Open Chemistry JupyterLab Chain Optimizations



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import openchemistry as oc



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mol = oc.import_structure('CCO', gen3d=False)

If the molecule doesn't have a 3D structure, it can be generated via open babel



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mol.structure.generate_3d(forcefield='mmff94', steps=150)

View the structure



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mol.structure.show()

View the cjson



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mol.structure.data()

Optimize the geometry with ANI



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image_name = 'openchemistry/torchani:1.2'
input_parameters = {}
result = mol.optimize(image_name, input_parameters)



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result.structure.show()

View the cjson



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result.structure.data()

Get the optimized geometry ID



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ani_optimized_id = result.optimized_geometry_id

Optimize the output from ANI with psi4



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image_name = 'openchemistry/psi4:1.2.1'
input_parameters = {
    'theory': 'dft',
    'functional': 'b3lyp',
    'basis': '6-31g'
}
result = mol.optimize(image_name, input_parameters, geometry_id=ani_optimized_id)



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result.structure.show()

View the cjson



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result.structure.data()

Get the optimized geometry ID



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psi4_optimized_id = result.optimized_geometry_id

Compare the optimized structures via RMSD



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oc.calculate_rmsd(mol, geometry_id1=ani_optimized_id, geometry_id2=psi4_optimized_id, heavy_atoms_only=True)