From f7b42cf36cd7697c022ba0c7cb855f9604797029 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 26 Jul 2023 12:04:39 +0200
Subject: [PATCH] fix: SCHWED-5954 report no ligands instead of raising an
error
---
modules/mol/alg/pymod/ligand_scoring.py | 20 ++++++++++++++--
modules/mol/alg/tests/test_ligand_scoring.py | 24 ++++++++++++++++++++
2 files changed, 42 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index c0743d196..c06a99959 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -265,7 +265,7 @@ class LigandScorer:
target_ligands,
rename_ligand_chain)
if len(self.target_ligands) == 0:
- raise ValueError("No ligands in the target")
+ LogWarning("No ligands in the target")
# Extract ligands from model
if model_ligands is None:
@@ -275,7 +275,9 @@ class LigandScorer:
model_ligands,
rename_ligand_chain)
if len(self.model_ligands) == 0:
- raise ValueError("No ligands in the model")
+ LogWarning("No ligands in the model")
+ if len(self.target_ligands) == 0:
+ raise ValueError("No ligand in the model and in the target")
self._chain_mapper = chain_mapper
self.resnum_alignments = resnum_alignments
@@ -764,6 +766,10 @@ class LigandScorer:
else:
mat2 = np.copy(mat2)
assignments = []
+ if 0 in mat1.shape:
+ # No model or target ligand
+ LogDebug("No model or target ligand, returning no assignment.")
+ return assignments
min_mat1 = LigandScorer._nanmin_nowarn(mat1)
while not np.isnan(min_mat1):
best_mat1 = np.argwhere(mat1 == min_mat1)
@@ -1252,6 +1258,7 @@ class LigandScorer:
Currently, the following reasons are reported:
+ * `no_ligand`: No ligand in the model.
* `binding_site`: no residue in proximity of the target ligand.
* `model_representation`: no representation of the reference binding
site was found in the model
@@ -1284,6 +1291,7 @@ class LigandScorer:
Currently, the following reasons are reported:
+ * `no_ligand`: No ligand in the target.
* `binding_site`: no residue in proximity of the target ligand.
* `model_representation`: no representation of the reference binding
site was found in the model
@@ -1413,6 +1421,10 @@ class LigandScorer:
if not ("unassigned" in ligand_details and ligand_details["unassigned"]):
raise RuntimeError("Ligand %s is mapped to %s" % (ligand, ligand_details["target_ligand"]))
+ # Were there any ligands in the target?
+ if len(self.target_ligands) == 0:
+ return ("no_ligand", "No ligand in the target")
+
# Do we have isomorphisms with the target?
for trg_lig_idx, assigned in enumerate(self._assignment_isomorphisms[:, ligand_idx]):
if np.isnan(assigned):
@@ -1465,6 +1477,10 @@ class LigandScorer:
raise RuntimeError("Ligand %s is mapped to %s.%s" % (
ligand, cname, rnum))
+ # Were there any ligands in the model?
+ if len(self.model_ligands) == 0:
+ return ("no_ligand", "No ligand in the model")
+
# Is it because there was no valid binding site or no representation?
if ligand in self._unassigned_target_ligands_reason:
return self._unassigned_target_ligands_reason[ligand]
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 961a28093..35de1ffb3 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -568,6 +568,30 @@ class TestLigandScoring(unittest.TestCase):
}
assert sc.lddt_pli["L_OXY"][1] is None
+ # With missing ligands
+ sc = LigandScorer(mdl.Select("cname=A"), trg, None, None)
+ assert sc.unassigned_target_ligands["E"][1] == ('no_ligand', 'No ligand in the model')
+
+ sc = LigandScorer(mdl, trg.Select("cname=A"), None, None)
+ assert sc.unassigned_model_ligands["L_2"][1] == ('no_ligand', 'No ligand in the target')
+
+ sc = LigandScorer(mdl.Select("cname=A"), trg, None, None,
+ unassigned=True, rmsd_assignment=True)
+ assert sc.unassigned_target_ligands["E"][1] == ('no_ligand', 'No ligand in the model')
+
+ sc = LigandScorer(mdl, trg.Select("cname=A"), None, None,
+ unassigned=True, rmsd_assignment=True)
+ assert sc.unassigned_model_ligands["L_2"][1] == ('no_ligand', 'No ligand in the target')
+
+ # However not everything must be missing
+ with self.assertRaises(ValueError):
+ sc = LigandScorer(mdl.Select("cname=A"), trg.Select("cname=A"), None, None,
+ unassigned=True, rmsd_assignment=True)
+
+
+
+
+
if __name__ == "__main__":
from ost import testutils
--
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