Added a species constraint for the max number of rings fused together

documentation/source/users/rmg/input.rst

@@ -1010,7 +1010,7 @@ all of RMG's reaction families. ::
         maximumRadicalElectrons=2,
         maximumSingletCarbenes=1,
         maximumCarbeneRadicals=0,
-        maximumIsotopicAtoms=2,
+        maximumFusedRings=3,
         allowSingletO2 = False,
         speciesCuttingThreshold=20,
     )
@@ -1020,6 +1020,8 @@ from either the input file, seed mechanisms, or reaction libraries to bypass the
 Note that this should be done with caution, since the constraints will still apply to subsequent
 products that form.
 
+``maximumFusedRings`` is the maximum number of rings in any fused ring system in the species.
+
 By default, the ``allowSingletO2`` flag is set to ``False``.  See :ref:`representing_oxygen` for more information.
 
 Note that ``speciesCuttingThreshold`` is set by default to 20 heavy atoms. This means that if a species containing 

documentation/source/users/rmg/modules/isotopes.rst

@@ -49,10 +49,6 @@ not match the same depository reactions, leading to inconsistent kinetics. If
 degeneracy errors arise when generating reactions from scratch, try using this
 option to see if it reduces errors in degeneracy.
 
-The arguement ``--maximumIsotopicAtoms [integer]`` limits the number of enriched
-atoms in any isotopologue in the model. This is beneficial for decreasing model 
-size, runtime of model creation and runtime necessary for analysis.
-
 Adding kinetic isotope effects which are described in this paper can be obtained
 through the argument ``--kineticIsotopeEffect simple``. Currently this is the
 only supported method, though this can be extended to other effects.

examples/rmg/MR_test/input.py

@@ -305,7 +305,5 @@
     #If this is false or missing, RMG will throw an error if the more less-stable form of O2 is entered 
     #which doesn't react in the RMG system. normally input O2 as triplet with SMILES [O][O]
     #allowSingletO2=False,
-    # maximum allowed number of non-normal isotope atoms:
-    #maximumIsotopicAtoms=2,
 )
 

examples/rmg/commented/input.py

@@ -285,8 +285,6 @@
     # If this is false or missing, RMG will throw an error if the more less-stable form of O2 is entered
     # which doesn't react in the RMG system. normally input O2 as triplet with SMILES [O][O]
     # allowSingletO2=False,
-    # maximum allowed number of non-normal isotope atoms:
-    # maximumIsotopicAtoms=2,
 )
 
 # optional block allows thermo to be estimated through quantum calculations

rmgpy/constraints.py

@@ -31,6 +31,7 @@
 
 from rmgpy.species import Species
 
+
 def pass_cutting_threshold(species):
     """
     Pass in either a `Species` or `Molecule` object and checks whether it passes 
@@ -58,6 +59,7 @@ def pass_cutting_threshold(species):
 
     return False
 
+
 def fails_species_constraints(species):
     """
     Pass in either a `Species` or `Molecule` object and checks whether it passes 
@@ -139,4 +141,9 @@ def fails_species_constraints(species):
         if struct.get_singlet_carbene_count() > 0 and struct.get_radical_count() > max_carbene_radicals:
             return True
 
+    max_fused_rings = species_constraints.get('maximumFusedRings', -1)
+    if max_fused_rings != -1 and struct.is_cyclic():
+        if struct.get_ring_count_in_largest_fused_ring_system() > max_fused_rings:
+            return True
+
     return False

rmgpy/molecule/molecule.py

@@ -2926,6 +2926,25 @@ def get_desorbed_molecules(self):
 
         return desorbed_molecules
 
+    def get_ring_count_in_largest_fused_ring_system(self) -> int:
+        """
+        Get the number of rings in the largest fused ring system in the molecule.
+        """
+        cython.declare(ring_counts=list, rings=list, ring_count=int)
+        polycycles = self.get_polycycles()
+        ring_counts = list()
+        for polycycle in polycycles:
+            rings, ring_count = list(), 0
+            for atom in polycycle:
+                cycles = self.get_all_cycles(atom)
+                for cycle in cycles:
+                    if cycle not in rings:
+                        rings.append(cycle)
+                        ring_count += 1
+            ring_counts.append(ring_count)
+        return max(ring_counts) if len(ring_counts) else 0
+
+
 # this variable is used to name atom IDs so that there are as few conflicts by 
 # using the entire space of integer objects
 atom_id_counter = -2 ** 15

rmgpy/rmg/input.py

@@ -1379,6 +1379,7 @@ def generated_species_constraints(**kwargs):
         'maximumRadicalElectrons',
         'maximumSingletCarbenes',
         'maximumCarbeneRadicals',
+        'maximumFusedRings',
         'allowSingletO2',
         'speciesCuttingThreshold',
     ]

scripts/rmg2to3.py

@@ -1796,7 +1796,6 @@
     # rmgpy.tools.isotopes
     'useOriginalReactions': 'use_original_reactions',
     'kineticIsotopeEffect': 'kinetic_isotope_effect',
-    'maximumIsotopicAtoms': 'maximum_isotopic_atoms',
     # rmgpy.tools.loader
     'generateImages': 'generate_images',
     'useJava': 'use_java',

test/rmgpy/molecule/moleculeTest.py

@@ -2956,3 +2956,14 @@ 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_ring_count_in_largest_fused_ring_system(self):
+        """Test that we can count the rings in the largest fused ring system."""
+        mol = Molecule(smiles="CCCC")
+        assert mol.get_ring_count_in_largest_fused_ring_system() == 0
+        mol = Molecule(smiles="c1ccccc1")
+        assert mol.get_ring_count_in_largest_fused_ring_system() == 0
+        mol = Molecule(smiles="c12ccccc1cccc2")
+        assert mol.get_ring_count_in_largest_fused_ring_system() == 2
+        mol = Molecule(smiles="C[C]1C2C(=O)C3CC4C(=O)C=C2CC143")
+        assert mol.get_ring_count_in_largest_fused_ring_system() == 4