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+--- Thread: Converting Smiles to Fingerprint with pandas iterrows/apply-function: (/thread-19559.html)
Converting Smiles to Fingerprint with pandas iterrows/apply-function: - Jompie96 - Jul-04-2019
Im trying to iterate my function over a column but it doesn't work properly. Could you guys show me where I have to correct my code?
Thats my Code
def SmilesToFPS(smiles):
mol = Chem.MolFromSmiles(smiles)
fps = FingerprintMols.FingerprintMol(mol)
#fpSize=1024, minPath=1, maxPath=7,
# bitsPerHash=2, useHs=True,
# tgtDensity=0.0, minSize=0,
# branchedPaths=True, useBondOrder=True,
# atomInvariants=0, fromAtoms=0, atomBits=None, bitInfo=None)
return print(fps.ToBitString())
for index, row in df_3.iterrows():
#for i, number in df_3['SmilesCode'].iteritems():
#this doesn't work.thats why I used .iterrows
try:
fingerprints = SmilesToFPS(smiles)
except:
fingerprints = 'ERROR'
print('\r', row['SmilesCode'], fingerprints, end='')
smiles_list.append(row['SmilesCode'])
fingerprint_list.append(fingerprints)
df_4 = pd.DataFrame({'SmilesCode' : smiles_list, 'Fingerprints' : fingerprint_list})I expect a Bitstring for every SmilesCode but I only get Errors for every row/SmilesCode. The defined function does work tho but not if I use it to iterate over my desired column! If I use the apply() function from pandas:
df_modDfObj = df_3.apply(SmilesToFPS)I get this error code:
ArgumentError: Python argument types in rdkit.Chem.rdmolops.RDKFingerprint(NoneType, int, int, int, int, int, float, int) did not match C++ signature: RDKFingerprint(RDKit::ROMol mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=True, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=True, bool useBondOrder=True, boost::python::api::object atomInvariants=0, boost::python::api::object fromAtoms=0, boost::python::api::object atomBits=None, boost::python::api::object bitInfo=None)
Im trying to iterate my function over a column but it doesn't work properly. Could you guys show me where I have to correct my code?
Thank you guys for your help!