Add method to add implicit hydrogens

pnnl · Sep 20, 2023 · 22025a8 · 22025a8
1 parent 8d2f450
commit 22025a8
Showing 1 changed file with 21 additions and 0 deletions.
diff --git a/isicle/geometry.py b/isicle/geometry.py
@@ -317,6 +317,27 @@ def _is_embedded(self):
             return True
         except:
             return False
+
+
+    def addHs(self):
+        """
+        Add implicit hydrogens to molecule.
+
+        Returns
+        -------
+         :obj:`~isicle.geometry.Geometry`
+            Molecule representation.
+
+        """
+
+        # Get copy of mol object
+        mol = self.to_mol()
+
+        # Add Hs with coordinates
+        mol = Chem.AddHs(mol, addCoords=True)
+
+        # Return new geometry instance
+        return self.__copy__(mol=mol)
 
     def initial_optimize(self, embed=False, forcefield="UFF", ff_iter=200):
         """