diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 41e906649512efe56ab9b2101b2b3772fa959494..e4b37ed65f2a279c466569c603bfba80eba6d079 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -451,8 +451,8 @@ class LigandScorer:
new_res = None
if res.entity.handle == old_entity.handle:
# Residue is part of the old_entity handle.
- # However it may not be in the copied one, for instance it may have been a view
- # We try to grab it grab it first, othewise we copyp it
+ # However, it may not be in the copied one, for instance it may have been a view
+ # We try to grab it first, otherwise we copy it
new_res = new_entity.FindResidue(res.chain.name, res.number)
if new_res and new_res.valid:
LogVerbose("Ligand residue %s already in entity" % res.handle.qualified_name)
@@ -1256,19 +1256,24 @@ class LigandScorer:
Assignment is the same as for the lDDT-PLI score (and is controlled
by the `rmsd_assignment` argument).
- Each sub-dictionary contains a tuple with information about the reason
- for the absence of assignment, in short and long format.
+ Each sub-dictionary contains a string from a controlled dictionary
+ about the reason for the absence of assignment.
Currently, the following reasons are reported:
- * `no_ligand`: no ligand in the model.
- * `disconnected`: ligand graph is disconnected.
- * `binding_site`: no residue in proximity of the target ligand.
+ * `no_ligand`: there was no ligand in the model.
+ * `disconnected`: the ligand graph was disconnected.
+ * `binding_site`: no residues were in proximity of the ligand.
* `model_representation`: no representation of the reference binding
- site was found in the model
- * `identity`: ligand was not found in the model (by isomorphism)
- * `stoichiometry`: ligand was assigned to an other model ligand
- (different stoichiometry)
+ site was found in the model. (I.e. the binding site was not modeled.
+ Remember: the binding site is defined in the target structure,
+ the position of the model ligand itself is ignored at this point.)
+ * `identity`: the ligand was not found in the model (by graph
+ isomorphism). Check your ligand connectivity, and enable the
+ `substructure_match` option if the target ligand is incomplete.
+ * `stoichiometry`: there was a possible assignment in the model, but
+ the model ligand was already assigned to a different target ligand.
+ This indicates different stoichiometries.
Some of these reasons can be overlapping, but a single reason will be
reported.
@@ -1295,14 +1300,22 @@ class LigandScorer:
Currently, the following reasons are reported:
- * `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
- * `identity`: ligand was not found in the target (by isomorphism)
- * `stoichiometry`: ligand was assigned to an other target ligand
- (different stoichiometry)
+ * `no_ligand`: there was no ligand in the target.
+ * `disconnected`: the ligand graph is disconnected.
+ * `binding_site`: a potential assignment was found in the target, but
+ there were no polymer residues in proximity of the ligand in the
+ target.
+ * `model_representation`: a potential assignment was found in the target,
+ but no representation of the binding site was found in the model.
+ (I.e. the binding site was not modeled. Remember: the binding site
+ is defined in the target structure, the position of the model ligand
+ itself is ignored at this point.)
+ * `identity`: the ligand was not found in the target (by graph
+ isomorphism). Check your ligand connectivity, and enable the
+ `substructure_match` option if the target ligand is incomplete.
+ * `stoichiometry`: there was a possible assignment in the target, but
+ the model target was already assigned to a different model ligand.
+ This indicates different stoichiometries.
Some of these reasons can be overlapping, but a single reason will be
reported.
@@ -1461,9 +1474,10 @@ class LigandScorer:
trg_ligand = self.target_ligands[trg_lig_idx]
return self._unassigned_target_ligands_reason[trg_ligand]
else:
- # Ligand was assigned to an other
- return ("stoichiometry", "Ligand was assigned to an other "
- "target ligand (different stoichiometry)")
+ # Ligand was already assigned
+ return ("stoichiometry",
+ "Ligand was already assigned to an other "
+ "model ligand (different stoichiometry)")
# Could not be assigned to any ligand - must be different
if self.substructure_match:
@@ -1521,8 +1535,9 @@ class LigandScorer:
self._assignment_isomorphisms[ligand_idx,model_lig_idx] = assigned
if assigned:
# Could have been assigned but was assigned to a different ligand
- return ("stoichiometry", "Ligand was assigned to an other "
- "model ligand (different stoichiometry)")
+ return ("stoichiometry",
+ "Ligand was already assigned to an other "
+ "target ligand (different stoichiometry)")
# Could not be assigned to any ligand - must be different
if self.substructure_match:
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 7207a32255fe790180fe230c43f1ce5fc343a1a4..9a279594c5dbe60927986e4e901ac936d8e8e66e 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -574,7 +574,7 @@ class TestLigandScoring(unittest.TestCase):
'L_OXY': {1: ('identity',
'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)')},
+ 'Ligand was already assigned to an other model ligand (different stoichiometry)')},
"L_CMO": {1: ('disconnected',
'Ligand graph is disconnected')}
}
@@ -584,7 +584,7 @@ class TestLigandScoring(unittest.TestCase):
'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)')},
+ 'Ligand was already assigned to an other target ligand (different stoichiometry)')},
'K': {1: ('identity',
'Ligand was not found in the model (by full graph isomorphism)')},
'L_NA': {1: ('binding_site',