Contributor modules

iSIM (Miranda-Quintana Group, Department of Chemistry, University of Florida)

iSIM (R35GM150620) performs comparisons of multiple molecules at the same time and yields the same value as the average pairwise comparisons of molecules represented by binary fingerprints.

from FPSim2.contrib.isim.isim_comp import (
    get_sim_dict,
    calculate_medoid,
    calculate_outlier,
    calculate_comp_sim,
)
from FPSim2 import FPSim2Engine

fp_filename = "chembl_35_v0.6.0.h5"
fpe = FPSim2Engine(fp_filename)

# get average similarity of the dataset
sim_dict = get_sim_dict(fpe)

# calculate medoid of the dataset
medoid = calculate_medoid(fpe)

# calculate outlier of the dataset
outlier = calculate_outlier(fpe)

# calculate complementary similarity
comp_sim = calculate_comp_sim(fpe)