new amide and sulfamide standardize rules.

query atom fixed.
cimm-kzn · Dec 2, 2020 · d415734 · d415734
1 parent 6a82e0d
commit d415734
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Showing 2 changed files with 49 additions and 3 deletions.
diff --git a/CGRtools/algorithms/standardize.py b/CGRtools/algorithms/standardize.py
@@ -23,6 +23,7 @@
 from ..containers import molecule, query  # cyclic imports resolve
 from ..containers.bonds import Bond
 from ..exceptions import ValenceError
+from ..periodictable import ListElement
 
 
 class Standardize:
@@ -1026,11 +1027,12 @@ def __standardize_rules():
 
         # Amide
         #
-        #       OH        O
+        #      [O,S]H    [O,S]
         #      /         //
         # N = C  >> NH - C
         #
-        atoms = ({'atom': 'C', 'hybridization': 2}, {'atom': 'O', 'neighbors': 1}, {'atom': 'N', 'hybridization': 2})
+        atoms = ({'atom': 'C', 'hybridization': 2}, {'atom': ListElement(['O', 'S']), 'neighbors': 1},
+                 {'atom': 'N', 'hybridization': 2})
         bonds = ((1, 2, 1), (1, 3, 2))
         atom_fix = {2: {'hybridization': 2}, 3: {'hybridization': 1}}
         bonds_fix = ((1, 2, 2), (1, 3, 1))
@@ -1215,6 +1217,50 @@ def __standardize_rules():
         bonds_fix = ((1, 2, 2),)
         rules.append((atoms, bonds, atom_fix, bonds_fix))
 
+        # amide S
+        #
+        #      A1,3                 A1,3
+        #      |                    |
+        #  N = S - [OH]  >>  [NH] - S = O
+        #
+        atoms = ({'atom': 'S', 'neighbors': (3, 5), 'hybridization': 2},
+                 {'atom': 'O', 'neighbors': 1}, {'atom': 'N', 'neighbors': (1, 2), 'hybridization': 2})
+        bonds = ((1, 2, 1), (1, 3, 2))
+        atom_fix = {2: {'hybridization': 2}, 3: {'hybridization': 1}}
+        bonds_fix = ((1, 2, 2), (1, 3, 1))
+        rules.append((atoms, bonds, atom_fix, bonds_fix))
+
+        # amide S(VI)
+        #
+        #     [OH]                O
+        #      |                 //
+        #  N = S = N  >>  [NH] - S - [NH]
+        #      |                 \\
+        #     [OH]                O
+        #
+        atoms = ({'atom': 'S', 'neighbors': 4}, {'atom': 'O', 'neighbors': 1},
+                 {'atom': 'N', 'neighbors': (1, 2), 'hybridization': 2}, {'atom': 'O', 'neighbors': 1},
+                 {'atom': 'N', 'neighbors': (1, 2), 'hybridization': 2})
+        bonds = ((1, 2, 1), (1, 3, 2), (1, 4, 1), (1, 5, 2))
+        atom_fix = {2: {'hybridization': 2}, 3: {'hybridization': 1}, 4: {'hybridization': 2}, 5: {'hybridization': 1}}
+        bonds_fix = ((1, 2, 2), (1, 3, 1), (1, 4, 2), (1, 5, 1))
+        rules.append((atoms, bonds, atom_fix, bonds_fix))
+
+        # amide S(VI)
+        #
+        #     [OH]                O
+        #      |                 //
+        #  N = S = A  >>  [NH] - S = A
+        #      |                 |
+        #      A                 A
+        #
+        atoms = ({'atom': 'S', 'neighbors': 4}, {'atom': 'O', 'neighbors': 1},
+                 {'atom': 'N', 'neighbors': (1, 2), 'hybridization': 2}, {'atom': 'A'}, {'atom': 'A'})
+        bonds = ((1, 2, 1), (1, 3, 2), (1, 4, 2), (1, 5, 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))
+
         # Silicate Selenite
         #
         #           O             O

diff --git a/CGRtools/periodictable/element/query.py b/CGRtools/periodictable/element/query.py
@@ -67,7 +67,7 @@ def ring_sizes(self) -> Tuple[int, ...]:
         Atom rings sizes.
         """
         try:
-            return self._graph()._rings_sizes[self._map] or self._graph().atoms_rings_sizes[self._map]
+            return self._graph()._rings_sizes[self._map]
         except AttributeError:
             raise IsNotConnectedAtom
         except KeyError: