Added fix_mol_electronic_configuration() to species

Also added get_atom_theoretical_charge()

Author: alongd

arc/species/species.py

@@ -1935,11 +1935,7 @@ def _scissors(self,
         added_radical = list()
         for mol, label in zip([mol1, mol2], [label1, label2]):
             for atom in mol.atoms:
-                theoretical_charge = elements.PeriodicSystem.valence_electrons[atom.symbol] \
-                                     - atom.get_total_bond_order() \
-                                     - atom.radical_electrons - \
-                                     2 * atom.lone_pairs
-                if theoretical_charge == atom.charge + 1:
+                if get_atom_theoretical_charge(atom) == atom.charge + 1:
                     # we're missing a radical electron on this atom
                     if label not in added_radical or label == 'H':
                         atom.radical_electrons += 1
@@ -2708,3 +2704,64 @@ def split_mol(mol: Molecule) -> Tuple[List[Molecule], List[List[int]]]:
         molecules.append(Molecule(atoms=[mol.atoms[index] for index in frag_indices]))
         fragments.append(frag_indices)
     return molecules, fragments
+
+
+def get_atom_theoretical_charge(atom: Atom) -> float:
+    """
+    Get the theoretical charge of an atom based on its electronic properties.
+
+    Args:
+        atom (Atom): The atom to check.
+
+    Returns:
+        float: The theoretical charge of the atom.
+    """
+    return elements.PeriodicSystem.valence_electrons[atom.symbol] \
+        - atom.get_total_bond_order() \
+        - atom.radical_electrons - \
+        2 * atom.lone_pairs
+
+
+def fix_mol_electronic_configuration(mol: Optional[Molecule] = None) -> Optional[Molecule]:
+    """
+    Fix the electronic configuration (number of radicals, lone pairs, and formal charges) of a Molecule object
+    that was perceived from xyz. Assumes the multiplicity attribute of the given molecule is correct.
+
+    Args:
+        mol (Molecule, optional): The molecule to fix.
+
+    Returns:
+        Molecule: The fixed molecule.
+    """
+    if mol is None:
+        return None
+    multiplicity = mol.multiplicity
+    n_radicals = mol.get_radical_count()
+    if n_radicals + 1 > mol.multiplicity:
+        # Find adjacent atoms with opposite-spin radicals, and pair the radicals up into a bond.
+        mols = mol.generate_resonance_structures(keep_isomorphic=False, filter_structures=True, save_order=True)
+        for structure in mols + [mol]:
+            structure.multiplicity = multiplicity
+        visited = list()
+        updated = False
+        for mol_1 in mols:
+            mol_1.multiplicity = mol.multiplicity
+            for atom_1 in mol_1.atoms:
+                if atom_1 not in visited and atom_1.radical_electrons >= 1:
+                    for atom_2, bond in atom_1.edges.items():
+                        if atom_2.radical_electrons >= 1:
+                            atom_1.radical_electrons -= 1
+                            atom_2.radical_electrons -= 1
+                            bond.order += 1
+                            visited.append(atom_2)
+                            updated = True
+                            break
+                visited.append(atom_1)
+            # Update formal charges.
+            for atom in mol_1.atoms:
+                theoretical_charge = get_atom_theoretical_charge(atom)
+                if theoretical_charge != atom.charge:
+                    atom.charge = theoretical_charge
+            if updated:
+                return mol_1
+        return mols[0]