now aromatize works with n-oxydes withput standardization.

new standardization rule added: enamine to imine.

CGRtools/algorithms/aromatics.py

@@ -226,6 +226,33 @@ def check_thiele(self, fast=True) -> bool:
             return False
         return True
 
+    def __fix_oxides(self):
+        atoms = self._atoms
+        bonds = self._bonds
+        atoms_order = self.atoms_order
+        connected_components = [set(x) for x in self.connected_components]
+
+        seen = set()
+        for q, af, bf in self.__oxyde_rules:
+            components, closures = q._compiled_query
+            for candidate in connected_components:
+                for mapping in q._get_mapping(components[0], closures, atoms, bonds, candidate - seen, atoms_order):
+                    match = set(mapping.values())
+                    if not match.isdisjoint(seen):  # skip intersected groups
+                        continue
+                    seen.update(match)
+
+                    for n, fix in af.items():
+                        n = mapping[n]
+                        for key, value in fix.items():
+                            getattr(self, key)[n] = value
+                    for n, m, b in bf:
+                        n = mapping[n]
+                        m = mapping[m]
+                        bonds[n][m]._Bond__order = b
+        if seen:
+            self.flush_cache()
+
     def __prepare_rings(self):
         atoms = self._atoms
         charges = self._charges
@@ -391,6 +418,7 @@ def __kekule_patch(self, patch):
             self._calc_implicit(n)
 
     def __kekule_full(self):
+        self.__fix_oxides()  # fix pyridine n-oxyde
         rings, pyroles, double_bonded = self.__prepare_rings()
         atoms = set(rings)
         components = []
@@ -580,5 +608,39 @@ def __freaks(self):
 
         return rules
 
+    @cached_property
+    def __oxyde_rules(self):
+        rules = []
+
+        # Aromatic N-Oxide
+        #
+        #  : N :  >>  : [N+] :
+        #    \\           \
+        #     O           [O-]
+        #
+        q = query.QueryContainer()
+        q.add_atom('N', neighbors=3, hybridization=4)
+        q.add_atom('O', neighbors=1)
+        q.add_bond(1, 2, 2)
+        atom_fix = {1: {'_charges': 1}, 2: {'_charges': -1, '_hybridizations': 1}}
+        bonds_fix = ((1, 2, 1),)
+        rules.append((q, atom_fix, bonds_fix))
+
+        # Aromatic N-Nitride?
+        #
+        #  : N :  >>  : [N+] :
+        #    \\           \
+        #     N           [N-]
+        #
+        q = query.QueryContainer()
+        q.add_atom('N', neighbors=3, hybridization=4)
+        q.add_atom('N', neighbors=(1, 2), hybridization=2)
+        q.add_bond(1, 2, 2)
+        atom_fix = {1: {'_charges': 1}, 2: {'_charges': -1, '_hybridizations': 1}}
+        bonds_fix = ((1, 2, 1),)
+        rules.append((q, atom_fix, bonds_fix))
+
+        return rules
+
 
 __all__ = ['Aromatize']

CGRtools/algorithms/standardize.py

@@ -33,11 +33,11 @@ def canonicalize(self) -> bool:
         """
         Convert molecule to canonical forms of functional groups and aromatic rings without explicit hydrogens.
         """
-        s = self.standardize(fix_stereo=False)
         k = self.kekule()
+        s = self.standardize(fix_stereo=False)
         h = self.implicify_hydrogens(fix_stereo=False)
         t = self.thiele()
-        return s or k or h or t
+        return k or s or h or t
 
     def standardize(self, *, fix_stereo=True, logging=False) -> bool:
         """
@@ -558,6 +558,20 @@ def __standardize_rules():
         bonds_fix = ()
         rules.append((atoms, bonds, atom_fix, bonds_fix))
 
+        #
+        #      RNH      RN
+        #      /        //
+        # C = C  >> C - C
+        #      \         \
+        #       A         A
+        #
+        atoms = ({'atom': 'C', 'neighbors': 3}, {'atom': 'N', 'hybridization': 1, 'neighbors': (1, 2)},
+                 {'atom': 'C', 'hybridization': 2}, {'atom': 'A'})
+        bonds = ((1, 2, 1), (1, 3, 2), (1, 4, 1))
+        atom_fix = {2: {'hybridization': 2}, 3: {'hybridization': 1}}
+        bonds_fix = ((1, 2, 2), (1, 3, 1))
+        rules.append((atoms, bonds, atom_fix, bonds_fix))
+
         # Nitrone
         #
         #      O          [O-]
@@ -968,30 +982,6 @@ def __standardize_rules():
         bonds_fix = ((1, 2, 2),)
         rules.append((atoms, bonds, atom_fix, bonds_fix))
 
-        # Aromatic N-Oxide
-        #
-        #  : N :  >>  : [N+] :
-        #    \\           \
-        #     O           [O-]
-        #
-        atoms = ({'atom': 'N', 'neighbors': 3, 'hybridization': 4}, {'atom': 'O', 'neighbors': 1})
-        bonds = ((1, 2, 2),)
-        atom_fix = {1: {'charge': 1}, 2: {'charge': -1, 'hybridization': 1}}
-        bonds_fix = ((1, 2, 1),)
-        rules.append((atoms, bonds, atom_fix, bonds_fix))
-
-        # Aromatic N-Nitride?
-        #
-        #  : N :  >>  : [N+] :
-        #    \\           \
-        #     N           [N-]
-        #
-        atoms = ({'atom': 'N', 'neighbors': 3, 'hybridization': 4}, {'atom': 'N', 'hybridization': 2})
-        bonds = ((1, 2, 2),)
-        atom_fix = {1: {'charge': 1}, 2: {'charge': -1, 'hybridization': 1}}
-        bonds_fix = ((1, 2, 1),)
-        rules.append((atoms, bonds, atom_fix, bonds_fix))
-
         # Nitroso
         #
         # - [N+] - [O-]  >>  - N = O