Check for enpty coordinates in RDKit converter (#4824)

* prevents assignment of coordinates if all positions are zero

Author: RMeli

package/CHANGELOG

@@ -14,14 +14,15 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, ChiahsinChu
+??/??/?? IAlibay, ChiahsinChu, RMeli
 
  * 2.9.0
 
 Fixes
 
 Enhancements
-  * Added `precision` for XYZWriter (Issue #4775, PR #4771)
+ * Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824)
+ * Added `precision` for XYZWriter (Issue #4775, PR #4771)
 
 Changes
 

package/MDAnalysis/converters/RDKit.py

@@ -363,9 +363,12 @@ def convert(self, obj, cache=True, NoImplicit=True, max_iter=200,
 
         # add a conformer for the current Timestep
         if hasattr(ag, "positions"):
-            if np.isnan(ag.positions).any():
-                warnings.warn("NaN detected in coordinates, the output "
-                              "molecule will not have 3D coordinates assigned")
+            if np.isnan(ag.positions).any() or np.allclose(
+                ag.positions, 0.0, rtol=0.0, atol=1e-12
+            ):
+                warnings.warn("NaN or empty coordinates detected in coordinates, "
+                              "the output molecule will not have 3D coordinates "
+                              "assigned")
             else:
                 # assign coordinates
                 conf = Chem.Conformer(mol.GetNumAtoms())

testsuite/MDAnalysisTests/converters/test_rdkit.py

@@ -331,7 +331,7 @@ def test_nan_coords(self):
         xyz = u.atoms.positions
         xyz[0][2] = np.nan
         u.atoms.positions = xyz
-        with pytest.warns(UserWarning, match="NaN detected"):
+        with pytest.warns(UserWarning, match="NaN .* detected"):
             mol = u.atoms.convert_to("RDKIT")
         with pytest.raises(ValueError, match="Bad Conformer Id"):
             mol.GetConformer()
@@ -692,6 +692,18 @@ def test_reorder_atoms(self, smi):
         expected = [a.GetSymbol() for a in mol.GetAtoms()]
         assert values == expected
 
+    @pytest.mark.parametrize("smi", [
+        "O=S(C)(C)=NC",
+    ])
+    def test_warn_empty_coords(self, smi):
+        mol = Chem.MolFromSmiles(smi)
+        mol = Chem.AddHs(mol)
+        # remove bond order and charges info
+        pdb = Chem.MolToPDBBlock(mol)
+        u = mda.Universe(StringIO(pdb), format="PDB")
+        with pytest.warns(match="NaN or empty coordinates detected"):
+            u.atoms.convert_to.rdkit()
+
     def test_pdb_names(self):
         u = mda.Universe(PDB_helix)
         mol = u.atoms.convert_to.rdkit()