These are instance methods, not class methods

rdkit-stubs/Chem/rdchem.pyi

@@ -37,8 +37,7 @@ class Atom:
     def ClearProp(cls, *args, **kwargs) -> Any: ...
     @classmethod
     def DescribeQuery(cls, RDKit) -> Any: ...
-    @classmethod
-    def GetAtomMapNum(cls) -> Any: ...
+    def GetAtomMapNum(self) -> int: ...
     def GetAtomicNum(self) -> int: ...
     @classmethod
     def GetBonds(cls, RDKit) -> Any: ...
@@ -58,8 +57,7 @@ class Atom:
     def GetFormalCharge(cls, RDKit) -> Any: ...
     @classmethod
     def GetHybridization(cls, RDKit) -> Any: ...
-    @classmethod
-    def GetIdx(cls) -> int: ...
+    def GetIdx(self) -> int: ...
     @classmethod
     def GetImplicitValence(cls, RDKit) -> Any: ...
     @classmethod
@@ -94,8 +92,7 @@ class Atom:
     def GetPropsAsDict(cls, RDKit) -> Any: ...
     @classmethod
     def GetQueryType(cls, RDKit) -> Any: ...
-    @classmethod
-    def GetSmarts(cls, doKekule: Optional[bool]=False, allHsExplicit: Optional[bool]=False, isomericSmiles: Optional[bool]=True) -> str: ...
+    def GetSmarts(self, doKekule: Optional[bool]=False, allHsExplicit: Optional[bool]=False, isomericSmiles: Optional[bool]=True) -> str: ...
     @classmethod
     def GetSymbol(cls, RDKit) -> Any: ...
     @classmethod
@@ -142,8 +139,7 @@ class Atom:
     def SetIntProp(cls, *args, **kwargs) -> Any: ...
     @classmethod
     def SetIsAromatic(cls, RDKit, bool) -> Any: ...
-    @classmethod
-    def SetIsotope(cls, arg1: int) -> None: ...
+    def SetIsotope(self, arg1: int) -> None: ...
     @classmethod
     def SetMonomerInfo(cls, *args, **kwargs) -> Any: ...
     @classmethod
@@ -269,8 +265,7 @@ class Bond:
     def GetEndAtom(cls, RDKit) -> Any: ...
     @classmethod
     def GetEndAtomIdx(cls, RDKit) -> Any: ...
-    @classmethod
-    def GetIdx(cls) -> int: ...
+    def GetIdx(self) -> int: ...
     @classmethod
     def GetIntProp(cls, *args, **kwargs) -> Any: ...
     @classmethod
@@ -532,11 +527,9 @@ class Mol:
     def Debug(cls, RDKit) -> Any: ...
     @classmethod
     def GetAromaticAtoms(cls, boost) -> Any: ...
-    @classmethod
-    def GetAtomWithIdx(cls, idx: int) -> Atom: ...
+    def GetAtomWithIdx(self, idx: int) -> Atom: ...
     def GetAtoms(self) -> Iterable[Atom]: ...
-    @classmethod
-    def GetAtomsMatchingQuery(cls, arg2: QueryAtom) -> Sequence[Atom]: ...
+    def GetAtomsMatchingQuery(self, arg2: QueryAtom) -> Sequence[Atom]: ...
     @classmethod
     def GetBondBetweenAtoms(cls, *args, **kwargs) -> Any: ...
     @classmethod
@@ -559,8 +552,7 @@ class Mol:
     def GetNumBonds(cls, RDKit) -> Any: ...
     @classmethod
     def GetNumConformers(cls, RDKit) -> Any: ...
-    @classmethod
-    def GetNumHeavyAtoms(cls) -> int: ...
+    def GetNumHeavyAtoms(self) -> int: ...
     @classmethod
     def GetProp(cls, *args, **kwargs) -> Any: ...
     @classmethod