Hi Paolo,
Very clear explanation. Thank you!!
Best,
Leon
On Mon, Nov 18, 2019 at 12:27 PM Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> Hi Leon,
>
> MMFFOptimizeMoleculeConfs() by default will distribute minimization tasks
> across all available CPU cores as it is multi-threaded at the C++ level,
> while ff.Minimize() will run single-threaded, unless you do the
> distribution of individual minimization tasks yourself in the Python layer
> (e.g., using Python multiprocessing.Pool or similar).
>
> Apart from that technical difference, there is no scientific difference in
> the calculation itself.
>
> Cheers,
> p.
> On 18/11/2019 17:05, topgunhaides . wrote:
>
> Hey guys,
>
> Are there any differences between the ff.minimize and
> MMFFGetMoleculeForceField for conformer optimization? Please see the
> forllowing example:
>
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> m = Chem.AddHs(Chem.MolFromSmiles('OCCCN'))
> cids = AllChem.EmbedMultipleConfs(m, 10, randomSeed=1)
> ps = AllChem.MMFFGetMoleculeProperties(m, mmffVariant='MMFF94s')
>
> for cid in cids:
> ff = AllChem.MMFFGetMoleculeForceField(m, ps, confId=cid)
> ff.Initialize()
> ff.Minimize(maxIts=1000)
> print(ff.CalcEnergy())
>
> optm = AllChem.MMFFOptimizeMoleculeConfs(m, maxIters=1000,
> mmffVariant='MMFF94s')
> print(optm)
>
> Both give me the same set of energies for generated conformers. Thank you!
>
> Best,
> Leon
>
>
>
>
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