % iso)
def _ResidueToGraph(residue, by_atom_index=False):
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index de7abda0c..7207a3225 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -572,7 +572,7 @@ class TestLigandScoring(unittest.TestCase):
'L_NA': {1: ('binding_site',
'No residue in proximity of the target ligand')},
'L_OXY': {1: ('identity',
- 'Ligand was not found in the target (by isomorphism)')},
+ 'Ligand was not found in the target (by full graph isomorphism)')},
'L_MG_2': {1: ('stoichiometry',
'Ligand was assigned to an other target ligand (different stoichiometry)')},
"L_CMO": {1: ('disconnected',
@@ -580,13 +580,13 @@ class TestLigandScoring(unittest.TestCase):
}
assert sc.unassigned_target_ligands == {
'G': {1: ('identity',
- 'Ligand was not found in the model (by isomorphism)')},
+ 'Ligand was not found in the model (by full graph isomorphism)')},
'H': {1: ('model_representation',
'No representation of the reference binding site was found in the model')},
'J': {1: ('stoichiometry',
'Ligand was assigned to an other model ligand (different stoichiometry)')},
'K': {1: ('identity',
- 'Ligand was not found in the model (by isomorphism)')},
+ 'Ligand was not found in the model (by full graph isomorphism)')},
'L_NA': {1: ('binding_site',
'No residue in proximity of the target ligand')},
"L_CMO": {1: ('disconnected',
--
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