espsim fast

def ShortGI(dist, charge1,charge2,):
    #These are precomputed coefficients:
    a=np.array([[ 15.90600036,   3.9534831 ,  17.61453176],
                [  3.9534831 ,   5.21580206,   1.91045387],
                [ 17.61453176,   1.91045387, 238.75820253]])
    b=np.array([[-0.02495   , -0.04539319, -0.00247124],
                [-0.04539319, -0.2513    , -0.00258662],
                [-0.00247124, -0.00258662, -0.0013    ]])
    
    a_flat = a.flatten()
    b_flat = b.flatten()
    dist = (dist**2).flatten()
    charges = (charge1[:,None]*charge2).flatten()
    
    return ((a_flat[:,None] * np.exp(dist * b_flat[:,None])).sum(0) * charges).sum()


def SimilarityMetric(intPrbPrb, intRefRef, intPrbRef,):
    numerator=intPrbRef
    denominator=intPrbPrb+intRefRef-intPrbRef
    return numerator/denominator


def mySim(refCoor, prbCoor, refCharge, prbCharge):
    distPrbPrb = cdist(prbCoor,prbCoor)
    distPrbRef = cdist(prbCoor,refCoor)
    distRefRef = cdist(refCoor,refCoor)
    
    intPrbPrb=ShortGI(distPrbPrb,prbCharge,prbCharge)
    intPrbRef=ShortGI(distPrbRef,prbCharge,refCharge)
    intRefRef=ShortGI(distRefRef,refCharge,refCharge)
    return SimilarityMetric(intPrbPrb,intRefRef,intPrbRef,'tanimoto')