Merge pull request #37 from TieuLongPhan/dev

Add solution for nitro reduction

Author: TieuLongPhan

CITATION.cff

@@ -0,0 +1,44 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Phan"
+  given-names: "Tieu-Long"
+  orcid: "https://orcid.org/0000-0000-0000-0000"
+- family-names: "Weinbauer"
+  given-names: "Klaus"
+  orcid: "https://orcid.org/0000-0000-0000-0000"
+- family-names: "Gärtner"
+  given-names: "Thomas"
+- family-names: "Merkle"
+  given-names: "Daniel"
+- family-names: "Andersen"
+  given-names: "Jakob L."
+- family-names: "Fagerberg"
+  given-names: "Rolf"
+- family-names: "Stadler"
+  given-names: "Peter F."
+title: "Reaction rebalancing: a novel approach to curating reaction databases"
+version: 1.0.0
+doi: 10.1186/s13321-024-00875-4
+preferred-citation:
+  authors:
+  - family-names: "Phan"
+    given-names: "Tieu-Long"
+    orcid: "https://orcid.org/0000-0000-0000-0000"
+  - family-names: "Weinbauer"
+    given-names: "Klaus"
+    orcid: "https://orcid.org/0000-0000-0000-0000"
+  - family-names: "Gärtner"
+    given-names: "Thomas"
+  - family-names: "Merkle"
+    given-names: "Daniel"
+  - family-names: "Andersen"
+    given-names: "Jakob L."
+  - family-names: "Fagerberg"
+    given-names: "Rolf"
+  - family-names: "Stadler"
+    given-names: "Peter F."
+  title: "Reaction rebalancing: a novel approach to curating reaction databases"
+  type: "article"
+  date-released: 2024-07-19
+  url: "https://doi.org/10.1186/s13321-024-00875-4"

synrbl/rule_based.py

@@ -65,6 +65,33 @@ def run(self, reactions, stats=None):
         both_side = BothSideReact(react_dict, product_dict, unbalance, diff_formula)
         diff_formula, unbalance = both_side.fit(n_jobs=self.n_jobs)
 
+        # Handle oxidation case
+        for index, formula in enumerate(diff_formula):
+            if unbalance[index] == "Both":
+                # Extract oxygen ratio if present, or skip to next iteration if absent.
+                water_ratio = formula.get("O")
+                if water_ratio is None:
+                    continue
+
+                hydrogen_change = 2 * water_ratio
+                additional_oxygen = ".O" * water_ratio
+
+                # Update the reactions list with additional oxygen on both specified keys.
+                reactions[index]["products"] += additional_oxygen
+                reactions[index][self.reaction_col] += additional_oxygen
+
+                # Remove the 'O' key as it's processed now.
+                del formula["O"]
+
+                formula["H"] = formula.get("H", 0) - hydrogen_change
+
+                # Check the new hydrogen count to update balance status.
+                if formula["H"] >= 0:
+                    unbalance[index] = "Products"
+                else:
+                    formula["H"] = -formula["H"]
+                    unbalance[index] = "Reactants"
+
         _reactions = pd.concat(
             [
                 pd.DataFrame(reactions),