Avoid splitting reaction SMILES at dative bonds

src/rxn/chemutils/extended_reaction_smiles.py

@@ -78,7 +78,9 @@ def convert(
         if remove_atom_maps:
             pure_smiles = remove_atom_mapping(pure_smiles)
 
-        reactant_groups = pure_smiles.split(">")
+        # We split at the ">" characters, only if they are not preceded by a "-",
+        # which would indicate a dative bond.
+        reactant_groups = re.split(r"(?<!-)>", pure_smiles)
         mols_groups = [group.split(".") for group in reactant_groups]
         mols_groups = [[mol for mol in group if mol] for group in mols_groups]
 

src/rxn/chemutils/reaction_equation.py

@@ -1,3 +1,4 @@
+import re
 from functools import partial
 from typing import (
     Callable,
@@ -75,9 +76,11 @@ def from_string(
         Convert a ReactionEquation from an "rxn" reaction SMILES.
         """
 
+        # We split at the ">" characters, only if they are not preceded by a "-",
+        # which would indicate a dative bond.
         groups = [
             multicomponent_smiles_to_list(smiles_group, fragment_bond=fragment_bond)
-            for smiles_group in reaction_string.split(">")
+            for smiles_group in re.split(r"(?<!-)>", reaction_string)
         ]
 
         try:

tests/test_extended_reaction_smiles.py

@@ -58,6 +58,20 @@ def test_from_reaction_smiles_with_fragments() -> None:
     assert reaction.products == ["OC1=CC=C2C3=C(C(=O)OC2=C1)C=C(COC)C=C3"]
 
 
+def test_from_reaction_smiles_with_dative_bond() -> None:
+    reaction_smiles = "COC(=O)CCBr.O=C[O-]->[K+].[OH-].[Na+]>>COC(=O)CCOC(=O)C |f:2.3|"
+
+    reaction = parse_extended_reaction_smiles(reaction_smiles)
+
+    assert reaction.reactants == [
+        "COC(=O)CCBr",
+        "O=C[O-]->[K+]",
+        "[OH-].[Na+]",
+    ]
+    assert reaction.agents == []
+    assert reaction.products == ["COC(=O)CCOC(=O)C"]
+
+
 def test_from_reaction_smiles_with_other_extended_information() -> None:
     # the part with "&1:", "c:", "H:", must not be considered for determination of fragments
     reaction_smiles = (

tests/test_reaction_equation.py

@@ -175,6 +175,21 @@ def test_equation_from_string_with_no_agent() -> None:
     assert reaction == expected_reaction
 
 
+def test_equation_from_string_with_dative_bond() -> None:
+    reaction_string = "COC(=O)CCBr.O=C([O-]->[K+])>>COC(=O)CCOC(=O)C"
+
+    reaction = ReactionEquation.from_string(reaction_string)
+
+    expected_reactants = ["COC(=O)CCBr", "O=C([O-]->[K+])"]
+    expected_agents: List[str] = []
+    expected_products = ["COC(=O)CCOC(=O)C"]
+    expected_reaction = ReactionEquation(
+        expected_reactants, expected_agents, expected_products
+    )
+
+    assert reaction == expected_reaction
+
+
 def test_iter_all_smiles() -> None:
     reaction_string = "COCO.[Na+].[OH-]>O>NCOC"
     reaction = ReactionEquation.from_string(reaction_string)