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Make UFFOptimizeMolecule optional #19

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RokasEl opened this issue Sep 18, 2024 · 1 comment
Open

Make UFFOptimizeMolecule optional #19

RokasEl opened this issue Sep 18, 2024 · 1 comment

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@RokasEl
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RokasEl commented Sep 18, 2024

UFFOptimize makes the conversion slow. If you'd like I can implement a MACE-OFF relaxation (which would be more accurate) as an optional dependency.

@PythonFZ
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I like the idea. We could adjust

def rdkit2ase(mol, seed: int = 42) -> ase.Atoms:
"""Convert an RDKit molecule to an ASE atoms object."""
mol = rdkit.Chem.AddHs(mol)
rdkit.Chem.AllChem.EmbedMolecule(mol, randomSeed=seed)
rdkit.Chem.AllChem.UFFOptimizeMolecule(mol)

to accept

  • an ASE calc for relaxation
  • a flag to enable/disable UFFOptimizeMolecule

I would prefer passing an ASE calc over directly adding mace, but I'd be in favour of adjusting the docstring to suggest using mace_mp as a great calc for the task.

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