[Rdkit-discuss] TanimotoSimilarity of Scaffolds

[serz sth]

Hey Guys,

 

I'm new to this forum and also new to python/rdkit, so I hope you'll be indulgent.

 

I wanna make a TanimotoSimilarity Comparison with compound-smiles that were put into a scaffolding form, e.g. 

'CC1C(CC2CC3CCCCC3C2)CCC2CCCCC21' 

So these scaffolds are stored in a DataFrame and I want to compare them one by one to find out if there are any outliers for a QSAR Model I'm feeding my compounds into.

 

My code looks like this (copied it mostly from the RDkit doc):

 


from rdkit import Chem, DataStructs, RDConfig

from rdkit.Chem import AllChem

from rdkit.Chem.Pharm2D import Gobbi_Pharm2D, Generate

 

ref = Chem.MolFromSmiles(df4.scaff[0])



mol1 = Chem.MolFromSmiles(df4.scaff[0])

mol1 = AllChem.AssignBondOrdersFromTemplate(ref, mol1)

mol2 = Chem.MolFromSmiles(df4.scaff[1])

mol2 = AllChem.AssignBondOrdersFromTemplate(ref, mol2)

# pharmacophore fingerprint

factory = Gobbi_Pharm2D.factory

fp1 = Generate.Gen2DFingerprint(mol1, factory, dMat=Chem.Get3DDistanceMatrix(mol1))

fp2 = Generate.Gen2DFingerprint(mol2, factory, dMat=Chem.Get3DDistanceMatrix(mol2))

# Tanimoto similarity

tani = DataStructs.TanimotoSimilarity(fp1, fp2)

print(tani)

 

But it doesn't work :( What do I need a reference for? So either I get a
ValueError: No matching found 
ValueError: Bad Conformer Id

Or, i get pass that, I get a



 

Can anybody help me? Thanks in Advance!

 

 

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss