Created cheat_sheet function to check if smiles is in cheat sheets (#679

)

I have updated the cheat sheets to include C2H3 and added a new function
called "cheat sheet." The test aims to confirm the accurate
representation of the C2H3 species when providing the SMILES notation in
both directions (C=[CH] / [CH]=C).

arc/species/conformers.py

@@ -41,7 +41,7 @@
 import sys
 import time
 from itertools import product
-from typing import List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 from openbabel import openbabel as ob
 from openbabel import pybel as pyb
@@ -115,7 +115,33 @@
                           'FF energy': 0,
                           'source': 'CHEAT_SHEET',
                           'torsion_dihedrals': {}},
-               }
+                '[CH]=C': {'xyz': converter.str_to_xyz("""C	0.0513140	0.7351300	0.0000000
+                                                          C	0.0513140	-0.5980320	0.0000000
+                                                          H	-0.7050560	1.5248940	0.0000000
+                                                          H	-0.8925320	-1.1684180	0.0000000
+                                                          H	0.9818240	-1.1790600	0.0000000"""),
+                         'index': 0,
+                          'FF energy': 0,
+                          'source': 'CHEAT_SHEET',
+                          'torsion_dihedrals': {}}
+              }
+
+def cheat_sheet(mol_list: Union[List[Molecule], Molecule]) -> Optional[List[Dict]]:
+    """
+    Check if the species is in the cheat sheet, and return its correct xyz if it is.
+
+    Args:
+        mol_list (Union[List[Molecule], Molecule]): Molecule objects to consider (or Molecule, resonance structures will be generated).
+    
+    Returns: Optional[lis[Dict]]
+    """
+    mol_list = [mol_list] if not isinstance(mol_list, list) else mol_list
+    for smiles in CHEAT_SHEET.keys():
+        cheat_mol = Molecule(smiles=smiles)
+        for mol in mol_list:
+            if cheat_mol.is_isomorphic(mol.copy(deep=True)):
+                return [CHEAT_SHEET[smiles]]
+    return None
 
 
 def generate_conformers(mol_list: Union[List[Molecule], Molecule],
@@ -177,12 +203,9 @@ def generate_conformers(mol_list: Union[List[Molecule], Molecule],
         - Lowest conformers
         - Lowest conformers and all new conformers.
     """
-    for mol in mol_list:
-        smiles = mol.copy(deep=True).to_smiles()
-        if smiles in CHEAT_SHEET:
-            if return_all_conformers:
-                return [CHEAT_SHEET[smiles]], [CHEAT_SHEET[smiles]]
-            return [CHEAT_SHEET[smiles]]
+    cheat = cheat_sheet(mol_list) 
+    if cheat is not None:
+        return cheat
     if isinstance(mol_list, Molecule):
         # Try generating resonance structures, but strictly keep atom order.
         success = False

arc/species/conformers_test.py

@@ -2577,6 +2577,25 @@ def test_determine_smallest_atom_index_in_scan(self):
             atom2=mol_1.atoms[20],
             mol=mol_1), 23)
 
+    def test_cheat_sheet(self):
+        """Test the cheat_sheet() method."""
+        expected_cheat_sheet_dict = [{'xyz': {'symbols': ('C', 'C', 'H', 'H', 'H'),
+                                             'isotopes': (12, 12, 1, 1, 1), 
+                                             'coords': ((0.051314, 0.73513, 0.0), 
+                                                        (0.051314, -0.598032, 0.0), 
+                                                        (-0.705056, 1.524894, 0.0), 
+                                                        (-0.892532, -1.168418, 0.0), 
+                                                        (0.981824, -1.17906, 0.0))}, 
+                                             'index': 0, 
+                                             'FF energy': 0, 
+                                             'source': 'CHEAT_SHEET', 
+                                             'torsion_dihedrals': {}}
+                                    ]
+        cheat_mol1 = Molecule(smiles='C=[CH]')
+        self.assertEqual(conformers.cheat_sheet([cheat_mol1]), expected_cheat_sheet_dict)
+        cheat_mol2 = Molecule(smiles='C')
+        self.assertIsNone(conformers.cheat_sheet([cheat_mol2]))
+
 
 if __name__ == '__main__':
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))