Stop embed_rdkit from returning a conformer-less molecule

``EmbedMultipleConfs`` does not only raise on failure - for some strained
species it returns normally having embedded zero conformers. ``embed_rdkit``
only guarded the raising path, so in that case it returned an RDMol with no
conformers and logged nothing at all. Every consumer of that object then reads
an empty list, and the first caller to index it gets
``IndexError: list index out of range`` with no record of where the molecule
came from. Reproduced on ``C1#CC1``, ``C1#CCC1`` and ``C1#CC#CC#C1``.

Treat zero conformers the same as an exception: log a warning naming the
species and return ``None``, which is what the ``RDMol | None`` return
annotation already promised and what the exception path already did.

All four callers already handle ``None`` and none of them is made worse by
receiving it: ``get_force_field_energies`` guards with ``if rd_mol is not
None``, ``get_force_field_energies_of_conformers`` returns early on ``None``,
``determine_chirality`` skips on ``rd_mol is None or not
rd_mol.GetNumConformers()``, and ``species.get_cheap_conformer`` passes it to
``rdkit_force_field``, which returns empty lists for ``None``. A conformer-less
molecule and ``None`` therefore produce the same downstream result, minus the
crash and plus a log line.

Author: calvinp0

arc/species/conformers.py

@@ -1465,7 +1465,8 @@ def embed_rdkit(label, mol, num_confs=None, xyz=None):
         xyz (dict, optional): The 3D coordinates.
 
     Returns:
-        RDMol | None: An RDKIt molecule with embedded conformers.
+        RDMol | None: An RDKIt molecule with embedded conformers,
+                      or ``None`` if no conformers could be embedded.
     """
     if num_confs is None and xyz is None:
         raise ConformerError(f'Either num_confs or xyz must be set when calling embed_rdkit() for {label}')
@@ -1482,6 +1483,10 @@ def embed_rdkit(label, mol, num_confs=None, xyz=None):
         except Exception as e:
             logger.warning(f'Could not embed conformers using RDKit for {label}, failed with: {e}')
             return None
+        if not rd_mol.GetNumConformers():
+            logger.warning(f'Could not embed conformers using RDKit for {label}, '
+                           f'RDKit returned no conformers without raising an error.')
+            return None
     elif xyz is not None:
         rd_conf = Chem.Conformer(rd_mol.GetNumAtoms())
         for i in range(rd_mol.GetNumAtoms()):

arc/species/conformers_test.py

@@ -681,6 +681,17 @@ def test_embed_rdkit_reports_why_embedding_failed(self):
         self.assertIsNone(rd_mol)
         self.assertIn('Bad Conformer Id', '\n'.join(captured.output))
 
+    def test_embed_rdkit_does_not_return_a_conformer_less_molecule(self):
+        """Test that an embedding which yields no conformers returns None rather than an unusable molecule"""
+        spc = ARCSpecies(label='c-C3H2', smiles='C1#CC1')
+        with self.assertLogs('arc', level='WARNING') as captured:
+            rd_mol = conformers.embed_rdkit(label='c-C3H2', mol=spc.mol, num_confs=5)
+            if rd_mol is not None:
+                xyzs = conformers.read_rdkit_embedded_conformers(label='c-C3H2', rd_mol=rd_mol)
+                self.assertIsInstance(xyzs[0], dict)
+        self.assertIsNone(rd_mol)
+        self.assertIn('c-C3H2', '\n'.join(captured.output))
+
     def test_rdkit_force_field_abandons_an_optimization_that_raises(self):
         """Test that a raising optimization is logged and attempted once per conformer"""
         rd_mol = conformers.embed_rdkit(label='CJ', mol=self.cj_spc.mol, num_confs=1)