Hi Antoine,
|rdkit.Chem.Pharm2D.Generate.||Gen2DFingerprint()| expects a single molecule
https://www.rdkit.org/docs/source/rdkit.Chem.Pharm2D.Generate.html?highlight=gen2dfingerprint#rdkit.Chem.Pharm2D.Generate.Gen2DFingerprint
while you are passing a list of molecules:
pharmacophorefps = Generate.Gen2DFingerprint(list(df['ROMol']), sigFactory)
HTH, cheers
p.
On 21/02/2020 16:22, Antoine Dumas wrote:
Hello,
I am trying to generate a set of pharmacophore fingerprints in python
using RDKIT from a list of SMILES (20k molecules)
No matter what I do the script keeps throwing an error saying my code
doesn’t match the C++ signature.
Here is a copy of my code as it stands right now
from __future__ import print_function
import os
import csv
import numpy as np
import pandas as pd
from rdkit import RDConfig, Chem, DataStructs, rdBase
from rdkit.Chem import rdFingerprintGenerator, rdMolDescriptors,
AllChem, rdFMCS, MACCSkeys, Draw, PandasTools, ChemicalFeatures,
rdDepictor
from rdkit.Chem.Fingerprints import FingerprintMols
from rdkit.Chem.Draw import IPythonConsole, MolDraw2D
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D, Generate
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
from IPython.display import SVG
from tabulate import tabulate
os.chdir(r'C:\Users\adumas\Desktop\')
input1 = r'C:\Users\adumas\Desktop\FILE.csv'
output = r'C:\Users\adumas\Desktop\FILE.csv'
df = pd.read_csv(input1, delimiter = ',', header = 0, index_col =
[''], names = ['','row ID','MOL_ID', 'SMILES',])
PandasTools.AddMoleculeColumnToFrame(df, smilesCol = 'SMILES')
SMILES = []
SMILES = df.iloc[0:,4]
ID = df.iloc[0:,1]
molecules = [Chem.MolFromSmiles(x) for x in SMILES]
fingerprints = [FingerprintMols.FingerprintMol(x) for x in molecules]
morganfps = rdFingerprintGenerator.GetFPs(list(df['ROMol']))
df['Morgan Fingerprint'] = morganfps
mcassfps = [MACCSkeys.GenMACCSKeys(x) for x in list(df['ROMol'])]
df['MCASS Fingerprint'] = mcassfps
fdefName = 'BaseFeatures.fdef'
featFactory = ChemicalFeatures.BuildFeatureFactory(fdefName)
sigFactory = SigFactory(featFactory, minPointCount=2, maxPointCount=9)
sigFactory.SetBins([(0,2),(2,5),(5,8)])
sigFactory.Init()
sigFactory.GetSigSize()
pharmacophorefps = Generate.Gen2DFingerprint(list(df['ROMol']),
sigFactory) ************* Line throwing error constantly no matter
whether I specify (SMILES, sigFactory) or (molecules, sigFactory) or
(df.iloc[0:,4], sigFactory)
df['Pharmacophore Fingerprints'] = pharmacophorefps
And the error it throws me every time no matter how I try to define
the list of smiles
*ArgumentError*: Python argument types in
rdkit.Chem.rdmolops.GetDistanceMatrix(Series, bool)
did not match C++ signature:
GetDistanceMatrix(class RDKit::ROMol {lvalue} mol, bool
useBO=False, bool useAtomWts=False, bool force=False, char const *
__ptr64 prefix='')
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