Hi all,
I have been playing with the diversity selection in RDKit. I am running
through a set of ~26,000 molecules to pick a set of 200 diverse molecules.
I saw some examples of how to do this in Python (my variant of their script
below), but the memory consumption is massive. I burned through ~15GB of
memory before I killed it off. Is this about what others have seen, or
should I move to doing this in C++ or Java (assuming that others have seen
a significantly lower level of memory consumption)?
Here is the script:
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import DataStructs
import gzip
from rdkit.Chem import Draw
from rdkit.SimDivFilters import rdSimDivPickers
zims = [x for x in Chem.ForwardSDMolSupplier(gzip.open('a.sdf.gz')) if x is
not None]
zims_fps=[AllChem.GetMorganFingerprintAsBitVect(x,2) for x in zims]
dm=[]
for i,fp in enumerate(zims_fps[:26000]): # only 1000 in the demo (in
the interest of time)
dm.extend(DataStructs.BulkTanimotoSimilarity(fp,zims_fps[1+1:26000],returnDistance=True))
dm = array(dm)
picker = rdSimDivPickers.MaxMinPicker()
ids = picker.Pick(dm,26000,200)
list(ids[:200])
Thanks in advance!
Matt
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