diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index c06a999593860be2ceb1ef95c1c15be7b954cb81..2a462b78df99c5e76e55afe54819516c14ee7229 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -652,6 +652,9 @@ class LigandScorer:
str(model_ligand), str(target_ligand)))
self._assignment_isomorphisms[target_i, model_i] = 0
continue
+ except DisconnectedGraphError:
+ # Disconnected graph is handled elsewhere
+ continue
substructure_match = len(symmetries[0][0]) != len(
model_ligand.atoms)
@@ -1258,7 +1261,8 @@ class LigandScorer:
Currently, the following reasons are reported:
- * `no_ligand`: No ligand in the model.
+ * `no_ligand`: no ligand in the model.
+ * `disconnected`: ligand graph is disconnected.
* `binding_site`: no residue in proximity of the target ligand.
* `model_representation`: no representation of the reference binding
site was found in the model
@@ -1291,7 +1295,8 @@ class LigandScorer:
Currently, the following reasons are reported:
- * `no_ligand`: No ligand in the target.
+ * `no_ligand`: no ligand in the target.
+ * `disconnected`: ligand graph is disconnected.
* `binding_site`: no residue in proximity of the target ligand.
* `model_representation`: no representation of the reference binding
site was found in the model
@@ -1425,6 +1430,11 @@ class LigandScorer:
if len(self.target_ligands) == 0:
return ("no_ligand", "No ligand in the target")
+ # Is the ligand disconnected?
+ graph = _ResidueToGraph(ligand)
+ if not networkx.is_connected(graph):
+ return ("disconnected", "Ligand graph is disconnected")
+
# Do we have isomorphisms with the target?
for trg_lig_idx, assigned in enumerate(self._assignment_isomorphisms[:, ligand_idx]):
if np.isnan(assigned):
@@ -1435,7 +1445,7 @@ class LigandScorer:
substructure_match=self.substructure_match,
by_atom_index=True,
return_symmetries=False)
- except NoSymmetryError:
+ except (NoSymmetryError, DisconnectedGraphError):
assigned = 0.
else:
assigned = 1.
@@ -1481,6 +1491,11 @@ class LigandScorer:
if len(self.model_ligands) == 0:
return ("no_ligand", "No ligand in the model")
+ # Is the ligand disconnected?
+ graph = _ResidueToGraph(ligand)
+ if not networkx.is_connected(graph):
+ return ("disconnected", "Ligand graph is disconnected")
+
# 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]
@@ -1495,7 +1510,7 @@ class LigandScorer:
substructure_match=self.substructure_match,
by_atom_index=True,
return_symmetries=False)
- except NoSymmetryError:
+ except (NoSymmetryError, DisconnectedGraphError):
assigned = 0.
else:
assigned = 1.
@@ -1563,7 +1578,8 @@ def SCRMSD(model_ligand, target_ligand, transformation=geom.Mat4(),
ligand.
:type substructure_match: :class:`bool`
:rtype: :class:`float`
- :raises: :class:`NoSymmetryError` when no symmetry can be found.
+ :raises: :class:`NoSymmetryError` when no symmetry can be found,
+ :class:`DisconnectedGraphError` when ligand graph is disconnected.
"""
symmetries = _ComputeSymmetries(model_ligand, target_ligand,
@@ -1637,9 +1653,9 @@ def _ComputeSymmetries(model_ligand, target_ligand, substructure_match=False,
target_graph = _ResidueToGraph(target_ligand, by_atom_index=by_atom_index)
if not networkx.is_connected(model_graph):
- raise RuntimeError("Disconnected graph for model ligand %s" % model_ligand)
+ raise DisconnectedGraphError("Disconnected graph for model ligand %s" % model_ligand)
if not networkx.is_connected(target_graph):
- raise RuntimeError("Disconnected graph for target ligand %s" % target_ligand)
+ raise DisconnectedGraphError("Disconnected graph for target ligand %s" % target_ligand)
# Note the argument order (model, target) which differs from spyrmsd.
# This is because a subgraph of model is isomorphic to target - but not the opposite
@@ -1683,5 +1699,10 @@ class NoSymmetryError(Exception):
"""
pass
+class DisconnectedGraphError(Exception):
+ """Exception to be raised when the ligand graph is disconnected.
+ """
+ pass
+
-__all__ = ["LigandScorer", "SCRMSD", "NoSymmetryError"]
+__all__ = ["LigandScorer", "SCRMSD", "NoSymmetryError", "DisconnectedGraphError"]
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 35de1ffb3d7fb0f272db95e6a2a9f0eaadd995f3..de7abda0c4e6313560c3a428b1b1c29467e9e3df 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -467,6 +467,20 @@ class TestLigandScoring(unittest.TestCase):
mdl_ed.Connect(new_atom1, new_atom2)
new_res.is_ligand = True
+ # Add CMO: disconnected
+ new_chain = mdl_ed.InsertChain("L_CMO")
+ mdl_ed.SetChainType(new_chain, mol.ChainType.CHAINTYPE_NON_POLY)
+ new_res = mdl_ed.AppendResidue(new_chain, "CMO")
+ new_atom1 = mdl_ed.InsertAtom(new_res, "O", geom.Vec3(0, 0, 0), "O")
+ new_atom2 = mdl_ed.InsertAtom(new_res, "C", geom.Vec3(1, 1, 1), "O")
+ new_res.is_ligand = True
+ new_chain = trg_ed.InsertChain("L_CMO")
+ trg_ed.SetChainType(new_chain, mol.ChainType.CHAINTYPE_NON_POLY)
+ new_res = trg_ed.AppendResidue(new_chain, "CMO")
+ new_atom1 = trg_ed.InsertAtom(new_res, "O", geom.Vec3(0, 0, 0), "O")
+ new_atom2 = trg_ed.InsertAtom(new_res, "C", geom.Vec3(1, 1, 1), "O")
+ new_res.is_ligand = True
+
# Add 3 MG in model: assignment/stoichiometry
mg_pos = [
mdl.geometric_center,
@@ -494,7 +508,7 @@ class TestLigandScoring(unittest.TestCase):
trg_zn = sc.target.FindResidue("H", 1)
assert sc._find_unassigned_target_ligand_reason(trg_zn)[0] == "model_representation"
assert sc.unassigned_target_ligands["H"][1][0] == "model_representation"
- # CMO: not identical to anything in the model
+ # AFB: not identical to anything in the model
trg_afb = sc.target.FindResidue("G", 1)
assert sc._find_unassigned_target_ligand_reason(trg_afb)[0] == "identity"
assert sc.unassigned_target_ligands["G"][1][0] == "identity"
@@ -502,6 +516,10 @@ class TestLigandScoring(unittest.TestCase):
trg_fg3d1 = sc.target.FindResidue("F", 1)
assert sc._find_unassigned_target_ligand_reason(trg_fg3d1)[0] == "stoichiometry"
assert sc.unassigned_target_ligands["F"][1][0] == "stoichiometry"
+ # CMO: disconnected
+ trg_cmo1 = sc.target.FindResidue("L_CMO", 1)
+ sc._find_unassigned_target_ligand_reason(trg_cmo1)[0] == "disconnected"
+ assert sc.unassigned_target_ligands["L_CMO"][1][0] == "disconnected"
# J.G3D1: assigned to L_2.G3D1 => error
trg_jg3d1 = sc.target.FindResidue("J", 1)
with self.assertRaises(RuntimeError):
@@ -537,6 +555,10 @@ class TestLigandScoring(unittest.TestCase):
with self.assertRaises(RuntimeError):
sc._find_unassigned_model_ligand_reason(mdl_mg_0)
assert "L_MG_0" not in sc.unassigned_model_ligands
+ # CMO: disconnected
+ mdl_cmo1 = sc.model.FindResidue("L_CMO", 1)
+ sc._find_unassigned_model_ligand_reason(mdl_cmo1)[0] == "disconnected"
+ assert sc.unassigned_model_ligands["L_CMO"][1][0] == "disconnected"
# Raises with an invalid ligand
with self.assertRaises(ValueError):
sc._find_unassigned_model_ligand_reason(sc.target_ligands[0])
@@ -552,7 +574,9 @@ class TestLigandScoring(unittest.TestCase):
'L_OXY': {1: ('identity',
'Ligand was not found in the target (by isomorphism)')},
'L_MG_2': {1: ('stoichiometry',
- 'Ligand was assigned to an other target ligand (different stoichiometry)')}
+ 'Ligand was assigned to an other target ligand (different stoichiometry)')},
+ "L_CMO": {1: ('disconnected',
+ 'Ligand graph is disconnected')}
}
assert sc.unassigned_target_ligands == {
'G': {1: ('identity',
@@ -564,7 +588,9 @@ class TestLigandScoring(unittest.TestCase):
'K': {1: ('identity',
'Ligand was not found in the model (by isomorphism)')},
'L_NA': {1: ('binding_site',
- 'No residue in proximity of the target ligand')}
+ 'No residue in proximity of the target ligand')},
+ "L_CMO": {1: ('disconnected',
+ 'Ligand graph is disconnected')}
}
assert sc.lddt_pli["L_OXY"][1] is None
@@ -589,10 +615,6 @@ class TestLigandScoring(unittest.TestCase):
unassigned=True, rmsd_assignment=True)
-
-
-
-
if __name__ == "__main__":
from ost import testutils
if testutils.DefaultCompoundLibIsSet():