Snippets

Biosig Lab Pharmacophores changes upon missense mutation

Created by Carlos Miranda Rodrigues
get_pharmacophores_difference.py
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import argparse

def main(aa_from,aa_to):
    fingerprint = {}
    fingerprint["A"] = [1,0,0,1,1,0,0,2]
    fingerprint["V"] = [3,0,0,1,1,0,0,2]
    fingerprint["L"] = [4,0,0,1,1,0,0,2]
    fingerprint["G"] = [0,0,0,1,1,0,0,2]
    fingerprint["S"] = [0,0,0,1,2,0,0,3]
    fingerprint["W"] = [10,0,0,1,2,9,0,2]
    fingerprint["T"] = [1,0,0,1,2,0,0,3]
    fingerprint["Q"] = [2,0,0,2,2,0,0,3]
    fingerprint["E"] = [2,0,2,3,1,0,0,3]
    fingerprint["C"] = [1,0,0,1,1,0,1,3]
    fingerprint["R"] = [3,2,0,1,4,0,0,3]
    fingerprint["P"] = [3,0,0,1,1,0,0,2]
    fingerprint["D"] = [1,0,2,3,1,0,0,3]
    fingerprint["F"] = [7,0,0,1,1,6,0,2]
    fingerprint["I"] = [4,0,0,1,1,0,0,2]
    fingerprint["H"] = [4,2,0,1,3,5,0,2]
    fingerprint["N"] = [1,0,0,2,3,0,0,3]
    fingerprint["M"] = [3,0,0,1,1,0,1,2]
    fingerprint["Y"] = [7,0,0,1,2,6,0,2]
    fingerprint["K"] = [3,1,0,1,2,0,0,3]
    #Hydrophobics,Positives,Negatives,Acceptors,Donnors,Aromatics,Sulfurs,Neutral
    vector_difference = [fingerprint[aa_from][i]-fingerprint[aa_to][i] for i in range(0,len(fingerprint[aa_from]))]
    print(vector_difference)
    return True

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='Pharmacophores changes upon missense mutation')
    parser.add_argument('-f', '--from', dest='aa_from', required=True, help='One letter code for wild-type residue')
    parser.add_argument('-t', '--to', dest='aa_to', required=True, help='One letter code for mutant residue')
    
    args = parser.parse_args()
    main(args.aa_from, args.aa_to)

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