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Add method to add implicit hydrogens #15

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Sep 20, 2023
Merged

Add method to add implicit hydrogens #15

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21 changes: 21 additions & 0 deletions isicle/geometry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
"""
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