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... for idx, mol in enumerate(tqdm(mols, desc="Processing molecules")): interchange = ff.create_interchange(mol.to_topology()) interchange.minimize() mol.conformers[0] = interchange.positions mol.to_file(f"minimized_mol_{idx}.sdf", file_format="sdf") ```
2. Warnings are sometimes emitted about protons/stereo/charges, those are from a performance heuristic and don’t change the chemistry of the inputs (we’re working on silencing these)
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