Hi Michal, Many thanks for the help! I am looking for an ensemble of conformers. My priority is to use RDKit to generate a large ensemble of conformers for each molecule. For large and flexiable molecules, will need a lot more than 10K (like 100K) to try to cover the entire conformational space.
I do not have to use MMFF to optimize all conformers, but I do want to use MMFF or UFF to get at least the energies of all conformers (which is also quite time-consuming, even without optimization). With the conformer energies, I can call some energy_filtering function to filter out conformers with high energies, etc. I am thinking that storing and processing a huge number of conformers could be the reason to slow things down, but not quite sure. Any suggestions are very welcome! Best, Leon On Wed, Dec 18, 2019 at 7:08 PM Michal Krompiec <michal.kromp...@gmail.com> wrote: > Are you looking for the global minimum or an ensemble of conformers? > Either way, this is already very fast. Bear in mind, however, that MMFF’s > accuracy isn’t great for this type of tasks (see for example > https://arxiv.org/pdf/1705.04308.pdf ). In other words, I don’t see a use > case for generation of 10k or more conformers with MMFF. And super-fast > generation of large conformational ensembles for arbitrary molecules just > isn’t realistic. > Best, > Michal > > On Wed, 18 Dec 2019 at 22:40, topgunhaides . <sunzhi....@gmail.com> wrote: > >> Hi guys, >> >> Can anyone give me some advices to improve the efficiency of the >> embedding code? See example below: >> >> >> import time >> from rdkit import Chem >> from rdkit.Chem import AllChem >> >> suppl = Chem.SDMolSupplier('cid831548.sdf') # medium size molecule (10 >> heavy atoms) >> >> for mol in suppl: >> mh = Chem.AddHs(mol, addCoords=True) >> >> # embedding >> start = time.time() >> AllChem.EmbedMultipleConfs(mh, numConfs=5000, maxAttempts=100, >> pruneRmsThresh=0.5, >> randomSeed=1, numThreads=0, >> enforceChirality=True, >> useExpTorsionAnglePrefs=True, >> useBasicKnowledge=True) >> cids = [conf.GetId() for conf in mh.GetConformers()] >> end = time.time() >> print("time eclipsed: ", end - start) >> >> >> The results: >> numConfs=1000, time eclipsed: 10 seconds >> numConfs=5000, time eclipsed: 66 seconds >> numConfs=10000, time eclipsed: 176 seconds >> >> I need to request a lot more than 10000 conformers per molecule and have >> a lot of molecules to process. >> I also wish to compute conformer energies and hopefully can do >> optimization (both are time consuming). So need to make my code as >> efficient as possible. Thank you! >> >> Best, >> Leon >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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