Fingerprints

ChEMBL makes a file containing pre-computed 2048 bit radius 2 Morgan fingerprints for each molecule available. It can be downloaded using:

import chembl_downloader

path = chembl_downloader.download_fps()

The version and other keyword arguments are also valid for this function.

Load fingerprints with chemfp

The following wraps the chembl_downloader.download_fps() function with chemfp’s fingerprint loader:

import chembl_downloader

arena = chembl_downloader.chemfp_load_fps()

The version and other keyword arguments are also valid for this function. More information on working with the chemfp.arena.FingerprintArena object can be found here.