Added cut_species_based_on_atom_indices function

This function uses the new, faster and more accurate method for performing the scissoring for atom mapping. Instead of assigning the BDE's to the relevant species, which causes issues when further scissions are performed, this function uses the atom indices to perform the scission.

arc/mapping/engine.py

@@ -1255,3 +1255,39 @@ def determine_bdes_indices_based_on_atom_labels(spc, bde):
         return atoms[1] in atoms[0].bonds.keys()
     else:
         return False
+
+
+def cut_species_based_on_atom_indices(species: List["ARCSpecies"], bdes: List[Tuple[int, int]]) -> List["ARCSpecies"]:
+    """
+    A function for scissoring species based on their atom indices.
+    Args:
+        species (List[ARCSpecies]): The species list that requires scission.
+        bdes (List[Tuple[int, int]]): A list of the atoms between which the bond should be scissored. The atoms are described using the atom labels, and not the actuall atom positions.
+    Returns:
+        List[ARCSpecies]: The species after scission.
+    """
+    if not bdes:
+        return species
+
+    for bde in bdes:
+        for index, spc in enumerate(species):
+            if determine_bdes_indices_based_on_atom_labels(spc, bde):
+                candidate = species.pop(index)
+                candidate.final_xyz = candidate.get_xyz()
+                if candidate.mol.copy(deep=True).smiles == "[H][H]":
+                    labels = [atom.label for atom in candidate.mol.copy(deep=True).atoms]
+                    try:
+                        H1 = candidate.scissors()[0]
+                    except SpeciesError:
+                        return None
+                    H2 = H1.copy()
+                    H2.mol.atoms[0].label = labels[0] if H1.mol.atoms[0].label != labels[0] else labels[1]
+                    species += [H1, H2]
+                else:
+                    try:
+                        species += candidate.scissors()
+                    except SpeciesError as e:
+                        print(e)
+                break
+
+    return species