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"
(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, ???)
In the first case, I do not get the point what is going wrong. With the
following conformer generation snippet, multiprocessing works perfect:
"
from multiprocessing import Pool
def generateconformations(m):
m = Chem.AddHs(m)
ids=AllChem.EmbedMultipleConfs(m,numConfs=10)
for id in ids:
AllChem.UFFOptimizeMolecule(m,confId=id)
return m
p4 = Pool(processes=4)
ms = [x for x in Chem.SDMolSupplier('blockbusters.sdf')]
cms4=p4.map(generateconformations,ms)
"
In the second case, I'm not sure how to properly pass the variables.
Cheers & Thanks,
Paul
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