OptimizeMolecule and OptimizeMoleculeConfs Argument?

[xiaoruiDong]

Hi everyone,

I am trying to use Chem.rdForceFieldHelpers.OptimizeMolecule and OptimizeMoleculeConfs in Python. I know there are things like MMFFOptimizeMolecule, but I hope to optimize molecules on a force field with constraints. However, I keep getting ArgumentError when using those functions. An example is provided below (constraint part neglected):

# Generate molecule
mol = Chem.MolFromSmiles('CCC[O]')
mol = Chem.AddHs(mol)
Chem.AllChem.EmbedMultipleConfs(mol, numConfs=10)

# Setup forcefield
mp = Chem.rdForceFieldHelpers.MMFFGetMoleculeProperties(mol)
ff = Chem.rdForceFieldHelpers.MMFFGetMoleculeForceField(mol, mp)

# Optimize
Chem.rdForceFieldHelpers.OptimizeMoleculeConfs(mol, ff, numThreads=1, maxIters=200)

The error I got is

ArgumentError: Python argument types in
    rdkit.Chem.rdForceFieldHelpers.OptimizeMoleculeConfs(Mol, ForceField)
did not match C++ signature:
    OptimizeMoleculeConfs(RDKit::ROMol {lvalue} mol, ForceFields::ForceField {lvalue} ff, int numThreads=1, int maxIters=200)

From my naive investigation, mol, numThreads, and maxIters should be good. Then, the assigned ff is problematic? I guess that this function is asking for ForceField but ff is actually pyForceField? Is that correct?

[greglandrum]

This looks like a bug in the OptimizeMoleculeConfs() functions. We'll take a look.

In the meantime, if you want to optimize all the conformers without providing the force field, you can do:

Chem.rdForceFieldHelpers.MMFFOptimizeMoleculeConfs(mol)

Or if you want to provide the force field (so that you can set constraints) you can loop over the conformers individually and provide the confId argument when you construct the force field.

[xiaoruiDong]

Thanks, I will post an issue for this!