Double-check SSSR to_rdkit_mol for fragment compat

Fragments will sometimes call `get_smallest_set_of_smallest_rings` (e.g.
for drawing), which will then call the _fragment_ version of
`to_rdkit_mol` (rather than Molecule, since Fragment inherits from
Molecule), which returns a _tuple_ rather than a _mol_. This causes
a crash.

I considerd just replacing this with `converter.to_rdkit_mol` without
the checks, but then you'd lose out on any fragment-related benefits
from to_rdkit_mol (for example, you need to replace the fragments with H
atoms).

This commit also adds a check so that the user is at least aware that
the default behavior is to change the kwarg to forcibly return
mapping=True for fragments.

Author: jonwzheng

rmgpy/molecule/fragment.py

@@ -504,7 +504,12 @@ def to_rdkit_mol(self, *args, **kwargs):
 
         mol0, mapping = self.get_representative_molecule("minimal", update=False)
 
-        kwargs["return_mapping"] = True
+        return_mapping = kwargs.get("return_mapping", False)
+        if return_mapping == False:
+            kwargs["return_mapping"] = True
+            logging.warning("Fragment to_rdkit_mol expects to return a tuple. "
+                            "Setting return_mapping = True; please double-check your code to ensure this is what you want.")
+
         rdmol, rdAtomIdx_mol0 = converter.to_rdkit_mol(
             mol0,
             *args,

rmgpy/molecule/molecule.py

@@ -2793,7 +2793,13 @@ def get_smallest_set_of_smallest_rings(self):
 
         sssr = []
         # Get the symmetric SSSR using RDKit
-        rdkit_mol = self.to_rdkit_mol(remove_h=False, sanitize="partial", save_order=True) 
+        rdkit_result = self.to_rdkit_mol(remove_h=False, sanitize="partial", save_order=True) 
+        
+        if isinstance(rdkit_result, tuple): # can be a tuple if Fragment version of to_rdkit_mol is used
+            rdkit_mol = rdkit_result[0]
+        else:
+            rdkit_mol = rdkit_result
+
         ring_info = Chem.GetSymmSSSR(rdkit_mol)
         for ring in ring_info:
             atom_ring = [self.atoms[idx] for idx in ring]