BTheDragonMaster · FriederikeBiermann · Aug 27, 2025 · Aug 27, 2025 · Aug 29, 2025 · Aug 29, 2025
diff --git a/raichu/cluster/terpene_cluster.py b/raichu/cluster/terpene_cluster.py
@@ -8,6 +8,7 @@
     TailoringRepresentation,
     IsomerizationRepresentation,
     MethylShiftRepresentation,
+    WaterQuenchingRepresentation,
 )
 from raichu.reactions.general_tailoring_reactions import (
     dephosphorylation,
@@ -31,6 +32,7 @@ def __init__(
         macrocyclisations: List[MacrocyclizationRepresentation] = None,
         double_bond_isomerisations: List[IsomerizationRepresentation] = None,
         methyl_shifts: List[MethylShiftRepresentation] = None,
+        water_quenching: List[WaterQuenchingRepresentation] = None,
         tailoring_representations: List[TailoringRepresentation] = None,
     ) -> None:
         super().__init__(tailoring_representations, macrocyclisations)
@@ -39,6 +41,7 @@ def __init__(
         self.precursor = precursor
         self.isomerization_representations = double_bond_isomerisations
         self.methyl_shift_representations = methyl_shifts
+        self.water_quenching_representations = water_quenching
 
         self.chain_intermediate = None
         self.tailored_product = None
@@ -49,6 +52,28 @@ def create_precursor(self) -> None:
         substrate = TerpeneCyclaseSubstrate(self.precursor)
         self.chain_intermediate = read_smiles(substrate.smiles)
 
+    def do_water_quenching(self):
+        if not self.water_quenching_representations:
+            return
+        initialized_water_quenching_atoms = self.initialize_modification_sites(
+            [
+                water_quenching_representation.modification_sites
+                for water_quenching_representation in self.water_quenching_representations
+            ]
+        )
+        for atom in initialized_water_quenching_atoms:
+
+            acceptor_atom = self.chain_intermediate.get_atom(atom[0])
+            # Check if acceptor atom has double bond
+
+            for bond in acceptor_atom.bonds:
+                # reduce one double bond
+                if bond.type == "double" or bond.type == "aromatic":
+                    self.chain_intermediate = double_bond_reduction(bond.neighbours[0], bond.neighbours[1], self.chain_intermediate)
+                    break
+            self.chain_intermediate = addition(acceptor_atom, "O", self.chain_intermediate)
+            self.chain_intermediate.refresh_structure(find_cycles=True)
+
     def do_double_bond_isomerization(self):
         if not self.isomerization_representations:
             return
@@ -77,7 +102,6 @@ def do_double_bond_isomerization(self):
                 new_double_bond_atom2,
             )
 
-
     def do_methyl_shift(self):
         if not self.methyl_shift_representations:
             return
@@ -88,25 +112,23 @@ def do_methyl_shift(self):
                 ]
             )
         for atoms in initialized_methyl_shift_atoms:
-                if len(atoms) != 2:
-                    continue
-                transferred_c = atoms[0]
-                # Assert its actually a methyl group
-                assert [atom.type for atom in transferred_c.neighbours].count("H") == 3
-                source = None
-                source = [
+            if len(atoms) != 2:
+                continue
+            transferred_c = atoms[0]
+            # Assert its actually a methyl group
+            assert [atom.type for atom in transferred_c.neighbours].count("H") == 3
+            source = None
+            source = [
                     atom for atom in transferred_c.neighbours if atom.type != "H"
                 ][0]
-                assert source
-                destination_c = atoms[1]
-                assert destination_c.has_neighbour("H")
-                assert transferred_c.type == "C" and destination_c.type == "C"
-
-                self.chain_intermediate = reductive_bond_breakage(source, transferred_c, self.chain_intermediate)
-                self.chain_intermediate = addition(destination_c, "C", self.chain_intermediate)
-                self.chain_intermediate.refresh_structure(find_cycles=True)
-
+            assert source
+            destination_c = atoms[1]
+            assert destination_c.has_neighbour("H")
+            assert transferred_c.type == "C" and destination_c.type == "C"
 
+            self.chain_intermediate = reductive_bond_breakage(source, transferred_c, self.chain_intermediate)
+            self.chain_intermediate = addition(destination_c, "C", self.chain_intermediate)
+            self.chain_intermediate.refresh_structure(find_cycles=True)
 
     def do_macrocyclization(self, sequential=True):
         initialized_macrocyclization_atoms = self.initialize_macrocyclization()

diff --git a/raichu/data/trans_at.py b/raichu/data/trans_at.py
@@ -7,15 +7,20 @@
     "ARST": [],
     "PYR": [("DUMMY_SC", None)],
     "ALPHAME_EDB": [("DUMMY_AMT", None), ("DUMMY_KR", None), ("DUMMY_EDH", None)],
+    "ALPHAME_ZDB": [("DUMMY_AMT", None), ("DUMMY_KR", None), ("DUMMY_ZDH", None)],
+    "ALPHAME_SHDB": [("DUMMY_AMT", None), ("DUMMY_KR", None), ("DUMMY_GDH", None)],
     "OXI": [],
     "AA": [],
     "ALPHAME_BETA_L_OH": [("DUMMY_AMT", None), ("DUMMY_KR", "B1")],
+    "NON_ELONGATING_ALPHAME_SHDB": [("DUMMY_KR", None), ("DUMMY_GDH", None), ("DUMMY_AMT", None)],
+    "NON_ELONGATING_BETA_L_OME": [("DUMMY_KR", "B1"), ("DUMMY_OMT", None)],
+    "NON_ELONGATING_BETA_OME": [("DUMMY_KR", None), ("DUMMY_OMT", None)],
     "NON_ELONGATING_BETA_L_OH": [("DUMMY_KR", "B1")],
     "RED_SHDB": [("DUMMY_KR", None), ("DUMMY_GDH", None)],
     "DB": [("DUMMY_KR", None), ("DUMMY_DH", None)],
     "KETO": [],
     "NON_ELONGATING": [],
-    "BETA_D_OH": [("DUMMY_KR", None)],
+    "BETA_D_OH": [("DUMMY_KR", "A1")],
     "BETA_L_OH": [("DUMMY_KR", "B1")],
     "BR": [
         ("DUMMY_KR", None),
@@ -34,7 +39,9 @@
         ("DUMMY_ER", None),
         ("DUMMY_AMT", None),
     ],
-    "BETA_D_OME": [("DUMMY_KR", None), ("DUMMY_OMT", None)],
+    "BETA_D_OME": [("DUMMY_KR", "A1"), ("DUMMY_OMT", None)],
+    "BETA_L_OME": [("DUMMY_KR", "B1"), ("DUMMY_OMT", None)],
+    "BETA_OME": [("DUMMY_KR", None), ("DUMMY_OMT", None)],
     "NON_ELONGATING_PYR": [("DUMMY_SC", None)],
     "BETA_ME": [
         ("DUMMY_KR", None),
@@ -72,6 +79,76 @@
     "ALPHAME_DB": [("DUMMY_KR", None), ("DUMMY_DH", None), ("DUMMY_AMT", None)],
     "ALPHAME_KETO": [("DUMMY_AMT", None)],
     "NON_ELONGATING_SHDB": [("DUMMY_KR", None), ("DUMMY_GDH", None)],
+    "NON_ELONGATING_BETA_OH_KETO": [],
+    "NON_ELONGATING_ALPHA_OH": [("DUMMY_AH", None)],
+    "NON_ELONGATING_EDB": [("DUMMY_KR", None), ("DUMMY_EDH", None)],
+    "NON_ELONGATING_ARST": [],
+    "NON_ELONGATING_OXI": [],
+    "NON_ELONGATING_AA": [],
+    "NON_ELONGATING_ALPHAME_BETA_L_OH": [("DUMMY_AMT", None), ("DUMMY_KR", "B1")],
+    "NON_ELONGATING_RED_SHDB": [("DUMMY_KR", None), ("DUMMY_GDH", None)],
+    "NON_ELONGATING_KETO": [],
+    "NON_ELONGATING_BETA_D_OH": [("DUMMY_KR", None)],
+    "NON_ELONGATING_BR": [
+        ("DUMMY_KR", None),
+        ("DUMMY_DH", None),
+        ("DUMMY_ER", None),
+        ("DUMMY_BR", None),
+    ],
+    "NON_ELONGATING_ALPHABETA_OH": [("DUMMY_AH", None), ("DUMMY_KR", None)],
+    "NON_ELONGATING_UNST": [],
+    "NON_ELONGATING_ST": [],
+    "NON_ELONGATING_MEOST": [],
+    "NON_ELONGATING_ACST": [],
+    "NON_ELONGATING_ALPHAME": [
+        ("DUMMY_KR", None),
+        ("DUMMY_DH", None),
+        ("DUMMY_ER", None),
+        ("DUMMY_AMT", None),
+    ],
+    "NON_ELONGATING_BETA_D_OME": [("DUMMY_KR", None), ("DUMMY_OMT", None)],
+    "NON_ELONGATING_BETA_ME": [
+        ("DUMMY_KR", None),
+        ("DUMMY_DH", None),
+        ("DUMMY_ER", None),
+        ("DUMMY_BMT", None),
+    ],
+    "NON_ELONGATING_BETA_OH_EDB": [("DUMMY_KR", None)],
+    "NON_ELONGATING_LACST": [],
+    "NON_ELONGATING_OUT": [],
+    "NON_ELONGATING_ZDB": [("DUMMY_KR", None), ("DUMMY_ZDH", None)],
+    "NON_ELONGATING_BETA_MEDB": [
+        ("DUMMY_KR", None),
+        ("DUMMY_EDH", None),
+        ("DUMMY_BMT", None),
+    ],
+    "NON_ELONGATING_MISCELLANEOUS": [],
+    "NON_ELONGATING_ALPHAME_BETA_D_OH": [("DUMMY_ALMT", None), ("DUMMY_KR", "A1")],
+    "NON_ELONGATING_ALPHAME_BETAOH": [("DUMMY_AMT", None), ("DUMMY_KR", None)],
+    "NON_ELONGATING_RED": [("DUMMY_KR", None), ("DUMMY_DH", None), ("DUMMY_ER", None)],
+    "NON_ELONGATING_EXOMETHYLENE": [
+        ("DUMMY_KR", None),
+        ("DUMMY_DH", None),
+        ("DUMMY_ER", None),
+        ("DUMMY_BMT", None),
+        ("DUMMY_EMO", None),
+    ],
+    "NON_ELONGATING_ALPHAME_ZDB": [
+        ("DUMMY_KR", None),
+        ("DUMMY_ZDH", None),
+        ("DUMMY_AMT", None),
+    ],
+    "NON_ELONGATING_ALPHA_D_ME_SHDB": [
+        ("DUMMY_KR", None),
+        ("DUMMY_GDH", None),
+        ("DUMMY_AMT", None),
+    ],
+    "NON_ELONGATING_ALPHAME_DB": [
+        ("DUMMY_KR", None),
+        ("DUMMY_DH", None),
+        ("DUMMY_AMT", None),
+    ],
+    "NON_ELONGATING_ALPHAME_KETO": [("DUMMY_AMT", None)],
 }
 
 
@@ -84,9 +161,15 @@
     "ARST": "PHENYLACETYL_COA",
     "PYR": "ACETYL_COA",
     "ALPHAME_EDB": "ACETYL_COA",
+    "ALPHAME_SHDB": "ACETYL_COA",
     "OXI": "ACETYL_COA",
+    "BETA_L_OME": "ACETYL_COA",
+    "BETA_OME": "ACETYL_COA",
     "AA": "GLYCINE",
     "ALPHAME_BETA_L_OH": "ACETYL_COA",
+    "NON_ELONGATING_ALPHAME_SHDB": "ACETYL_COA",
+    "NON_ELONGATING_BETA_L_OME": "ACETYL_COA",
+    "NON_ELONGATING_BETA_OME": "ACETYL_COA",
     "NON_ELONGATING_BETA_L_OH": "ACETYL_COA",
     "RED_SHDB": "ACETYL_COA",
     "DB": "ACETYL_COA",
@@ -124,6 +207,39 @@
     "ALPHAME_DB": "ACETYL_COA",
     "ALPHAME_KETO": "ACETYL_COA",
     "NON_ELONGATING_SHDB": "ACETYL_COA",
+    "NON_ELONGATING_BETA_OH_KETO": "ACETYL_COA",
+    "NON_ELONGATING_ALPHA_OH": "ACETYL_COA",
+    "NON_ELONGATING_EDB": "ACETYL_COA",
+    "NON_ELONGATING_ARST": "PHENYLACETYL_COA",
+    "NON_ELONGATING_OXI": "ACETYL_COA",
+    "NON_ELONGATING_AA": "GLYCINE",
+    "NON_ELONGATING_ALPHAME_BETA_L_OH": "ACETYL_COA",
+    "NON_ELONGATING_RED_SHDB": "ACETYL_COA",
+    "NON_ELONGATING_KETO": "ACETYL_COA",
+    "NON_ELONGATING_BETA_D_OH": "ACETYL_COA",
+    "NON_ELONGATING_BR": "ACETYL_COA",
+    "NON_ELONGATING_ALPHABETA_OH": "ACETYL_COA",
+    "NON_ELONGATING_UNST": "PROPIONYL_COA",
+    "NON_ELONGATING_ST": "ACETYL_COA",
+    "NON_ELONGATING_MEOST": "METHOXYFORMYL_COA",
+    "NON_ELONGATING_ACST": "ACETYL_COA",
+    "NON_ELONGATING_ALPHAME": "ACETYL_COA",
+    "NON_ELONGATING_BETA_D_OME": "ACETYL_COA",
+    "NON_ELONGATING_BETA_ME": "ACETYL_COA",
+    "NON_ELONGATING_BETA_OH_EDB": "ACETYL_COA",
+    "NON_ELONGATING_LACST": "LACTYL_COA",
+    "NON_ELONGATING_OUT": "ACETYL_COA",
+    "NON_ELONGATING_ZDB": "ACETYL_COA",
+    "NON_ELONGATING_BETA_MEDB": "ACETYL_COA",
+    "NON_ELONGATING_MISCELLANEOUS": "ACETYL_COA",
+    "NON_ELONGATING_ALPHAME_BETA_D_OH": "ACETYL_COA",
+    "NON_ELONGATING_ALPHAME_BETAOH": "ACETYL_COA",
+    "NON_ELONGATING_RED": "ACETYL_COA",
+    "NON_ELONGATING_EXOMETHYLENE": "ACETYL_COA",
+    "NON_ELONGATING_ALPHAME_ZDB": "ACETYL_COA",
+    "NON_ELONGATING_ALPHA_D_ME_SHDB": "ACETYL_COA",
+    "NON_ELONGATING_ALPHAME_DB": "ACETYL_COA",
+    "NON_ELONGATING_ALPHAME_KETO": "ACETYL_COA",
 }
 
 TRANSATOR_CLADE_TO_ELONGATING = {
@@ -135,9 +251,15 @@
     "ARST": True,
     "PYR": True,
     "ALPHAME_EDB": True,
+    "ALPHAME_SHDB": True,
     "OXI": True,
+    "BETA_L_OME": True,
+    "BETA_OME": True,
     "AA": True,
     "ALPHAME_BETA_L_OH": True,
+    "NON_ELONGATING_ALPHAME_SHDB": False,
+    "NON_ELONGATING_BETA_L_OME": False,
+    "NON_ELONGATING_BETA_OME": False,
     "NON_ELONGATING_BETA_L_OH": False,
     "RED_SHDB": True,
     "DB": True,
@@ -175,4 +297,37 @@
     "ALPHAME_DB": True,
     "ALPHAME_KETO": True,
     "NON_ELONGATING_SHDB": False,
+    "NON_ELONGATING_BETA_OH_KETO": False,
+    "NON_ELONGATING_ALPHA_OH": False,
+    "NON_ELONGATING_EDB": False,
+    "NON_ELONGATING_ARST": False,
+    "NON_ELONGATING_OXI": False,
+    "NON_ELONGATING_AA": False,
+    "NON_ELONGATING_ALPHAME_BETA_L_OH": False,
+    "NON_ELONGATING_RED_SHDB": False,
+    "NON_ELONGATING_KETO": False,
+    "NON_ELONGATING_BETA_D_OH": False,
+    "NON_ELONGATING_BR": False,
+    "NON_ELONGATING_ALPHABETA_OH": False,
+    "NON_ELONGATING_UNST": False,
+    "NON_ELONGATING_ST": False,
+    "NON_ELONGATING_MEOST": False,
+    "NON_ELONGATING_ACST": False,
+    "NON_ELONGATING_ALPHAME": False,
+    "NON_ELONGATING_BETA_D_OME": False,
+    "NON_ELONGATING_BETA_ME": False,
+    "NON_ELONGATING_BETA_OH_EDB": False,
+    "NON_ELONGATING_LACST": False,
+    "NON_ELONGATING_OUT": False,
+    "NON_ELONGATING_ZDB": False,
+    "NON_ELONGATING_BETA_MEDB": False,
+    "NON_ELONGATING_MISCELLANEOUS": False,
+    "NON_ELONGATING_ALPHAME_BETA_D_OH": False,
+    "NON_ELONGATING_ALPHAME_BETAOH": False,
+    "NON_ELONGATING_RED": False,
+    "NON_ELONGATING_EXOMETHYLENE": False,
+    "NON_ELONGATING_ALPHAME_ZDB": False,
+    "NON_ELONGATING_ALPHA_D_ME_SHDB": False,
+    "NON_ELONGATING_ALPHAME_DB": False,
+    "NON_ELONGATING_ALPHAME_KETO": False,
 }
diff --git a/raichu/domain/domain_types.py b/raichu/domain/domain_types.py
@@ -219,6 +219,45 @@ class KSDomainSubtype(Enum):
     ALPHAME_DB = 48
     ALPHAME_KETO = 49
     NON_ELONGATING_SHDB = 50
+    ALPHAME_SHDB = 51
+    BETA_L_OME = 52
+    BETA_OME = 53
+    NON_ELONGATING_AA = 54
+    NON_ELONGATING_ACST = 55
+    NON_ELONGATING_ALPHABETA_OH = 56
+    NON_ELONGATING_ALPHAME = 57
+    NON_ELONGATING_ALPHAME_BETAOH = 58
+    NON_ELONGATING_ALPHAME_BETA_D_OH = 59
+    NON_ELONGATING_ALPHAME_BETA_L_OH = 60
+    NON_ELONGATING_ALPHAME_DB = 61
+    NON_ELONGATING_ALPHAME_KETO = 62
+    NON_ELONGATING_ALPHAME_SHDB = 63
+    NON_ELONGATING_ALPHAME_ZDB = 64
+    NON_ELONGATING_ALPHA_D_ME_SHDB = 65
+    NON_ELONGATING_ALPHA_OH = 66
+    NON_ELONGATING_ARST = 67
+    NON_ELONGATING_BETA_D_OH = 68
+    NON_ELONGATING_BETA_D_OME = 69
+    NON_ELONGATING_BETA_L_OME = 70
+    NON_ELONGATING_BETA_ME = 71
+    NON_ELONGATING_BETA_MEDB = 72
+    NON_ELONGATING_BETA_OH_EDB = 73
+    NON_ELONGATING_BETA_OH_KETO = 74
+    NON_ELONGATING_BETA_OME = 75
+    NON_ELONGATING_BR = 76
+    NON_ELONGATING_EDB = 77
+    NON_ELONGATING_EXOMETHYLENE = 78
+    NON_ELONGATING_KETO = 79
+    NON_ELONGATING_LACST = 80
+    NON_ELONGATING_MEOST = 81
+    NON_ELONGATING_MISCELLANEOUS = 82
+    NON_ELONGATING_OUT = 83
+    NON_ELONGATING_OXI = 84
+    NON_ELONGATING_RED = 85
+    NON_ELONGATING_RED_SHDB = 86
+    NON_ELONGATING_ST = 87
+    NON_ELONGATING_UNST = 88
+    NON_ELONGATING_ZDB = 89
 
     @staticmethod
     def from_string(label: str) -> "KSDomainSubtype":

diff --git a/raichu/general.py b/raichu/general.py
@@ -83,6 +83,9 @@ def draw_terpene_structure_from_terpene_cluster(terpene_cluster: TerpeneCluster,
     terpene_cluster.draw_product(
         as_string=False, out_file=os.path.join(out_folder, "precursor_test_terpene.svg"))
     terpene_cluster.do_macrocyclization()
+    terpene_cluster.do_double_bond_isomerization()
+    terpene_cluster.do_methyl_shift()
+    terpene_cluster.do_water_quenching()
     terpene_cluster.draw_product(
         as_string=False, out_file=os.path.join(out_folder, "macroyclisation_test_terpene.svg"))
     terpene_cluster.do_tailoring()

diff --git a/raichu/representations.py b/raichu/representations.py
@@ -36,6 +36,12 @@ class MethylShiftRepresentation:
     modification_sites: List[List[str]]
 
 
+@dataclass
+class WaterQuenchingRepresentation:
+    # Should be the atom to receive OH
+    modification_sites: List[List[str]]
+
+
 @dataclass
 class DomainRepresentation:
     gene_name: Union[str, None]

diff --git a/raichu/test/integration/test_trans_at_pks.py b/raichu/test/integration/test_trans_at_pks.py
@@ -21,7 +21,7 @@ def test_extensive_KS_subtypes():
     # Check if final structure is correct
     assert (
         structure_to_smiles(cluster.chain_intermediate)
-        == r"OC(=O)C[C@H](O)CC(=C)C[C@@H](O1)CC(C[*])CC1C(C)C=C[C@H](O2)CC(OC)C2C(=O)C=C[C@H](O)C"
+        == r"OC(=O)C[C@H](O)CC(=C)C[C@@H](O1)CC(C[*])CC1C(C)C=C[C@H](O2)C[C@@H](OC)C2C(=O)C=C[C@H](O)C"
     )