Hi Anthony, Can you share the molecule that you're having trouble with?
As for the pharmacophore definitions: we don't have a great set of definitions available, but the one I normally suggest would be to use either the ones in RDConfig.RDDataDir+'/BaseFeatures.fdef' or the feature factory which is available from Chem.Pharm2D.Gobbi_Pharm2D: from rdkit.Chem.Pharm2D import Gobbi_Pharm2D sigFactory = Gobbi_Pharm2D.factory sigFactory.SetBins([(0,2),(2,5),(5,8)]) sigFactory.Init() Tutorials: the only one I'm aware of is the material in the Getting Started guide: https://www.rdkit.org/docs/GettingStartedInPython.html#d-pharmacophore-fingerprints but I suspect you've found that already Best, -greg On Wed, Oct 13, 2021 at 10:39 PM Anthony Nash <anthony.n...@ndcn.ox.ac.uk> wrote: > 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 > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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