I am new with openbabel and need your help. I have a list of SMILES and for each compound, I need to calculate different fingerprint types provided by openbabel. I installed the package but there is no information for how to calculate fingerprints.
I read the webpage of openbabel however it mentions about similarity search in a ligand set. I dont need the similarity search right now, just let me know how to calculate 4 types of fingerprints for my SMILES list.
On Apr 15, 2017, at 22:24, Mehmet Aziz YIRIK <[hidden email]> wrote:
> I need to calculate different fingerprint types provided by openbabel. ... how to calculate 4 types of fingerprints for my SMILES list.
You didn't say if you want to do that from the command-line or from a programming language like C++ or Python. I'll assume that you want to use the command-line, and that you want your output in FPS format.
Use "-ofps" to say you want the output in FPS format.
Use "-xf" to specify the fingerprint type, specifically, "-xfFP2" means to compute FP2 fingerprints (this is the default), "-xfFP3" computes FP3 fingerprints, "-xfFP4" computes FP4 fingerprints, and "-xfMACCS" computes the MACCS fingerprints: