Hi Paul,
Your reuse of the variable num_confs inside the loop is causing that
monotonic decrease. So, if a molecule returns 190 conformers, the next
iteration has you only asking for 190 conformers. And so on.
Best,
David
On Wed, Oct 25, 2017 at 12:36 PM, Paul Hawkins <phawk...@eyesopen.com>
wrote:
> Hello,
>
>
> I have run into a problem with using the RDKit to generate conformers of
> molecules. I am using the following code:
>
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> from timeit import default_timer as timer
>
>
>
> def GenerateDGConfs(m,num_confs,rms):
> start_time = timer()
> ids = AllChem.EmbedMultipleConfs(m, numConfs=num_confs,
> pruneRmsThresh=rms, maxAttempts=200,enforceChirality=True)
> for id in ids:
> AllChem.MMFFOptimizeMolecule(m, confId=id)
>
> end_time = timer()
> time_diff = end_time - start_time
> # print ("Normal DG = %0.2f" % time_diff)
>
> return m, list(ids), time_diff
>
>
> w = Chem.SDWriter("%s/%s" % (rootdir,"My_conformers.sdf))
>
>
> suppl = Chem.SDMolSupplier("%s/%s" % (rootdir,"My_molecules.sdf"))
> num_confs = 200
> rmsd = 0.5
>
>
> for mol in suppl:
>
> if mol is None: continue
>
> Chem.AssignAtomChiralTagsFromStructure(mol)
> mol1 = Chem.AddHs(mol)
>
> conf_mol, id_list, time_diff = GenerateDGConfs(mol1,num_confs,rmsd)
> num_confs = conf_mol.GetNumConformers()
> for id in id_list:
> w.write(conf_mol, confId=id)
>
>
>
> w.flush()
> w.close()
>
>
> What I see from this is as I go through the molecules in the input file
> the number of conformers returned declines monotonically, starting close to
> the 200 I set as a maximum to around 10 after a few thousand molecules have
> been processed (this applies whether I use 'normal' DG or the ETKDG method.
> As I am a new user of RDKit I am sure I missed something obvious but I
> cannot see it.
>
> Also, once I generate the conformers what is best way to cluster them by
> RMSD so that each conformer has a minimum RMSD to all the others in the set?
>
>
> Any help would be gratefully received.
>
>
>
> Paul.
>
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