Bddap/getnumatoms (#7)

* Mol.GetNumAtoms, Mol.GetConformers, Conformer.GetNumAtoms

* version bump

* BuildFeatureFactoryFromString

* add RemoveHs

rdkit-stubs/Chem/rdMolChemicalFeatures.pyi

@@ -1,6 +1,4 @@
-from typing import Any, ClassVar
-
-from typing import overload
+from typing import Any, ClassVar, overload
 
 class MolChemicalFeature:
     @classmethod
@@ -50,5 +48,5 @@ class MolChemicalFeatureFactory:
     def __reduce__(cls) -> Any: ...
 
 def BuildFeatureFactory(*args, **kwargs) -> Any: ...
-def BuildFeatureFactoryFromString(*args, **kwargs) -> Any: ...
+def BuildFeatureFactoryFromString(arg1: str) -> MolChemicalFeatureFactory: ...
 def GetAtomMatch(boost) -> Any: ...

rdkit-stubs/Chem/rdchem.pyi

@@ -421,8 +421,7 @@ class Conformer:
     def GetId(cls, RDKit) -> Any: ...
     @classmethod
     def GetIntProp(cls, *args, **kwargs) -> Any: ...
-    @classmethod
-    def GetNumAtoms(cls, RDKit) -> Any: ...
+    def GetNumAtoms(self) -> int: ...
     @classmethod
     def GetOwningMol(cls, RDKit) -> Any: ...
     def GetPositions(
@@ -534,7 +533,7 @@ class Mol:
     @classmethod
     def GetAromaticAtoms(cls, boost) -> Any: ...
     def GetAtomWithIdx(self, idx: int) -> Atom: ...
-    def GetAtoms(self) -> Iterable[Atom]: ...
+    def GetAtoms(self) -> Sequence[Atom]: ...
     def GetAtomsMatchingQuery(self, arg2: QueryAtom) -> Sequence[Atom]: ...
     @classmethod
     def GetBondBetweenAtoms(cls, *args, **kwargs) -> Any: ...
@@ -545,14 +544,12 @@ class Mol:
     @classmethod
     def GetBoolProp(cls, *args, **kwargs) -> Any: ...
     def GetConformer(self, id: int = -1) -> Conformer: ...
-    @classmethod
-    def GetConformers(cls, boost) -> Any: ...
+    def GetConformers(self) -> Sequence[Conformer]: ...
     @classmethod
     def GetDoubleProp(cls, *args, **kwargs) -> Any: ...
     @classmethod
     def GetIntProp(cls, *args, **kwargs) -> Any: ...
-    @classmethod
-    def GetNumAtoms(cls, RDKit) -> Any: ...
+    def GetNumAtoms(self, onlyHeavy: int = -1, onlyExplicit: bool = True) -> int: ...
     @classmethod
     def GetNumBonds(cls, RDKit) -> Any: ...
     @classmethod

rdkit-stubs/Chem/rdmolops.pyi

@@ -1,4 +1,4 @@
-from typing import Any, ClassVar, Sequence
+from typing import Any, ClassVar, Sequence, overload
 
 from rdkit.Chem.rdchem import Mol
 from rdkit.Chem.rdMolDescriptors import AtomPairsParameters
@@ -247,7 +247,19 @@ def PathToSubmol(RDKit, boost) -> Any: ...
 def PatternFingerprint(RDKit) -> Any: ...
 def RDKFingerprint(*args, **kwargs) -> Any: ...
 def RemoveAllHs(RDKit) -> Any: ...
-def RemoveHs(RDKit) -> Any: ...
+@overload
+def RemoveHs(
+    mol: Mol,
+    implicitOnly: bool = False,
+    updateExplicitCount: bool = False,
+    sanitize: bool = True,
+) -> Mol: ...
+@overload
+def RemoveHs(
+    mol: Mol,
+    params: RemoveHsParameters,
+    sanitize: bool = True,
+) -> Mol: ...
 def RemoveStereochemistry(RDKit) -> Any: ...
 def RenumberAtoms(RDKit, boost) -> Any: ...
 def ReplaceCore(mol, core, match) -> Any: ...

setup.py

@@ -29,7 +29,7 @@ def list_package_files() -> List[str]:
 
 setup(
     name="rdkit-stubs",
-    version="0.6",
+    version="0.7",
     description="type stubs for rdkit",
     author="Andrew Dirksen, Ryan Rightmer",
     author_email="[email protected], [email protected]",