fix: SCHWED-5783 element case is unspecified in OST

modules/mol/alg/pymod/ligand_scoring.py

@@ -738,12 +738,12 @@ def ResidueToGraph(residue, by_atom_index=False):
     :type by_atom_index: :class:`bool`
     :rtype: :class:`~networkx.classes.graph.Graph`
 
-    Nodes are labeled with the Atom's :attr:`~ost.mol.AtomHandle.element`.
+    Nodes are labeled with the Atom's :attr:`~ost.mol.AtomHandle.mass`.
     """
     nxg = networkx.Graph()
 
     for atom in residue.atoms:
-        nxg.add_node(atom.name, element=atom.element)
+        nxg.add_node(atom.name, element=atom.mass)
 
     # This will list all edges twice - once for every atom of the pair.
     # But as of NetworkX 3.0 adding the same edge twice has no effect, so we're good.

modules/mol/alg/tests/test_ligand_scoring.py

@@ -167,6 +167,11 @@ class TestLigandScoring(unittest.TestCase):
         sym = ost.mol.alg.ligand_scoring._ComputeSymmetries(mdl_g3d, trg_g3d1, by_atom_index=True)
         assert len(sym) == 72
 
+        # Test that we can match ions read from SDF
+        sdf_lig = io.LoadEntity(os.path.join('testfiles', "1r8q_ligand_0.sdf"))
+        sym = ost.mol.alg.ligand_scoring._ComputeSymmetries(trg_mg1, sdf_lig.residues[0], by_atom_index=True)
+        assert len(sym) == 1
+
         # Test that it works with views and only consider atoms in the view
         # Skip PA, PB and O[1-3]A and O[1-3]B in target and model
         # We assume atom index are fixed and won't change