Hi RDKitters,
I'm trying to use RDKit to fragment a large set of molecules ~1.5m. So I wrote
a simple script (below) to handle SMILES and fragment it, I then chunked my
file in 20 pieces, wrote a 4 line bash script to handle the 20 chunks and then
pressed the go button. The problem that I'm having is the memory allocation to
these processes. I have been running the job for about 30 minutes and I've got
one process which is using 2.43 GB of memory (and growing) yet some of the
processes don't appear to be growing at all, static at 34.5 MB, which is what I
would expect (N.B. the chunks will be heterogeneous). I am wondering if anyone
knows where my leak might be.
Apologies for all the del statements in the following script, I was being over
zealous to remove any possibilities.
from rdkit import Chem
from rdkit.Chem import Recap
import sys
#sys.path.append('/Users/nfirth/Desktop/MOARF/')
#from parallellSmartsFragmenter import AdjustAromaticNs, makeMolFromSmiles
f = open(sys.argv[1], 'rb')
g = open('%s_fragmented.txt' %sys.argv[1][:-4], 'wb')
for line in f:
#mol = makeMolFromSmiles(line.rstrip())
try:
mol = Chem.MolFromSmiles(line.rstrip())
except:
del mol
continue
if(mol is None):
del mol
continue
hierarch = Recap.RecapDecompose(mol)
del mol
ks = hierarch.GetLeaves().keys()
del hierarch
if(len(ks)):
for x in ks:
g.write('%s\n' %x)
else:
g.write(line)
del ks
Many thanks in advance.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
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