You beat me by seconds ... I hate it when you do that ;-) -----Original Message----- From: Greg Landrum [mailto:[email protected]] Sent: Tuesday, October 11, 2011 4:23 PM To: [email protected] Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] multiprocessing & rdkit
Hi Paul, On Tue, Oct 11, 2011 at 7:55 AM, <[email protected]> wrote: > > Dear RDkitters, > > I'm trying to use Python's multiprocessing module in conjunction with > RDKit. > > It should be applied in 2 cases: > (1) fingerprint calculation > & > (2) Picking Diverse Molecules > > > > (1) > " > from multiprocessing import Pool > p4 = Pool(processes=4) > def fps_calc(m): > fps = [GetMorganFingerprint(x,3) for x in m] > return fps > fps = p4.map(fps_calc,ms) > " > ==> > "TypeError: 'Mol' object is not iterable" I think what you want to do here is: #------------------- def fps_calc(m): fp = GetMorganFingerprint(m,3) return fp fps = p4.map(fps_calc,ms) #------------------- The map method takes a function and a sequence of objects, it applies that function to each object in the sequence. > (2) > " > from multiprocessing import Pool > p4 = Pool(processes=4) > def distij(i,j,fps=fps): > return 1-DataStructs.DiceSimilarity(fps[i],fps[j]) > > def DivSelection(distij,nfps,quantity_train): > picker = MaxMinPicker() > picked_indices = picker.LazyPick(distij,nfps,quantity_train) > return picked_indices > " > pickIndices = p4.map(DivSelection, ???) The MaxMinPicker does not have any way to do the parallelization with multiprocessing. -greg ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
