diff --git a/.conda/meta.yaml b/.conda/meta.yaml
index 20466c88d3..bb0cf0be93 100644
--- a/.conda/meta.yaml
+++ b/.conda/meta.yaml
@@ -64,7 +64,6 @@ requirements:
     - conda-forge::gprof2dot
     - conda-forge::numdifftools
     - conda-forge::quantities !=0.16.0,!=0.16.1
-    - conda-forge::ringdecomposerlib-python
     - rmg::pydas >=1.0.3
     - rmg::pydqed >=1.0.3
     - rmg::symmetry
@@ -114,7 +113,6 @@ requirements:
     - conda-forge::gprof2dot
     - conda-forge::numdifftools
     - conda-forge::quantities !=0.16.0,!=0.16.1
-    - conda-forge::ringdecomposerlib-python
     - rmg::pydas >=1.0.3
     - rmg::pydqed >=1.0.3
     - rmg::symmetry
@@ -165,7 +163,6 @@ test:
     - conda-forge::gprof2dot
     - conda-forge::numdifftools
     - conda-forge::quantities !=0.16.0,!=0.16.1
-    - conda-forge::ringdecomposerlib-python
     - rmg::pydas >=1.0.3
     - rmg::pydqed >=1.0.3
     - rmg::symmetry
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index e815da269d..260101d46e 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -63,7 +63,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: [macos-13, macos-latest, ubuntu-latest]
         include-rms: ["", "with RMS"]
         exclude:
diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 7c6a7b32f5..4be38424af 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -17,7 +17,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-13, macos-latest]
         numpy-version: ["1.26"]
-        python-version: ["3.9"]
+        python-version: ["3.9", "3.10", "3.11"]
     runs-on: ${{ matrix.os }}
     name: Build ${{ matrix.os }} Python ${{ matrix.python-version }} Numpy ${{ matrix.numpy-version }}
     defaults:
diff --git a/environment.yml b/environment.yml
index da840c1ab4..200c853c60 100644
--- a/environment.yml
+++ b/environment.yml
@@ -84,7 +84,6 @@ dependencies:
   # bug in quantities, see:
   # https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2694#issuecomment-2489286263
   - conda-forge::quantities !=0.16.0,!=0.16.1
-  - conda-forge::ringdecomposerlib-python
 
 # packages we maintain
   - rmg::pydas >=1.0.3
diff --git a/rmgpy/data/thermo.py b/rmgpy/data/thermo.py
index 4bd050f529..9179c3a10a 100644
--- a/rmgpy/data/thermo.py
+++ b/rmgpy/data/thermo.py
@@ -467,7 +467,7 @@ def is_ring_partial_matched(ring, matched_group):
     else:
         submol_ring, _ = convert_ring_to_sub_molecule(ring)
         sssr = submol_ring.get_smallest_set_of_smallest_rings()
-        sssr_grp = matched_group.get_smallest_set_of_smallest_rings()
+        sssr_grp = matched_group.make_sample_molecule().get_smallest_set_of_smallest_rings()
         if sorted([len(sr) for sr in sssr]) == sorted([len(sr_grp) for sr_grp in sssr_grp]):
             return False
         else:
diff --git a/rmgpy/molecule/adjlist.py b/rmgpy/molecule/adjlist.py
index 852d7bc9d0..8e654d0334 100644
--- a/rmgpy/molecule/adjlist.py
+++ b/rmgpy/molecule/adjlist.py
@@ -1093,7 +1093,7 @@ def to_adjacency_list(atoms, multiplicity, metal='', facet='', label=None, group
                 # numbers if doesn't work
                 try:
                     adjlist += bond.get_order_str()
-                except ValueError:
+                except (ValueError, TypeError):
                     adjlist += str(bond.get_order_num())
             adjlist += '}'
 
diff --git a/rmgpy/molecule/converter.pxd b/rmgpy/molecule/converter.pxd
index 25752cfd2d..24258a81f4 100644
--- a/rmgpy/molecule/converter.pxd
+++ b/rmgpy/molecule/converter.pxd
@@ -29,7 +29,7 @@ cimport rmgpy.molecule.molecule as mm
 cimport rmgpy.molecule.element as elements
 
 
-cpdef to_rdkit_mol(mm.Molecule mol, bint remove_h=*, bint return_mapping=*, bint sanitize=*, bint save_order=?)
+cpdef to_rdkit_mol(mm.Molecule mol, bint remove_h=*, bint return_mapping=*, object sanitize=*, bint save_order=?)
 
 cpdef mm.Molecule from_rdkit_mol(mm.Molecule mol, object rdkitmol, bint raise_atomtype_exception=?)
 
diff --git a/rmgpy/molecule/converter.py b/rmgpy/molecule/converter.py
index 7182b20499..a2e792a0a4 100644
--- a/rmgpy/molecule/converter.py
+++ b/rmgpy/molecule/converter.py
@@ -38,6 +38,7 @@
 import cython
 # Assume that rdkit is installed
 from rdkit import Chem
+from rdkit.Chem.rdchem import KekulizeException, AtomKekulizeException
 # Test if openbabel is installed
 try:
     from openbabel import openbabel
@@ -70,7 +71,9 @@ def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_o
     for index, atom in enumerate(mol.vertices):
         if atom.element.symbol == 'X':
             rd_atom = Chem.rdchem.Atom('Pt')  # not sure how to do this with linear scaling when this might not be Pt
-        else:
+        elif atom.element.symbol in ['R', 'L']:
+            rd_atom = Chem.rdchem.Atom(0)
+        else:   
             rd_atom = Chem.rdchem.Atom(atom.element.symbol)
         if atom.element.isotope != -1:
             rd_atom.SetIsotope(atom.element.isotope)
@@ -96,8 +99,9 @@ def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_o
             else:
                 label_dict[label] = [saved_index]
     rd_bonds = Chem.rdchem.BondType
+    # no vdW bond in RDKit, so "ZERO" or "OTHER" might be OK
     orders = {'S': rd_bonds.SINGLE, 'D': rd_bonds.DOUBLE, 'T': rd_bonds.TRIPLE, 'B': rd_bonds.AROMATIC,
-              'Q': rd_bonds.QUADRUPLE}
+              'Q': rd_bonds.QUADRUPLE, 'vdW': rd_bonds.ZERO, 'H': rd_bonds.HYDROGEN, 'R': rd_bonds.UNSPECIFIED} 
     # Add the bonds
     for atom1 in mol.vertices:
         for atom2, bond in atom1.edges.items():
@@ -107,7 +111,10 @@ def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_o
             index2 = atoms.index(atom2)
             if index1 < index2:
                 order_string = bond.get_order_str()
-                order = orders[order_string]
+                if order_string is None:
+                    order = rd_bonds.UNSPECIFIED
+                else:
+                    order = orders[order_string]
                 rdkitmol.AddBond(index1, index2, order)
 
     # Make editable mol into a mol and rectify the molecule
@@ -119,8 +126,14 @@ def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_o
     for atom in rdkitmol.GetAtoms():
         if atom.GetAtomicNum() > 1:
             atom.SetNoImplicit(True)
-    if sanitize:
+    if sanitize == True:
         Chem.SanitizeMol(rdkitmol)
+    elif sanitize == "partial":
+        try:
+            Chem.SanitizeMol(rdkitmol, sanitizeOps=Chem.SANITIZE_ALL ^ Chem.SANITIZE_PROPERTIES)
+        except (KekulizeException, AtomKekulizeException):
+            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)
     if return_mapping:
diff --git a/rmgpy/molecule/draw.py b/rmgpy/molecule/draw.py
index ad6f0e6070..89aa83d6f2 100644
--- a/rmgpy/molecule/draw.py
+++ b/rmgpy/molecule/draw.py
@@ -155,7 +155,7 @@ def clear(self):
         self.surface = None
         self.cr = None
 
-    def draw(self, molecule, file_format, target=None):
+    def draw(self, molecule, file_format, target=None, use_rdkit=True):
         """
         Draw the given `molecule` using the given image `file_format` - pdf, svg, ps, or
         png. If `path` is given, the drawing is saved to that location on disk. The
@@ -165,6 +165,9 @@ def draw(self, molecule, file_format, target=None):
         This function returns the Cairo surface and context used to create the
         drawing, as well as a bounding box for the molecule being drawn as the
         tuple (`left`, `top`, `width`, `height`).
+
+        If `use_rdkit` is True, then the RDKit 2D coordinate generation is used to generate the coordinates.
+        If `use_rdkit` is False, then the molecule is drawn using our (deprecated) original algorithm.
         """
 
         # The Cairo 2D graphics library (and its Python wrapper) is required for
@@ -219,13 +222,13 @@ def draw(self, molecule, file_format, target=None):
                 if molecule.contains_surface_site():
                     try:
                         self._connect_surface_sites()
-                        self._generate_coordinates()
+                        self._generate_coordinates(use_rdkit=use_rdkit)
                         self._disconnect_surface_sites()
                     except AdsorbateDrawingError as e:
                         self._disconnect_surface_sites()
-                        self._generate_coordinates(fix_surface_sites=False)
+                        self._generate_coordinates(fix_surface_sites=False, use_rdkit=use_rdkit)
                 else:
-                    self._generate_coordinates()
+                    self._generate_coordinates(use_rdkit=use_rdkit)
                 self._replace_bonds(old_bond_dictionary)
 
                 # Generate labels to use
@@ -341,7 +344,7 @@ def _find_ring_groups(self):
                 if not found:
                     self.ringSystems.append([cycle])
 
-    def _generate_coordinates(self, fix_surface_sites=True):
+    def _generate_coordinates(self, fix_surface_sites=True, use_rdkit=True):
         """
         Generate the 2D coordinates to be used when drawing the current
         molecule. The function uses rdKits 2D coordinate generation.
@@ -372,15 +375,34 @@ def _generate_coordinates(self, fix_surface_sites=True):
                 self.coordinates[1, :] = [0.5, 0.0]
             return self.coordinates
 
-        # Decide whether we can use RDKit or have to generate coordinates ourselves
-        for atom in self.molecule.atoms:
-            if atom.charge != 0:
-                use_rdkit = False
-                break
-        else:  # didn't break
-            use_rdkit = True
+        if use_rdkit == True:
+            # Use RDKit 2D coordinate generation:
+
+            # Generate the RDkit molecule from the RDkit molecule, use geometry
+            # in order to match the atoms in the rdmol with the atoms in the
+            # RMG molecule (which is required to extract coordinates).
+            self.geometry = Geometry(None, None, self.molecule, None)
+
+            rdmol, rd_atom_idx = self.geometry.rd_build()
+            AllChem.Compute2DCoords(rdmol)
+
+            # Extract the coordinates from each atom.
+            for atom in atoms:
+                index = rd_atom_idx[atom]
+                point = rdmol.GetConformer(0).GetAtomPosition(index)
+                coordinates[index, :] = [point.x * 0.6, point.y * 0.6]
+
+            # RDKit generates some molecules more vertically than horizontally,
+            # Especially linear ones. This will reflect any molecule taller than
+            # it is wide across the line y=x
+            ranges = np.ptp(coordinates, axis=0)
+            if ranges[1] > ranges[0]:
+                temp = np.copy(coordinates)
+                coordinates[:, 0] = temp[:, 1]
+                coordinates[:, 1] = temp[:, 0]
 
-        if not use_rdkit:
+        else:
+            logging.warning("Using deprecated molecule drawing algorithm; undesired behavior may occur. Consider using use_rdkit=True.")
             if len(self.cycles) > 0:
                 # Cyclic molecule
                 backbone = self._find_cyclic_backbone()
@@ -438,32 +460,6 @@ def _generate_coordinates(self, fix_surface_sites=True):
             # minimize likelihood of overlap
             self._generate_neighbor_coordinates(backbone)
 
-        else:
-            # Use RDKit 2D coordinate generation:
-
-            # Generate the RDkit molecule from the RDkit molecule, use geometry
-            # in order to match the atoms in the rdmol with the atoms in the
-            # RMG molecule (which is required to extract coordinates).
-            self.geometry = Geometry(None, None, self.molecule, None)
-
-            rdmol, rd_atom_idx = self.geometry.rd_build()
-            AllChem.Compute2DCoords(rdmol)
-
-            # Extract the coordinates from each atom.
-            for atom in atoms:
-                index = rd_atom_idx[atom]
-                point = rdmol.GetConformer(0).GetAtomPosition(index)
-                coordinates[index, :] = [point.x * 0.6, point.y * 0.6]
-
-            # RDKit generates some molecules more vertically than horizontally,
-            # Especially linear ones. This will reflect any molecule taller than
-            # it is wide across the line y=x
-            ranges = np.ptp(coordinates, axis=0)
-            if ranges[1] > ranges[0]:
-                temp = np.copy(coordinates)
-                coordinates[:, 0] = temp[:, 1]
-                coordinates[:, 1] = temp[:, 0]
-
         # For surface species
         if fix_surface_sites and self.molecule.contains_surface_site():
             if len(self.molecule.atoms) == 1:
diff --git a/rmgpy/molecule/fragment.py b/rmgpy/molecule/fragment.py
index d4fa0acf4d..6d1b40fe6a 100644
--- a/rmgpy/molecule/fragment.py
+++ b/rmgpy/molecule/fragment.py
@@ -490,11 +490,13 @@ def get_formula(self):
 
         return formula
 
-    def to_rdkit_mol(self, remove_h=False, return_mapping=True, save_order=False):
+    def to_rdkit_mol(self, *args, **kwargs):
         """
         Convert a molecular structure to a RDKit rdmol object.
         """
-        if remove_h:
+        remove_h = kwargs.get('remove_h', False)
+
+        if remove_h == True:
             # because we're replacing
             # cutting labels with hydrogens
             # so do not allow removeHs to be True
@@ -502,12 +504,16 @@ def to_rdkit_mol(self, remove_h=False, return_mapping=True, save_order=False):
 
         mol0, mapping = self.get_representative_molecule("minimal", update=False)
 
+        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,
-            remove_h=remove_h,
-            return_mapping=return_mapping,
-            sanitize=True,
-            save_order=save_order,
+            *args,
+            **kwargs
         )
 
         rdAtomIdx_frag = {}
@@ -587,7 +593,7 @@ def get_aromatic_rings(self, rings=None, save_order=False):
         """
         Returns all aromatic rings as a list of atoms and a list of bonds.
 
-        Identifies rings using `Graph.get_smallest_set_of_smallest_rings()`, then uses RDKit to perceive aromaticity.
+        Identifies rings, then uses RDKit to perceive aromaticity.
         RDKit uses an atom-based pi-electron counting algorithm to check aromaticity based on Huckel's Rule.
         Therefore, this method identifies "true" aromaticity, rather than simply the RMG bond type.
 
@@ -911,7 +917,7 @@ def sliceitup_arom(self, molecule, size_threshold=None):
         _, cutting_label_list = self.detect_cutting_label(molecule_smiles)
         # transfer to rdkit molecule for substruct matching
         f = self.from_smiles_like_string(molecule_smiles)
-        molecule_to_cut, rdAtomIdx_frag = f.to_rdkit_mol()
+        molecule_to_cut, rdAtomIdx_frag = f.to_rdkit_mol(remove_h=False, return_mapping=True)
 
         # replace CuttingLabel to special Atom (metal) in rdkit
         for atom, idx in rdAtomIdx_frag.items():
@@ -1037,7 +1043,7 @@ def sliceitup_aliph(self, molecule, size_threshold=None):
         _, cutting_label_list = self.detect_cutting_label(molecule_smiles)
         # transfer to rdkit molecule for substruct matching
         f = self.from_smiles_like_string(molecule_smiles)
-        molecule_to_cut, rdAtomIdx_frag = f.to_rdkit_mol()
+        molecule_to_cut, rdAtomIdx_frag = f.to_rdkit_mol(remove_h=False, return_mapping=True)
 
         # replace CuttingLabel to special Atom (metal) in rdkit
         for atom, idx in rdAtomIdx_frag.items():
diff --git a/rmgpy/molecule/graph.pxd b/rmgpy/molecule/graph.pxd
index 696aa0b07d..31499a9fb5 100644
--- a/rmgpy/molecule/graph.pxd
+++ b/rmgpy/molecule/graph.pxd
@@ -127,16 +127,6 @@ cdef class Graph(object):
     cpdef bint _is_chain_in_cycle(self, list chain) except -2
 
     cpdef list get_all_cyclic_vertices(self)
-    
-    cpdef list get_all_polycyclic_vertices(self)
-    
-    cpdef list get_polycycles(self)
-    
-    cpdef list get_monocycles(self)
-    
-    cpdef tuple get_disparate_cycles(self)
-
-    cpdef tuple _merge_cycles(self, list cycle_sets)
 
     cpdef list get_all_cycles(self, Vertex starting_vertex)
 
@@ -146,13 +136,7 @@ cdef class Graph(object):
 
     cpdef list _explore_cycles_recursively(self, list chain, list cycles)
 
-    cpdef list get_smallest_set_of_smallest_rings(self)
-
-    cpdef list get_relevant_cycles(self)
-
     cpdef list sort_cyclic_vertices(self, list vertices)
-
-    cpdef int get_max_cycle_overlap(self)
     
     cpdef list get_largest_ring(self, Vertex vertex)
     
diff --git a/rmgpy/molecule/graph.pyx b/rmgpy/molecule/graph.pyx
index 207470c4e5..89760d7c4a 100644
--- a/rmgpy/molecule/graph.pyx
+++ b/rmgpy/molecule/graph.pyx
@@ -35,8 +35,6 @@ are the components of a graph.
 
 import itertools
 
-import py_rdl
-
 from rmgpy.molecule.vf2 cimport VF2
 
 ################################################################################
@@ -623,178 +621,6 @@ cdef class Graph(object):
                 cyclic_vertices.append(vertex)
         return cyclic_vertices
 
-    cpdef list get_all_polycyclic_vertices(self):
-        """
-        Return all vertices belonging to two or more cycles, fused or spirocyclic.
-        """
-        cdef list sssr, vertices, polycyclic_vertices
-        sssr = self.get_smallest_set_of_smallest_rings()
-        polycyclic_vertices = []
-        if sssr:
-            vertices = []
-            for cycle in sssr:
-                for vertex in cycle:
-                    if vertex not in vertices:
-                        vertices.append(vertex)
-                    else:
-                        if vertex not in polycyclic_vertices:
-                            polycyclic_vertices.append(vertex)
-        return polycyclic_vertices
-
-    cpdef list get_polycycles(self):
-        """
-        Return a list of cycles that are polycyclic.
-        In other words, merge the cycles which are fused or spirocyclic into 
-        a single polycyclic cycle, and return only those cycles. 
-        Cycles which are not polycyclic are not returned.
-        """
-        cdef list polycyclic_vertices, continuous_cycles, sssr
-        cdef set polycyclic_cycle
-        cdef Vertex vertex
-
-        sssr = self.get_smallest_set_of_smallest_rings()
-        if not sssr:
-            return []
-
-        polycyclic_vertices = self.get_all_polycyclic_vertices()
-
-        if not polycyclic_vertices:
-            # no polycyclic vertices detected
-            return []
-        else:
-            # polycyclic vertices found, merge cycles together
-            # that have common polycyclic vertices            
-            continuous_cycles = []
-            for vertex in polycyclic_vertices:
-                # First check if it is in any existing continuous cycles
-                for cycle in continuous_cycles:
-                    if vertex in cycle:
-                        polycyclic_cycle = cycle
-                        break
-                else:
-                    # Otherwise create a new cycle
-                    polycyclic_cycle = set()
-                    continuous_cycles.append(polycyclic_cycle)
-
-                for cycle in sssr:
-                    if vertex in cycle:
-                        polycyclic_cycle.update(cycle)
-
-            # convert each set to a list
-            continuous_cycles = [list(cycle) for cycle in continuous_cycles]
-            return continuous_cycles
-
-    cpdef list get_monocycles(self):
-        """
-        Return a list of cycles that are monocyclic.
-        """
-        cdef list polycyclic_vertices, sssr, monocyclic_cycles, polycyclic_sssr
-        cdef Vertex vertex
-
-        sssr = self.get_smallest_set_of_smallest_rings()
-        if not sssr:
-            return []
-
-        polycyclic_vertices = self.get_all_polycyclic_vertices()
-
-        if not polycyclic_vertices:
-            # No polycyclic_vertices detected, all the rings from get_smallest_set_of_smallest_rings
-            # are monocyclic
-            return sssr
-
-        polycyclic_sssr = []
-        for vertex in polycyclic_vertices:
-            for cycle in sssr:
-                if vertex in cycle:
-                    if cycle not in polycyclic_sssr:
-                        polycyclic_sssr.append(cycle)
-
-        # remove the polycyclic cycles from the list of SSSR, leaving behind just the monocyclics
-        monocyclic_cycles = sssr
-        for cycle in polycyclic_sssr:
-            monocyclic_cycles.remove(cycle)
-        return monocyclic_cycles
-
-    cpdef tuple get_disparate_cycles(self):
-        """
-        Get all disjoint monocyclic and polycyclic cycle clusters in the molecule.
-        Takes the RC and recursively merges all cycles which share vertices.
-        
-        Returns: monocyclic_cycles, polycyclic_cycles
-        """
-        cdef list rc, cycle_list, cycle_sets, monocyclic_cycles, polycyclic_cycles
-        cdef set cycle_set
-
-        rc = self.get_relevant_cycles()
-
-        if not rc:
-            return [], []
-
-        # Convert cycles to sets
-        cycle_sets = [set(cycle_list) for cycle_list in rc]
-
-        # Merge connected cycles
-        monocyclic_cycles, polycyclic_cycles = self._merge_cycles(cycle_sets)
-
-        # Convert cycles back to lists
-        monocyclic_cycles = [list(cycle_set) for cycle_set in monocyclic_cycles]
-        polycyclic_cycles = [list(cycle_set) for cycle_set in polycyclic_cycles]
-
-        return monocyclic_cycles, polycyclic_cycles
-
-    cpdef tuple _merge_cycles(self, list cycle_sets):
-        """
-        Recursively merges cycles that share common atoms.
-        
-        Returns one list with unmerged cycles and one list with merged cycles.
-        """
-        cdef list unmerged_cycles, merged_cycles, matched, u, m
-        cdef set cycle, m_cycle, u_cycle
-        cdef bint merged, new
-
-        unmerged_cycles = []
-        merged_cycles = []
-
-        # Loop through each cycle
-        for cycle in cycle_sets:
-            merged = False
-            new = False
-
-            # Check if it's attached to an existing merged cycle
-            for m_cycle in merged_cycles:
-                if not m_cycle.isdisjoint(cycle):
-                    m_cycle.update(cycle)
-                    merged = True
-                    # It should only match one merged cycle, so we can break here
-                    break
-            else:
-                # If it doesn't match any existing merged cycles, initiate a new one
-                m_cycle = cycle.copy()
-                new = True
-
-            # Check if the new merged cycle is attached to any of the unmerged cycles
-            matched = []
-            for i, u_cycle in enumerate(unmerged_cycles):
-                if not m_cycle.isdisjoint(u_cycle):
-                    m_cycle.update(u_cycle)
-                    matched.append(i)
-                    merged = True
-            # Remove matched cycles from list of unmerged cycles
-            for i in reversed(matched):
-                del unmerged_cycles[i]
-
-            if merged and new:
-                merged_cycles.append(m_cycle)
-            elif not merged:
-                unmerged_cycles.append(cycle)
-
-        # If any rings were successfully merged, try to merge further
-        if len(merged_cycles) > 1:
-            u, m = self._merge_cycles(merged_cycles)
-            merged_cycles = u + m
-
-        return unmerged_cycles, merged_cycles
-
     cpdef list get_all_cycles(self, Vertex starting_vertex):
         """
         Given a starting vertex, returns a list of all the cycles containing
@@ -969,71 +795,6 @@ cdef class Graph(object):
         # At this point we should have discovered all of the cycles involving the current chain
         return cycles
 
-    cpdef list get_smallest_set_of_smallest_rings(self):
-        """
-        Returns the smallest set of smallest rings as a list of lists.
-        Uses RingDecomposerLib for ring perception.
-
-        Kolodzik, A.; Urbaczek, S.; Rarey, M.
-        Unique Ring Families: A Chemically Meaningful Description
-        of Molecular Ring Topologies.
-        J. Chem. Inf. Model., 2012, 52 (8), pp 2013-2021
-
-        Flachsenberg, F.; Andresen, N.; Rarey, M.
-        RingDecomposerLib: An Open-Source Implementation of
-        Unique Ring Families and Other Cycle Bases.
-        J. Chem. Inf. Model., 2017, 57 (2), pp 122-126
-        """
-        cdef list sssr
-        cdef object graph, data, cycle
-
-        graph = py_rdl.Graph.from_edges(
-            self.get_all_edges(),
-            _get_edge_vertex1,
-            _get_edge_vertex2,
-        )
-
-        data = py_rdl.wrapper.DataInternal(graph.get_nof_nodes(), graph.get_edges().keys())
-        data.calculate()
-
-        sssr = []
-        for cycle in data.get_sssr():
-            sssr.append(self.sort_cyclic_vertices([graph.get_node_for_index(i) for i in cycle.nodes]))
-
-        return sssr
-
-    cpdef list get_relevant_cycles(self):
-        """
-        Returns the set of relevant cycles as a list of lists.
-        Uses RingDecomposerLib for ring perception.
-
-        Kolodzik, A.; Urbaczek, S.; Rarey, M.
-        Unique Ring Families: A Chemically Meaningful Description
-        of Molecular Ring Topologies.
-        J. Chem. Inf. Model., 2012, 52 (8), pp 2013-2021
-
-        Flachsenberg, F.; Andresen, N.; Rarey, M.
-        RingDecomposerLib: An Open-Source Implementation of
-        Unique Ring Families and Other Cycle Bases.
-        J. Chem. Inf. Model., 2017, 57 (2), pp 122-126
-        """
-        cdef list rc
-        cdef object graph, data, cycle
-
-        graph = py_rdl.Graph.from_edges(
-            self.get_all_edges(),
-            _get_edge_vertex1,
-            _get_edge_vertex2,
-        )
-
-        data = py_rdl.wrapper.DataInternal(graph.get_nof_nodes(), graph.get_edges().keys())
-        data.calculate()
-
-        rc = []
-        for cycle in data.get_rcs():
-            rc.append(self.sort_cyclic_vertices([graph.get_node_for_index(i) for i in cycle.nodes]))
-
-        return rc
 
     cpdef list sort_cyclic_vertices(self, list vertices):
         """
@@ -1062,24 +823,6 @@ cdef class Graph(object):
 
         return ordered
 
-    cpdef int get_max_cycle_overlap(self):
-        """
-        Return the maximum number of vertices that are shared between
-        any two cycles in the graph. For example, if there are only
-        disparate monocycles or no cycles, the maximum overlap is zero;
-        if there are "spiro" cycles, it is one; if there are "fused"
-        cycles, it is two; and if there are "bridged" cycles, it is
-        three.
-        """
-        cdef list cycles
-        cdef int max_overlap, overlap, i, j
-
-        cycles = self.get_smallest_set_of_smallest_rings()
-        max_overlap = 0
-        for i, j in itertools.combinations(range(len(cycles)), 2):
-            overlap = len(set(cycles[i]) & set(cycles[j]))
-            max_overlap = max(overlap, max_overlap)
-        return max_overlap
 
     cpdef list get_largest_ring(self, Vertex vertex):
         """
diff --git a/rmgpy/molecule/molecule.pxd b/rmgpy/molecule/molecule.pxd
index 8bbf3a5aa6..b1d35d7fda 100644
--- a/rmgpy/molecule/molecule.pxd
+++ b/rmgpy/molecule/molecule.pxd
@@ -307,4 +307,20 @@ cdef class Molecule(Graph):
 
     cpdef list get_desorbed_molecules(self)
 
+    cpdef list get_smallest_set_of_smallest_rings(self)
+
+    cpdef list get_relevant_cycles(self)
+
+    cpdef list get_all_polycyclic_vertices(self)
+
+    cpdef list get_polycycles(self)
+
+    cpdef list get_monocycles(self)
+
+    cpdef tuple get_disparate_cycles(self)
+
+    cpdef tuple _merge_cycles(self, list cycle_sets)
+
+    cpdef int get_max_cycle_overlap(self)
+
 cdef atom_id_counter
diff --git a/rmgpy/molecule/molecule.py b/rmgpy/molecule/molecule.py
index 1a32f07add..548292e19f 100644
--- a/rmgpy/molecule/molecule.py
+++ b/rmgpy/molecule/molecule.py
@@ -768,7 +768,7 @@ def is_specific_case_of(self, other):
 
     def get_order_str(self):
         """
-        returns a string representing the bond order
+        Returns a string representing the bond order. Returns None if bond order does not have a string representation.
         """
         if self.is_single():
             return 'S'
@@ -787,7 +787,8 @@ def get_order_str(self):
         elif self.is_reaction_bond():
             return 'R'
         else:
-            raise ValueError("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):
         """
@@ -1891,7 +1892,10 @@ def from_adjacency_list(self, adjlist, saturate_h=False, raise_atomtype_exceptio
         self.vertices, self.multiplicity, self.metal, self.facet = from_adjacency_list(adjlist, group=False, saturate_h=saturate_h,
                                                                check_consistency=check_consistency)
         self.update_atomtypes(raise_exception=raise_atomtype_exception)
-        self.identify_ring_membership()
+
+        # identify ring membership iff it's not a suspicious molecule
+        if not self.is_electron():
+            self.identify_ring_membership()
 
         # Check if multiplicity is possible
         n_rad = self.get_radical_count()
@@ -2048,6 +2052,10 @@ def to_rdkit_mol(self, *args, **kwargs):
         """
         Convert a molecular structure to a RDKit rdmol object.
         """
+        # RDKit doesn't support electron
+        if self.is_electron():
+            raise ValueError("Cannot convert electron molecule to RDKit Mol object")
+        
         return converter.to_rdkit_mol(self, *args, **kwargs)
 
     def to_adjacency_list(self, label='', remove_h=False, remove_lone_pairs=False, old_style=False):
@@ -2328,6 +2336,10 @@ def is_aryl_radical(self, aromatic_rings=None, save_order=False):
         and this process may involve atom order change by default. Set ``save_order`` to
         ``True`` to force the atom order unchanged.
         """
+        # RDKit does not support electron
+        if self.is_electron():
+            return False
+        
         cython.declare(atom=Atom, total=int, aromatic_atoms=set, aryl=int)
         if aromatic_rings is None:
             aromatic_rings = self.get_aromatic_rings(save_order=save_order)[0]
@@ -2518,6 +2530,10 @@ def count_aromatic_rings(self):
 
         Returns an integer corresponding to the number or aromatic rings.
         """
+        # RDKit does not support electron
+        if self.is_electron():
+            return 0
+        
         cython.declare(rings=list, count=int, ring=list, bonds=list, bond=Bond)
         rings = self.get_relevant_cycles()
         count = 0
@@ -2536,7 +2552,7 @@ def get_aromatic_rings(self, rings=None, save_order=False):
         """
         Returns all aromatic rings as a list of atoms and a list of bonds.
 
-        Identifies rings using `Graph.get_smallest_set_of_smallest_rings()`, then uses RDKit to perceive aromaticity.
+        Identifies rings, then uses RDKit to perceive aromaticity.
         RDKit uses an atom-based pi-electron counting algorithm to check aromaticity based on Huckel's Rule.
         Therefore, this method identifies "true" aromaticity, rather than simply the RMG bond type.
 
@@ -2546,6 +2562,10 @@ def get_aromatic_rings(self, rings=None, save_order=False):
         By default, the atom order will be sorted to get consistent results from different runs. The atom order can
         be saved when dealing with problems that are sensitive to the atom map.
         """
+        # RDKit does not support electron
+        if self.is_electron():
+            return [], []
+        
         cython.declare(rd_atom_indices=dict, ob_atom_ids=dict, aromatic_rings=list, aromatic_bonds=list)
         cython.declare(ring0=list, i=cython.int, atom1=Atom, atom2=Atom)
 
@@ -2635,18 +2655,17 @@ def get_aromatic_rings(self, rings=None, save_order=False):
 
     def get_deterministic_sssr(self):
         """
-        Modified `Graph` method `get_smallest_set_of_smallest_rings` by sorting calculated cycles
-        by short length and then high atomic number instead of just short length (for cases where
-        multiple cycles with same length are found, `get_smallest_set_of_smallest_rings` outputs
-        non-determinstically).
-        
-        For instance, molecule with this smiles: C1CC2C3CSC(CO3)C2C1, will have non-deterministic
+        Sorts calculated cycles by short length and then high atomic number instead of just short length.
+        Originally created as an alternative to `get_smallest_set_of_smallest_rings` before it was converted
+        to use only RDKit Functions.
+
+        For instance, previously molecule with this smiles: C1CC2C3CSC(CO3)C2C1, would have non-deterministic
         output from `get_smallest_set_of_smallest_rings`, which leads to non-deterministic bicyclic decomposition.
         Using this new method can effectively prevent this situation.
 
         Important Note: This method returns an incorrect set of SSSR in certain molecules (such as cubane).
-        It is recommended to use the main `Graph.get_smallest_set_of_smallest_rings` method in new applications.
-        Alternatively, consider using `Graph.get_relevant_cycles` for deterministic output.
+        It is recommended to use the main `Molecule.get_smallest_set_of_smallest_rings` method in new applications.
+        Alternatively, consider using `Molecule.get_relevant_cycles` for deterministic output.
 
         In future development, this method should ideally be replaced by some method to select a deterministic
         set of SSSR from the set of Relevant Cycles, as that would be a more robust solution.
@@ -2750,6 +2769,249 @@ def get_deterministic_sssr(self):
 
         return cycle_list
 
+    def get_smallest_set_of_smallest_rings(self):
+        """
+        Returns the smallest set of smallest rings (SSSR) as a list of lists of Atom objects.
+        Uses RDKit's built-in ring perception (GetSymmSSSR).
+
+        References:
+            Kolodzik, A.; Urbaczek, S.; Rarey, M.
+            Unique Ring Families: A Chemically Meaningful Description
+            of Molecular Ring Topologies.
+            J. Chem. Inf. Model., 2012, 52 (8), pp 2013-2021
+
+            Flachsenberg, F.; Andresen, N.; Rarey, M.
+            RingDecomposerLib: An Open-Source Implementation of
+            Unique Ring Families and Other Cycle Bases.
+            J. Chem. Inf. Model., 2017, 57 (2), pp 122-126
+        """
+        # RDKit does not support electron
+        if self.is_electron():
+            return []
+        
+        from rdkit import Chem
+        
+        sssr = []
+        # Get the symmetric SSSR using RDKit
+        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]
+            sorted_ring = self.sort_cyclic_vertices(atom_ring)
+            sssr.append(sorted_ring)
+        return sssr
+
+    def get_relevant_cycles(self):
+        """
+        Returns the set of relevant cycles as a list of lists of Atom objects.
+        Uses RDKit's RingInfo to approximate relevant cycles.
+
+        References:
+            Kolodzik, A.; Urbaczek, S.; Rarey, M.
+            Unique Ring Families: A Chemically Meaningful Description
+            of Molecular Ring Topologies.
+            J. Chem. Inf. Model., 2012, 52 (8), pp 2013-2021
+
+            Flachsenberg, F.; Andresen, N.; Rarey, M.
+            RingDecomposerLib: An Open-Source Implementation of
+            Unique Ring Families and Other Cycle Bases.
+            J. Chem. Inf. Model., 2017, 57 (2), pp 122-126
+        """
+        # RDKit does not support electron
+        if self.is_electron():
+            return []
+        
+        rc = []        
+        mol = converter.to_rdkit_mol(self, remove_h=False, sanitize="partial", save_order=True)
+        ring_info = mol.GetRingInfo()
+        atom_rings = ring_info.AtomRings()
+        for ring in atom_rings:
+            atom_ring = [self.atoms[idx] for idx in ring]
+            sorted_ring = self.sort_cyclic_vertices(atom_ring)
+            # Filter for "relevant" cycles (e.g., rings up to size 7)
+            if len(sorted_ring) <= 7:
+                rc.append(sorted_ring)
+        return rc
+
+    def get_all_polycyclic_vertices(self):
+        """
+        Return all vertices belonging to two or more cycles, fused or spirocyclic.
+        """
+        sssr = self.get_smallest_set_of_smallest_rings()
+        polycyclic_vertices = []
+        if sssr:
+            vertices = []
+            for cycle in sssr:
+                for vertex in cycle:
+                    if vertex not in vertices:
+                        vertices.append(vertex)
+                    else:
+                        if vertex not in polycyclic_vertices:
+                            polycyclic_vertices.append(vertex)
+        return polycyclic_vertices
+
+    def get_polycycles(self):
+        """
+        Return a list of cycles that are polycyclic.
+        In other words, merge the cycles which are fused or spirocyclic into 
+        a single polycyclic cycle, and return only those cycles. 
+        Cycles which are not polycyclic are not returned.
+        """
+        sssr = self.get_smallest_set_of_smallest_rings()
+        if not sssr:
+            return []
+
+        polycyclic_vertices = self.get_all_polycyclic_vertices()
+
+        if not polycyclic_vertices:
+            # no polycyclic vertices detected
+            return []
+        else:
+            # polycyclic vertices found, merge cycles together
+            # that have common polycyclic vertices            
+            continuous_cycles = []
+            for vertex in polycyclic_vertices:
+                # First check if it is in any existing continuous cycles
+                for cycle in continuous_cycles:
+                    if vertex in cycle:
+                        polycyclic_cycle = cycle
+                        break
+                else:
+                    # Otherwise create a new cycle
+                    polycyclic_cycle = set()
+                    continuous_cycles.append(polycyclic_cycle)
+
+                for cycle in sssr:
+                    if vertex in cycle:
+                        polycyclic_cycle.update(cycle)
+
+            # convert each set to a list
+            continuous_cycles = [list(cycle) for cycle in continuous_cycles]
+            return continuous_cycles
+
+    def get_monocycles(self):
+        """
+        Return a list of cycles that are monocyclic.
+        """
+        sssr = self.get_smallest_set_of_smallest_rings()
+        if not sssr:
+            return []
+
+        polycyclic_vertices = self.get_all_polycyclic_vertices()
+
+        if not polycyclic_vertices:
+            # No polycyclic_vertices detected, all the rings from get_smallest_set_of_smallest_rings
+            # are monocyclic
+            return sssr
+
+        polycyclic_sssr = []
+        for vertex in polycyclic_vertices:
+            for cycle in sssr:
+                if vertex in cycle:
+                    if cycle not in polycyclic_sssr:
+                        polycyclic_sssr.append(cycle)
+
+        # remove the polycyclic cycles from the list of SSSR, leaving behind just the monocyclics
+        monocyclic_cycles = sssr
+        for cycle in polycyclic_sssr:
+            monocyclic_cycles.remove(cycle)
+        return monocyclic_cycles
+
+    def get_disparate_cycles(self):
+        """
+        Get all disjoint monocyclic and polycyclic cycle clusters in the molecule.
+        Takes the RC and recursively merges all cycles which share vertices.
+        
+        Returns: monocyclic_cycles, polycyclic_cycles
+        """
+        rc = self.get_relevant_cycles()
+
+        if not rc:
+            return [], []
+
+        # Convert cycles to sets
+        cycle_sets = [set(cycle_list) for cycle_list in rc]
+
+        # Merge connected cycles
+        monocyclic_cycles, polycyclic_cycles = self._merge_cycles(cycle_sets)
+
+        # Convert cycles back to lists
+        monocyclic_cycles = [list(cycle_set) for cycle_set in monocyclic_cycles]
+        polycyclic_cycles = [list(cycle_set) for cycle_set in polycyclic_cycles]
+
+        return monocyclic_cycles, polycyclic_cycles
+
+    def _merge_cycles(self, cycle_sets):
+        """
+        Recursively merges cycles that share common atoms.
+        
+        Returns one list with unmerged cycles and one list with merged cycles.
+        """
+        unmerged_cycles = []
+        merged_cycles = []
+
+        # Loop through each cycle
+        for cycle in cycle_sets:
+            merged = False
+            new = False
+
+            # Check if it's attached to an existing merged cycle
+            for m_cycle in merged_cycles:
+                if not m_cycle.isdisjoint(cycle):
+                    m_cycle.update(cycle)
+                    merged = True
+                    # It should only match one merged cycle, so we can break here
+                    break
+            else:
+                # If it doesn't match any existing merged cycles, initiate a new one
+                m_cycle = cycle.copy()
+                new = True
+
+            # Check if the new merged cycle is attached to any of the unmerged cycles
+            matched = []
+            for i, u_cycle in enumerate(unmerged_cycles):
+                if not m_cycle.isdisjoint(u_cycle):
+                    m_cycle.update(u_cycle)
+                    matched.append(i)
+                    merged = True
+            # Remove matched cycles from list of unmerged cycles
+            for i in reversed(matched):
+                del unmerged_cycles[i]
+
+            if merged and new:
+                merged_cycles.append(m_cycle)
+            elif not merged:
+                unmerged_cycles.append(cycle)
+
+        # If any rings were successfully merged, try to merge further
+        if len(merged_cycles) > 1:
+            u, m = self._merge_cycles(merged_cycles)
+            merged_cycles = u + m
+
+        return unmerged_cycles, merged_cycles
+
+    def get_max_cycle_overlap(self):
+        """
+        Return the maximum number of vertices that are shared between
+        any two cycles in the graph. For example, if there are only
+        disparate monocycles or no cycles, the maximum overlap is zero;
+        if there are "spiro" cycles, it is one; if there are "fused"
+        cycles, it is two; and if there are "bridged" cycles, it is
+        three.
+        """
+        cycles = self.get_smallest_set_of_smallest_rings()
+        max_overlap = 0
+        for i, j in itertools.combinations(range(len(cycles)), 2):
+            overlap = len(set(cycles[i]) & set(cycles[j]))
+            max_overlap = max(overlap, max_overlap)
+        return max_overlap
+
     def kekulize(self):
         """
         Kekulizes an aromatic molecule.
diff --git a/rmgpy/qm/molecule.py b/rmgpy/qm/molecule.py
index 45cf457b67..3c6009601a 100644
--- a/rmgpy/qm/molecule.py
+++ b/rmgpy/qm/molecule.py
@@ -147,7 +147,7 @@ def rd_build(self):
         """
         Import rmg molecule and create rdkit molecule with the same atom labeling.
         """
-        return self.molecule.to_rdkit_mol(remove_h=False, return_mapping=True)
+        return self.molecule.to_rdkit_mol(remove_h=False, return_mapping=True, sanitize="partial")
 
     def rd_embed(self, rdmol, num_conf_attempts):
         """
diff --git a/rmgpy/statmech/ndTorsions.py b/rmgpy/statmech/ndTorsions.py
index 7ee4e31135..c71675a18b 100644
--- a/rmgpy/statmech/ndTorsions.py
+++ b/rmgpy/statmech/ndTorsions.py
@@ -35,8 +35,9 @@
 
 import numdifftools as nd
 import numpy as np
-from scipy import integrate as inte
 from scipy import interpolate
+from scipy.integrate import simpson
+
 from sklearn import linear_model
 from sklearn.preprocessing import PolynomialFeatures
 
@@ -614,7 +615,7 @@ def f(*phis):
             Imat[coords] = f(*rphis[np.array(coords)])
         
         for i in range(len(self.pivots)):
-            Imat = inte.simps(Imat, rphis)
+            Imat = simpson(Imat, rphis)
             
         intg = Imat
         
diff --git a/setup.py b/setup.py
index 78a8e3eeda..ff7c0770ad 100644
--- a/setup.py
+++ b/setup.py
@@ -145,8 +145,9 @@
     description='Reaction Mechanism Generator',
     author='William H. Green and the RMG Team',
     author_email='rmg_dev@mit.edu',
-    url='https://reactionmechanismgenerator.github.io',
-    python_requires='>=3.9,<3.10',
+    url='http://reactionmechanismgenerator.github.io',
+    python_requires='>=3.9,<3.12',
+
     packages=find_packages(where='.', include=["rmgpy*"]) + find_packages(where='.', include=["arkane*"]),
     scripts=scripts,
     entry_points={
diff --git a/test/rmgpy/molecule/atomtypeTest.py b/test/rmgpy/molecule/atomtypeTest.py
index fb9ab3c5ed..200922b9a4 100644
--- a/test/rmgpy/molecule/atomtypeTest.py
+++ b/test/rmgpy/molecule/atomtypeTest.py
@@ -165,7 +165,7 @@ def test_make_sample_molecule(self):
             except:
                 logging.exception(f"Couldn't make sample molecule for atomType {name}")
                 failed.append(name)
-        assert not failed, f"Couldn't make sample molecules for types {', '.join(failed)}"
+        assert len(failed) == 0, f"Couldn't make sample molecules for types {', '.join(failed)}"
 
     @pytest.mark.skip(reason="WIP")
     def test_make_sample_molecule_wip(self):
diff --git a/test/rmgpy/molecule/drawTest.py b/test/rmgpy/molecule/drawTest.py
index 6c416f171d..dec288ab79 100644
--- a/test/rmgpy/molecule/drawTest.py
+++ b/test/rmgpy/molecule/drawTest.py
@@ -297,4 +297,102 @@ def test_draw_bidentate_adsorbate(self):
             surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(molecule, file_format="png", target=path)
             assert os.path.exists(path), "File doesn't exist"
             os.unlink(path)
-            assert isinstance(surface, ImageSurface)
\ No newline at end of file
+            assert isinstance(surface, ImageSurface)
+
+    def test_draw_bidentate_with_charge_separation(self):
+        molecule = Molecule().from_adjacency_list(
+            """
+1 X u0 p0 c0 {3,S}
+2 X u0 p0 c0 {4,D}
+3 O u0 p2 c0 {1,S} {4,S}
+4 N u0 p0 c+1 {3,S} {2,D} {5,S}
+5 O u0 p3 c-1 {4,S}
+        """
+        )
+        try:
+            from cairocffi import PDFSurface
+        except ImportError:
+            from cairo import PDFSurface
+        surface, _cr, (_xoff, _yoff, _width, _height) = self.drawer.draw(molecule, file_format="pdf")
+        assert isinstance(surface, PDFSurface)
+
+    def test_draw_cation(self):
+        try:
+            from cairocffi import PDFSurface
+        except ImportError:
+            from cairo import PDFSurface
+        path = "test_molecule.pdf"
+        if os.path.exists(path):
+            os.unlink(path)
+        polycycle = Molecule(smiles="C1=NC2=C(N1)C(=O)[NH2+]C(=N2)N")
+        surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(polycycle, file_format="pdf", target=path)
+        assert isinstance(surface, PDFSurface)
+        assert width > height
+        os.unlink(path)
+
+    def test_draw_anion(self):
+        try:
+            from cairocffi import PDFSurface
+        except ImportError:
+            from cairo import PDFSurface
+        path = "test_molecule.pdf"
+        if os.path.exists(path):
+            os.unlink(path)
+        polycycle = Molecule(smiles="c1ccc2c3ccccc3[CH-]c2c1")
+        surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(polycycle, file_format="pdf", target=path)
+        assert isinstance(surface, PDFSurface)
+        assert width > height
+        os.unlink(path)
+
+    def test_draw_zwitterion(self):
+        try:
+            from cairocffi import PDFSurface
+        except ImportError:
+            from cairo import PDFSurface
+        path = "test_molecule.pdf"
+        if os.path.exists(path):
+            os.unlink(path)
+        polycycle = Molecule(smiles="[NH3+]CC(=O)[O-]")
+        surface, _cr, (_xoff, _yoff, width, height) = self.drawer.draw(polycycle, file_format="pdf", target=path)
+        assert isinstance(surface, PDFSurface)
+        assert width > height
+        os.unlink(path)
+
+    def test_draw_cation_on_surface(self):
+        molecule = Molecule().from_adjacency_list(
+            """
+1 X u0 p0 c0 {3,S}
+2 X u0 p0 c0 {3,S}
+3 O u0 p1 c+1 {1,S} {2,S} {4,S}
+4 H u0 p0 c0 {3,S}
+        """
+        )
+        try:
+            from cairocffi import PDFSurface
+        except ImportError:
+            from cairo import PDFSurface
+        path = "test_molecule.pdf"
+        if os.path.exists(path):
+            os.unlink(path)
+        surface, _cr, (_xoff, _yoff, _width, _height) = self.drawer.draw(molecule, file_format="pdf", target=path)
+        assert isinstance(surface, PDFSurface)
+        os.unlink(path)
+
+
+    def test_draw_anion_on_surface(self):
+        molecule = Molecule().from_adjacency_list(
+            """
+1 X u0 p0 c0 {2,S}
+2 O u0 p3 c-1 {1,S}
+        """
+        )
+        try:
+            from cairocffi import PDFSurface
+        except ImportError:
+            from cairo import PDFSurface
+        path = "test_molecule.pdf"
+        if os.path.exists(path):
+            os.unlink(path)
+        surface, _cr, (_xoff, _yoff, _width, _height) = self.drawer.draw(molecule, file_format="pdf", target=path)
+        assert isinstance(surface, PDFSurface)
+        os.unlink(path)
diff --git a/test/rmgpy/molecule/fragmentTest.py b/test/rmgpy/molecule/fragmentTest.py
index 1975b442f6..5f59efd6a3 100644
--- a/test/rmgpy/molecule/fragmentTest.py
+++ b/test/rmgpy/molecule/fragmentTest.py
@@ -747,7 +747,7 @@ def test_get_representative_molecule(self):
 
     def test_to_rdkit_mol(self):
         fragment = rmgpy.molecule.fragment.Fragment().from_smiles_like_string("CCR")
-        rdmol, _ = fragment.to_rdkit_mol()
+        rdmol, _ = fragment.to_rdkit_mol(remove_h=False, return_mapping=True)
 
         assert rdmol.GetNumAtoms() == 8
 
diff --git a/test/rmgpy/molecule/graphTest.py b/test/rmgpy/molecule/graphTest.py
index f7781d3ae7..da4daafefc 100644
--- a/test/rmgpy/molecule/graphTest.py
+++ b/test/rmgpy/molecule/graphTest.py
@@ -608,25 +608,6 @@ def test_get_all_cyclic_vertices(self):
         self.graph.add_edge(edge)  # To create a cycle
         assert len(self.graph.get_all_cyclic_vertices()) == 4
 
-    def test_get_all_polycylic_vertices(self):
-        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
-        self.graph.add_edge(edge)  # To create a cycle
-        assert self.graph.get_all_polycyclic_vertices() == []
-        edge2 = Edge(self.graph.vertices[0], self.graph.vertices[5])
-        self.graph.add_edge(edge2)  # Create another cycle to generate two fused cycles
-        assert len(self.graph.get_all_polycyclic_vertices()) == 2
-        # Add new vertices and edges to generate a spirocyclic cycle
-        vertices = [Vertex() for _ in range(2)]
-        for vertex in vertices:
-            self.graph.add_vertex(vertex)
-        edges = [
-            Edge(self.graph.vertices[5], self.graph.vertices[6]),
-            Edge(self.graph.vertices[6], self.graph.vertices[7]),
-            Edge(self.graph.vertices[5], self.graph.vertices[7]),
-        ]
-        for edge in edges:
-            self.graph.add_edge(edge)
-        assert len(self.graph.get_all_polycyclic_vertices()) == 3
 
     def test_get_all_cycles(self):
         """
@@ -673,255 +654,6 @@ def test_get_all_simple_cycles_of_size(self):
         cycle_list = self.graph.get_all_simple_cycles_of_size(6)
         assert len(cycle_list) == 0
 
-    def test_get_smallest_set_of_smallest_rings(self):
-        """
-        Test the Graph.get_smallest_set_of_smallest_rings() method.
-        """
-        cycle_list = self.graph.get_smallest_set_of_smallest_rings()
-        assert len(cycle_list) == 0
-        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
-        self.graph.add_edge(edge)  # To create a cycle
-        cycle_list = self.graph.get_smallest_set_of_smallest_rings()
-        assert len(cycle_list) == 1
-        assert len(cycle_list[0]) == 4
-
-    def test_get_relevant_cycles(self):
-        """
-        Test the Graph.get_relevant_cycles() method.
-        """
-        cycle_list = self.graph.get_relevant_cycles()
-        assert len(cycle_list) == 0
-        # Create a cycle of length 4
-        edge = Edge(self.graph.vertices[0], self.graph.vertices[3])
-        self.graph.add_edge(edge)
-        # Create a second cycle of length 4
-        edge = Edge(self.graph.vertices[0], self.graph.vertices[5])
-        self.graph.add_edge(edge)
-        # Create a bridge forming multiple cycles of length 4
-        edge = Edge(self.graph.vertices[1], self.graph.vertices[4])
-        self.graph.add_edge(edge)
-
-        # SSSR should be 3 cycles of length 4
-        cycle_list = self.graph.get_smallest_set_of_smallest_rings()
-        assert len(cycle_list) == 3
-        size_list = sorted([len(cycle) for cycle in cycle_list])
-        assert size_list == [4, 4, 4]
-
-        # RC should be 5 cycles of length 4
-        cycle_list = self.graph.get_relevant_cycles()
-        assert len(cycle_list) == 5
-        size_list = sorted([len(cycle) for cycle in cycle_list])
-        assert size_list == [4, 4, 4, 4, 4]
-
-    def test_cycle_list_order_sssr(self):
-        """
-        Test that get_smallest_set_of_smallest_rings return vertices in the proper order.
-
-        There are methods such as symmetry and molecule drawing which rely
-        on the fact that subsequent list entries are connected.
-        """
-        # Create a cycle of length 5
-        edge = Edge(self.graph.vertices[0], self.graph.vertices[4])
-        self.graph.add_edge(edge)
-        # Test SSSR
-        sssr = self.graph.get_smallest_set_of_smallest_rings()
-        assert len(sssr) == 1
-        assert len(sssr[0]) == 5
-        for i in range(5):
-            assert self.graph.has_edge(sssr[0][i], sssr[0][i - 1])
-
-    def test_cycle_list_order_relevant_cycles(self):
-        """
-        Test that get_relevant_cycles return vertices in the proper order.
-
-        There are methods such as symmetry and molecule drawing which rely
-        on the fact that subsequent list entries are connected.
-        """
-        # Create a cycle of length 5
-        edge = Edge(self.graph.vertices[0], self.graph.vertices[4])
-        self.graph.add_edge(edge)
-        # Test RC
-        rc = self.graph.get_relevant_cycles()
-        assert len(rc) == 1
-        assert len(rc[0]) == 5
-        for i in range(5):
-            assert self.graph.has_edge(rc[0][i], rc[0][i - 1])
-
-    def test_get_polycyclic_rings(self):
-        """
-        Test that the Graph.get_polycycles() method returns only polycyclic rings.
-        """
-        vertices = [Vertex() for _ in range(27)]
-        bonds = [
-            (0, 1),
-            (1, 2),
-            (2, 3),
-            (3, 4),
-            (4, 5),
-            (5, 6),
-            (6, 7),
-            (7, 8),
-            (8, 9),
-            (9, 10),
-            (10, 11),
-            (11, 12),
-            (12, 13),
-            (13, 14),
-            (14, 15),
-            (14, 12),
-            (12, 16),
-            (16, 10),
-            (10, 17),
-            (17, 18),
-            (18, 19),
-            (9, 20),
-            (20, 21),
-            (21, 7),
-            (6, 22),
-            (22, 23),
-            (22, 4),
-            (23, 3),
-            (23, 24),
-            (24, 25),
-            (25, 1),
-        ]
-        edges = []
-        for bond in bonds:
-            edges.append(Edge(vertices[bond[0]], vertices[bond[1]]))
-
-        graph = Graph()
-        for vertex in vertices:
-            graph.add_vertex(vertex)
-        for edge in edges:
-            graph.add_edge(edge)
-        graph.update_connectivity_values()
-
-        sssr = graph.get_smallest_set_of_smallest_rings()
-        assert len(sssr) == 6
-        polycyclic_vertices = set(graph.get_all_polycyclic_vertices())
-        expected_polycyclic_vertices = set([vertices[index] for index in [3, 23, 4, 22, 12]])
-
-        assert polycyclic_vertices == expected_polycyclic_vertices
-
-        continuous_rings = graph.get_polycycles()
-        expected_continuous_rings = [
-            [vertices[index] for index in [1, 2, 3, 4, 5, 6, 22, 23, 24, 25]],
-            # [vertices[index] for index in [7,8,9,21,20]], # This is a nonpolycyclic ring
-            [vertices[index] for index in [10, 11, 12, 13, 14, 16]],
-        ]
-
-        # Convert to sets for comparison purposes
-        continuous_rings = [set(ring) for ring in continuous_rings]
-        expected_continuous_rings = [set(ring) for ring in expected_continuous_rings]
-        for ring in expected_continuous_rings:
-            assert ring in continuous_rings
-
-    def test_get_max_cycle_overlap(self):
-        """
-        Test that get_max_cycle_overlap returns the correct overlap numbers
-        for different graphs.
-        """
-
-        def make_graph(edge_inds):
-            nvert = max(max(inds) for inds in edge_inds) + 1
-            vertices = [Vertex() for _ in range(nvert)]
-            graph = Graph(vertices)
-            for idx1, idx2 in edge_inds:
-                graph.add_edge(Edge(vertices[idx1], vertices[idx2]))
-            return graph
-
-        linear = make_graph([(0, 1), (1, 2)])
-        mono = make_graph([(0, 1), (0, 2), (1, 2), (2, 3), (3, 4), (3, 5), (4, 5)])
-        spiro = make_graph([(0, 1), (0, 2), (1, 2), (2, 3), (2, 4), (3, 4)])
-        fused = make_graph([(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)])
-        bridged = make_graph([(0, 1), (0, 2), (1, 3), (1, 4), (2, 3), (2, 5), (4, 5)])
-        cube = make_graph(
-            [
-                (0, 1),
-                (0, 2),
-                (0, 4),
-                (1, 3),
-                (1, 5),
-                (2, 3),
-                (2, 6),
-                (3, 7),
-                (4, 5),
-                (4, 6),
-                (5, 7),
-                (6, 7),
-            ]
-        )
-
-        assert linear.get_max_cycle_overlap() == 0
-        assert mono.get_max_cycle_overlap() == 0
-        assert spiro.get_max_cycle_overlap() == 1
-        assert fused.get_max_cycle_overlap() == 2
-        assert bridged.get_max_cycle_overlap() == 3
-        # With the current algorithm for maximum overlap determination, a cube
-        # only has an overlap of 2, because the set of relevant cycles
-        # contains the six four-membered faces. This could be changed in the
-        # future.
-        assert cube.get_max_cycle_overlap() == 2
-
-    def test_get_largest_ring(self):
-        """
-        Test that the Graph.get_polycycles() method returns only polycyclic rings.
-        """
-        vertices = [Vertex() for _ in range(27)]
-        bonds = [
-            (0, 1),
-            (1, 2),
-            (2, 3),
-            (3, 4),
-            (4, 5),
-            (5, 6),
-            (6, 7),
-            (9, 10),
-            (10, 11),
-            (11, 12),
-            (12, 13),
-            (13, 14),
-            (14, 15),
-            (12, 16),
-            (10, 17),
-            (17, 18),
-            (18, 19),
-            (9, 20),
-            (20, 21),
-            (6, 22),
-            (22, 23),
-            (22, 8),
-            (8, 4),
-            (23, 3),
-            (23, 24),
-            (24, 25),
-            (25, 1),
-        ]
-        edges = []
-        for bond in bonds:
-            edges.append(Edge(vertices[bond[0]], vertices[bond[1]]))
-
-        graph = Graph()
-        for vertex in vertices:
-            graph.add_vertex(vertex)
-        for edge in edges:
-            graph.add_edge(edge)
-        graph.update_connectivity_values()
-
-        rings = graph.get_polycycles()
-        assert len(rings) == 1
-
-        # ensure the last ring doesn't include vertex 8, since it isn't in the
-        # longest ring. Try two different items since one might contain the vertex 8
-        long_ring = graph.get_largest_ring(rings[0][0])
-        long_ring2 = graph.get_largest_ring(rings[0][1])
-
-        if len(long_ring) > len(long_ring2):
-            longest_ring = long_ring
-        else:
-            longest_ring = long_ring2
-
-        assert len(longest_ring) == len(rings[0]) - 1
 
     def test_sort_cyclic_vertices(self):
         """Test that sort_cyclic_vertices works properly for a valid input."""
diff --git a/test/rmgpy/molecule/moleculeTest.py b/test/rmgpy/molecule/moleculeTest.py
index 9621d6fc7d..d41bd09993 100644
--- a/test/rmgpy/molecule/moleculeTest.py
+++ b/test/rmgpy/molecule/moleculeTest.py
@@ -2310,7 +2310,7 @@ def test_large_mol_creation(self):
     def test_get_polycyclic_rings(self):
         """
         Test that polycyclic rings within a molecule are returned properly in the function
-        `Graph().get_polycycles()`
+        `Molecule.get_polycycles()`
         """
         # norbornane
         m1 = Molecule(smiles="C1CC2CCC1C2")
@@ -2414,7 +2414,7 @@ def test_get_disparate_rings(self):
     def test_get_smallest_set_of_smallest_rings(self):
         """
         Test that SSSR within a molecule are returned properly in the function
-        `Graph().get_smallest_set_of_smallest_rings()`
+        `Molecule().get_smallest_set_of_smallest_rings()`
         """
 
         m1 = Molecule(smiles="C12CCC1C3CC2CC3")
@@ -3043,3 +3043,133 @@ def test_remove_van_der_waals_bonds(self):
         assert len(mol.get_all_edges()) == 2
         mol.remove_van_der_waals_bonds()
         assert len(mol.get_all_edges()) == 1
+
+    def test_get_relevant_cycles(self):
+        """
+        Test the Molecule.get_relevant_cycles() method.
+        """
+        mol = Molecule(smiles="CCCC")
+        cycle_list = mol.get_relevant_cycles()
+        assert len(cycle_list) == 0
+        
+        # Create a cycle of length 4
+        mol = Molecule(smiles="C1CCC1")
+        cycle_list = mol.get_relevant_cycles()
+        assert len(cycle_list) == 1
+        assert len(cycle_list[0]) == 4
+
+        # TODO: test bridged bicycle
+
+    def test_cycle_list_order_sssr(self):
+        """
+        Test that get_smallest_set_of_smallest_rings return vertices in the proper order.
+
+        There are methods such as symmetry and molecule drawing which rely
+        on the fact that subsequent list entries are connected.
+        """
+        # Create a cycle of length 5
+        mol = Molecule(smiles="C1CCCC1")
+        # Test SSSR
+        sssr = mol.get_smallest_set_of_smallest_rings()
+        assert len(sssr) == 1
+        assert len(sssr[0]) == 5
+        for i in range(5):
+            assert mol.has_bond(sssr[0][i], sssr[0][i - 1])
+
+    def test_cycle_list_order_relevant_cycles(self):
+        """
+        Test that get_relevant_cycles return vertices in the proper order.
+
+        There are methods such as symmetry and molecule drawing which rely
+        on the fact that subsequent list entries are connected.
+        """
+        # Create a cycle of length 5
+        mol = Molecule(smiles="C1CCCC1")
+        # Test RC
+        rc = mol.get_relevant_cycles()
+        assert len(rc) == 1
+        assert len(rc[0]) == 5
+        for i in range(5):
+            assert mol.has_bond(rc[0][i], rc[0][i - 1])
+
+    def test_get_max_cycle_overlap(self):
+        """
+        Test that get_max_cycle_overlap returns the correct overlap numbers
+        for different molecules.
+        """
+        # Linear molecule
+        linear = Molecule(smiles="CCC")
+        assert linear.get_max_cycle_overlap() == 0
+        
+        # Monocyclic molecule
+        mono = Molecule(smiles="C1CCCC1")
+        assert mono.get_max_cycle_overlap() == 0
+        
+        # Spirocyclic molecule
+        spiro = Molecule(smiles="C1CCC2(CC1)CC2")
+        assert spiro.get_max_cycle_overlap() == 1
+        
+        # Fused bicyclic molecule
+        fused = Molecule(smiles="C1C2C(CCC1)CCCC2")
+        assert fused.get_max_cycle_overlap() == 2
+        
+        # Bridged bicyclic molecule
+        bridged = Molecule(smiles="C1CC2CCC1C2")
+        assert bridged.get_max_cycle_overlap() == 3
+        
+        # Cube-like molecule (cubane)
+        cube = Molecule(smiles="C12C3C4C1C5C2C3C45")
+        # With the current algorithm for maximum overlap determination, a cube
+        # only has an overlap of 2, because the set of relevant cycles
+        # contains the six four-membered faces. This could be changed in the
+        # future.
+        assert cube.get_max_cycle_overlap() == 2
+
+    def test_get_all_polycyclic_vertices(self):
+        """
+        Test that get_all_polycyclic_vertices returns the correct vertices.
+        """
+        # Simple linear molecule
+        mol = Molecule(smiles="CCC")
+        polycyclic_vertices = mol.get_all_polycyclic_vertices()
+        assert len(polycyclic_vertices) == 0
+        
+        # Monocyclic molecule
+        mol = Molecule(smiles="C1CCCC1")
+        polycyclic_vertices = mol.get_all_polycyclic_vertices()
+        assert len(polycyclic_vertices) == 0
+        
+        # Fused bicyclic molecule
+        # TODO: don't just test length, test the actual vertices
+        mol = Molecule(smiles="C1C2C(CCC1)CCCC2")
+        polycyclic_vertices = mol.get_all_polycyclic_vertices()
+        assert len(polycyclic_vertices) > 0
+        
+        # Spirocyclic molecule
+        # TODO: don't just test length, test the actual vertices
+        mol = Molecule(smiles="C1CCC2(CC1)CC2")
+        polycyclic_vertices = mol.get_all_polycyclic_vertices()
+        assert len(polycyclic_vertices) > 0
+
+    def test_get_largest_ring(self):
+        """
+        Test that Molecule.get_largest_ring() method returns the largest ring.
+        """
+        # Create a complex polycyclic molecule
+        mol = Molecule(smiles="C14CCCCCC(C(CCC1CC2CCCCCCC2)CC3CCC3)C4")
+
+        # Get polycyclic rings
+        rings = mol.get_polycycles()
+        assert len(rings) == 1
+
+        long_ring = mol.get_largest_ring(rings[0][0])
+        long_ring2 = mol.get_largest_ring(rings[0][1])
+
+        # get the longer of the two rings
+        if len(long_ring) > len(long_ring2):
+            longest_ring = long_ring
+        else:
+            longest_ring = long_ring2
+
+        # longest ring should be one atom shorter than the full polycyclic ring
+        assert len(longest_ring) == len(rings[0]) - 1
\ No newline at end of file
diff --git a/utilities.py b/utilities.py
index 10178c10df..1d47b33453 100644
--- a/utilities.py
+++ b/utilities.py
@@ -50,7 +50,6 @@ def check_dependencies():
     missing = {
         'openbabel': _check_openbabel(),
         'pydqed': _check_pydqed(),
-        'pyrdl': _check_pyrdl(),
         'rdkit': _check_rdkit(),
         'symmetry': _check_symmetry(),
     }
@@ -104,22 +103,6 @@ def _check_pydqed():
     return missing
 
 
-def _check_pyrdl():
-    """Check for pyrdl"""
-    missing = False
-
-    try:
-        import py_rdl
-    except ImportError:
-        print('{0:<30}{1}'.format('pyrdl', 'Not found. Necessary for ring perception algorithms.'))
-        missing = True
-    else:
-        location = py_rdl.__file__
-        print('{0:<30}{1}'.format('pyrdl', location))
-
-    return missing
-
-
 def _check_rdkit():
     """Check for RDKit"""
     missing = False