Use rdkit for SSSR and RCs (bug fix + Python upgrade)

Currently we use `RingDecomposerLib` for finding the Smallest Set of Smallest Rings and getting the Relevant Cycles. This package does not support Python 3.10+ and is thus blocking further upgrades to RMG.

@KnathanM in particular is looking to get RMG to Python 3.11 so as to add support for ChemProp v2.

I believe we can just use RDKit to do these operations instead. The original paper mentions that the functionality was being moved upstream to RDKit. With the help of AI I've taken just a first pass at reimplementing, with the special note that:
 - I opted to use the Symmetric SSSR in place of the 'true' SSSR. This is because the latter is non-unique (see [RDKit's "The SSSR Problem"](https://www.rdkit.org/docs/GettingStartedInPython.html#the-sssr-problem)). This should actually resolve  #2562
 - I need to read more about the "Relevant Cycles"

This PR will be a draft for now, as it is predicated on Python 3.9 already being available (which it nearly is in #2741)

Author: JacksonBurns

.github/workflows/CI.yml

@@ -56,7 +56,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         os: [macos-13, macos-latest, ubuntu-latest]
         include-rms: ["", "with RMS"]
         exclude:

environment.yml

@@ -83,7 +83,6 @@ 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

rmgpy/molecule/graph.pyx

@@ -35,7 +35,7 @@ are the components of a graph.
 
 import itertools
 
-import py_rdl
+from rdkit import Chem
 
 from rmgpy.molecule.vf2 cimport VF2
 
@@ -971,68 +971,57 @@ cdef class Graph(object):
 
     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]))
-
+        Returns the smallest set of smallest rings (SSSR) as a list of lists of atom indices.
+        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
+        """
+        cdef list sssr = []
+        cdef object ring_info, ring
+        # Get the symmetric SSSR using RDKit
+        ring_info = Chem.GetSymmSSSR(self)
+        for ring in ring_info:
+            # Convert ring (tuple of atom indices) to sorted list
+            sorted_ring = self.sort_cyclic_vertices(list(ring))
+            sssr.append(sorted_ring)
         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]))
-
+        Returns the set of relevant cycles as a list of lists of atom indices.
+        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
+        """
+        cdef list rc = []
+        cdef object mol = self
+        cdef object ring_info = mol.GetRingInfo()
+        cdef object atom_rings = ring_info.AtomRings()
+        cdef object ring
+        for ring in atom_rings:
+            # Convert ring (tuple of atom indices) to sorted list
+            sorted_ring = self.sort_cyclic_vertices(list(ring))
+            # Filter for "relevant" cycles (e.g., rings up to size 7)
+            if len(sorted_ring) <= 7:
+                rc.append(sorted_ring)
         return rc
 
     cpdef list sort_cyclic_vertices(self, list vertices):

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