How to convert Smiles to Fingerprint with rdkit?

Question

I have to convert a list of Smiles in a list of Fingerprints with rdkit. But I don't know how. I searched for solutions in the internet, but there is actually no Example working... Does anyone has experience with the conversion from a list of Smiles from molecules to the Fingerprints?

Thanks!

What have you tried so far? What were the problems with the examples? Which fingerprints do you want to use? — rapelpy, Jun 24 '19 at 17:37
Where have you been looking? There is clear documentation on the rdkit website: [Fingerprints](http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity) — Oliver Scott, Jun 28 '19 at 08:57

score 1 · Answer 1 · answered May 11 '21 at 18:21

You can try this:

from rdkit import Chem

smiles_list = ["O=C(NCc1cc(OC)c(O)cc1)CCCC/C=C/C(C)C", "CC(C)CCCCCC(=O)NCC1=CC(=C(C=C1)O)OC", "c1(C=O)cc(OC)c(O)cc1"]

# create a list of mols
mols = [Chem.MolFromSmiles(smiles) for smiles in smiles_list]

# create a list of fingerprints from mols
fps = [Chem.RDKFingerprint(mol) for mol in mols]

RDKit has variety of built-in functionality for generating molecular fingerprints, I have shown example of generating topological fingerprints here. Please refer to this doc for other options.

How to convert Smiles to Fingerprint with rdkit?

1 Answers1