Hello everyone,
We have been writing a script that searches though a large number of molecules
within different files for a common substructure. To speed this up we have been
attempting to run this script in parallel-see scripts below. However online the
tutorial notes make reference to problems with using the SDMolSupplier in
parallel, we were wondering what is the issue and how we could circumvent them
to speed up some of our calculations.
Non-parallel
from __future__ import print_function
from rdkit import Chem
import os
from progressbar import ProgressBar
pbar=ProgressBar()
matches = []
directory = 'Q:\Data2'
patt = Chem.MolFromSmarts('NC(N****NC=O)=O')
for file in pbar(os.listdir(directory)):
filename = os.fsdecode(file)
if filename.endswith(".sdf"):
f = os.path.join(directory,filename)
suppl= Chem.SDMolSupplier(f)
for mol in suppl:
if mol is None: continue
if mol.HasSubstructMatch(patt):
matches.append(mol)
w = Chem.SDWriter(r'C:\Users\tom.watts\Desktop\datasmarts4c.sdf')
for m in matches: w.write(m)
print(filename)
Parallel
pbar=ProgressBar()
matches = []
directory = 'E:\Data'
patt = Chem.MolFromSmarts('NC(N****NC=O)=O')
w = Chem.SDWriter(r'C:\Users\tom.watts\Desktop\SearchDataNonly.sdf')
l=[]
for file in pbar(os.listdir(directory)):
filename = os.fsdecode(file)
if filename.endswith(".sdf"):
f = os.path.join(directory,filename)
l.append(f)
num_cores = multiprocessing.cpu_count()
print(num_cores)
lock = multiprocessing.Lock()
def Search(i):
suppl= Chem.SDMolSupplier(i)
for mol in suppl:
if mol is None: continue
if mol.HasSubstructMatch(patt):
matches.append(mol)
return matches
results = Parallel(n_jobs=20)(delayed(Search)(i) for i in l)
We also wish to use a second script that opens one SDF file and then runs a
loop over each molecule in the file. This is currently done serially and we
were wondering if it could be made parallel.
suppl = Chem.SDMolSupplier('Red3.sdf')
for mol in suppl:
patt = Chem.MolFromSmarts('NC(N)=O')
num=mol.GetSubstructMatches(patt)
logger.debug(Chem.MolToSmiles(mol))
h=len(num)
m3=Chem.AddHs(mol)
cids =AllChem.EmbedMultipleConfs(m3, numConfs)
Any comments can be useful.
Thanks a lot,
Stamatia Zavitsanou
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