Merge remote-tracking branch 'origin/main' into docker_bashrc

Author: calvinp0

arc/species/species.py

@@ -287,6 +287,7 @@ class ARCSpecies(object):
         multi_species: (str): The multi-species set this species belongs to. Used for running a set of species
                               simultaneously in a single ESS input file.
         symmetry_number (int): The external symmetry number of the species, calculated from mol_list.
+        index (int): An optional index for the species.
     """
 
     def __init__(self,
@@ -366,6 +367,7 @@ def __init__(self,
         self.project_directory = project_directory
         self.label = label
         self.symmetry_number = None
+        self.index = None
 
         if species_dict is not None:
             # Reading from a dictionary (it's possible that the dict contains only a 'yml_path' argument, check first)
@@ -678,6 +680,8 @@ def as_dict(self,
             species_dict['arkane_file'] = self.arkane_file
         if not self.consider_all_diastereomers:
             species_dict['consider_all_diastereomers'] = self.consider_all_diastereomers
+        if self.index is not None:
+            species_dict['index'] = self.index
         if self.is_ts:
             if len(self.ts_guesses):
                 species_dict['ts_guesses'] = [tsg.as_dict() for tsg in self.ts_guesses]
@@ -827,6 +831,7 @@ def from_dict(self, species_dict):
         self.ts_conf_spawned = species_dict['ts_conf_spawned'] if 'ts_conf_spawned' in species_dict \
             else False if self.is_ts else None
         self.adjlist = species_dict['adjlist'] if 'adjlist' in species_dict else None
+        self.index = species_dict['index'] if 'index' in species_dict else None
         if self.is_ts:
             self.ts_number = species_dict['ts_number'] if 'ts_number' in species_dict else None
             self.ts_guesses_exhausted = species_dict['ts_guesses_exhausted'] if 'ts_guesses_exhausted' in species_dict else False

arc/species/species_test.py

@@ -2767,6 +2767,20 @@ def test_hash(self):
         self.assertEqual(len(s), 2)
         self.assertIn(self.spc1, s)
 
+    def test_species_indexing(self):
+        """Test species indexing in ARCSpecies."""
+        spc_a = ARCSpecies(label='spc_a', smiles='C')
+        spc_b = ARCSpecies(label='spc_b', smiles='CC')
+        spc_c = ARCSpecies(label='spc_c', smiles='CCC')
+
+        species_list = [spc_a, spc_b, spc_c]
+        for index, spc in enumerate(species_list):
+            spc.index = index
+
+        self.assertEqual(spc_a.index, 0)
+        self.assertEqual(spc_b.index, 1)
+        self.assertEqual(spc_c.index, 2)
+
 
 class TestTSGuess(unittest.TestCase):
     """