Change debug level of RDKit-related warnings

Some compounds with resonance form resonance hybrids, which create
non-integer bond orders that then call ring perception (via
get_symmetry_number). Because non-integer bond orders are not
recognized, we handle them as `unspecified`. Alternatively, the
kekulization rules for RMG may sometimes differ from those of RDKit,
which also logged a warning.

For ring perception, these 'warnings' do not impact performance, and for
nearly all users should not raise any concerns. So this demotes the
logging level from `warning` to `debug`

Author: jonwzheng

rmgpy/molecule/converter.py

@@ -132,7 +132,7 @@ def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_o
         try:
             Chem.SanitizeMol(rdkitmol, sanitizeOps=Chem.SANITIZE_ALL ^ Chem.SANITIZE_PROPERTIES)
         except (KekulizeException, AtomKekulizeException):
-            logging.warning("Kekulization failed; sanitizing without Kekulize")
+            logging.debug("Kekulization failed; sanitizing without Kekulize")
             Chem.SanitizeMol(rdkitmol, sanitizeOps=Chem.SANITIZE_ALL ^ Chem.SANITIZE_PROPERTIES ^ Chem.SANITIZE_KEKULIZE)
     if remove_h:
         rdkitmol = Chem.RemoveHs(rdkitmol, sanitize=sanitize)

rmgpy/molecule/molecule.py

@@ -787,7 +787,7 @@ def get_order_str(self):
         elif self.is_reaction_bond():
             return 'R'
         else:
-            logging.warning("Bond order {} does not have string representation.".format(self.order))
+            logging.debug("Bond order {} does not have string representation; treating as unspecified.".format(self.order))
             return None
 
     def set_order_str(self, new_order):