Adapter Module¶

The adapter module provides bidirectional conversion between MolPy structures and external molecular libraries, primarily RDKit.

Key Features¶

• Convert between RDKit Mol objects and MolPy Atomistic structures
• Generate 3D coordinates using RDKit's ETKDG method
• Optimize geometries with MMFF/UFF force fields
• Generate 2D molecular drawings (SVG)
• Stable atom mapping for round-trip conversion

In [1]:

from rdkit import Chem

from molpy.adapter import RDKitWrapper, atomistic_to_mol, mol_to_atomistic

# Create a molecule from SMILES
mol = Chem.MolFromSmiles("CCO")

# Convert to MolPy Atomistic
atomistic = mol_to_atomistic(mol)
print(f"Converted molecule with {len(atomistic.atoms)} atoms")

# Create wrapper for bidirectional conversion
wrapper = RDKitWrapper.from_mol(mol)

# Generate 3D coordinates
wrapper.generate_3d(optimize=True)

# Access the MolPy structure
atomistic_3d = wrapper.inner
print("Generated 3D structure with coordinates")

from rdkit import Chem from molpy.adapter import RDKitWrapper, atomistic_to_mol, mol_to_atomistic # Create a molecule from SMILES mol = Chem.MolFromSmiles("CCO") # Convert to MolPy Atomistic atomistic = mol_to_atomistic(mol) print(f"Converted molecule with {len(atomistic.atoms)} atoms") # Create wrapper for bidirectional conversion wrapper = RDKitWrapper.from_mol(mol) # Generate 3D coordinates wrapper.generate_3d(optimize=True) # Access the MolPy structure atomistic_3d = wrapper.inner print("Generated 3D structure with coordinates")

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[1], line 1
----> 1 from rdkit import Chem
      3 from molpy.adapter import RDKitWrapper, atomistic_to_mol, mol_to_atomistic
      5 # Create a molecule from SMILES

ModuleNotFoundError: No module named 'rdkit'

Converting from Atomistic to RDKit¶

You can also convert MolPy structures to RDKit:

In [2]:

# Convert Atomistic back to RDKit
mol_from_atomistic = atomistic_to_mol(atomistic_3d)
print(f"RDKit molecule has {mol_from_atomistic.GetNumAtoms()} atoms")

# Generate 2D drawing
svg = wrapper.draw(show=False)
print("Generated 2D molecular drawing")

# Convert Atomistic back to RDKit mol_from_atomistic = atomistic_to_mol(atomistic_3d) print(f"RDKit molecule has {mol_from_atomistic.GetNumAtoms()} atoms") # Generate 2D drawing svg = wrapper.draw(show=False) print("Generated 2D molecular drawing")

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[2], line 2
      1 # Convert Atomistic back to RDKit
----> 2 mol_from_atomistic = atomistic_to_mol(atomistic_3d)
      3 print(f"RDKit molecule has {mol_from_atomistic.GetNumAtoms()} atoms")
      5 # Generate 2D drawing

NameError: name 'atomistic_to_mol' is not defined