Hi,
Problem solved (the sample script was missing a few lines of code). Sorry about
that. A fully functional script is below.
Best regards,
Konrad
===== begin active_fragments.py =====
from rdkit import Chem
from rdkit.ML.InfoTheory import InfoBitRanker
from rdkit.Chem import FragmentCatalog
from rdkit import RDConfig
import os
suppl = Chem.SDMolSupplier('bzr.sdf')
sdms = [x for x in suppl]
acts = [float(x.GetProp('ACTIVITY')) for x in sdms]
fName=os.path.join(RDConfig.RDDataDir,'FunctionalGroups.txt')
fparams = FragmentCatalog.FragCatParams(1,6,fName)
# fparams.GetNumFuncGroups()
fcat = FragmentCatalog.FragCatalog(fparams)
fcgen = FragmentCatalog.FragCatGenerator()
fpgen = FragmentCatalog.FragFPGenerator()
for m in sdms: nAdded=fcgen.AddFragsFromMol(m,fcat)
fps = [fpgen.GetFPForMol(x,fcat) for x in sdms]
ranker = InfoBitRanker(len(fps[0]),2)
for i,fp in enumerate(fps):
act = int(acts[i]>7)
ranker.AccumulateVotes(fp,act)
top5 = ranker.GetTopN(5)
for id,gain,n0,n1 in top5:
print(int(id),'%.3f '%gain,int(n0),int(n1))
===== end active_fragments.py =====
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