Dear all,
I'm afraid that I'm struggling to understand precisely how to build a 2D
pharmacophore fingerprint. I thought I had it, but my code sits in a running
state indefinitely.
This is the code:
fdefNameStr: str = "MinimalFeatures.fdef"
featFactory = ChemicalFeatures.BuildFeatureFactory(fdefNameStr)
sigFactory = SigFactory(featFactory, minPointCount=2, maxPointCount=3,
trianglePruneBins=False)
sigFactory.SetBins([(0,2),(2,5),(5,8)])
sigFactory.Init()
sigFactory.GetSignature()
pharmFPList = []
for keyCase in caseDrugDictionary:
caseDrug = caseDrugDictionary[keyCase]
mol = caseDrug.getRDKitMol()
drugNameStr = caseDrug.getDrugName()
pharmFP = Generate.Gen2DFingerprint(mol, sigFactory)
pharmFPList.append(pharmFP)
Firstly, the code runs indefinitely (2 hrs and still running) when it executes:
pharmFP = Generate.Gen2DFingerprint(mol, sigFactory)
Secondly, I would be extremely grateful if someone could explain whether
"MinimalFeatures.fdef" is the right file? I downloaded it from GitHub, but I'm
uncertain of its use. I've gone through the RDKit API and RDKit book. Are there
any descriptive RDKit Pharmacophore tutorials?
Many thanks
Anthony
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