dmis-lab/ReSimNet

ECFP fingerprint computation

sabrina-rashid opened this issue · 1 comments

sabrina-rashid commented

How are you computing ECFP fingerprints? I am using the following command to compute fingerprint for the first compound in the AABA.csv file. But it does not seem to match with what you have in that file. Any help would be much appreciated.

from rdkit import Chem
mol = Chem.MolFromSmiles("Cn1cc(N+[O-])c(=O)n(C)c1=O")
fp = Chem.RDKFingerprint(mol)
a = fp.ToBitString()

Thanks,

mjjeon commented

How are you computing ECFP fingerprints? I am using the following command to compute fingerprint for the first compound in the AABA.csv file. But it does not seem to match with what you have in that file. Any help would be much appreciated.

from rdkit import Chem
mol = Chem.MolFromSmiles("Cn1cc(N+[O-])c(=O)n(C)c1=O")
fp = Chem.RDKFingerprint(mol)
a = fp.ToBitString()

Thanks,

Hi,
I used the following codes to get ECFP fingerprints. Hope it is helpful.

mol = Chem.MolFromSmiles(smilesstr)
fp_obj = AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=2048, useChirality=True)
arr = np.zeros((1,))
DataStructs.ConvertToNumpyArray(fp_obj, arr)

If you have further questions, please let me know.
Thanks,