score_dms.py

import math

def stat_test( lower_avg, lower_err, upper_avg, upper_err ):
    # not a real funciton but shoudl return a p value that the 
    # lower_avg < upper_avg
    raise TypeError("not implemented")
    
    
    
    
    
def score( structure, reacts, react_errors, critical=0.01 ):
    assert critical >= 0 and critical <= 1, f"Critical value must be on range [0-1]"
    paired, unpaired = [], []
    for idx, db in enumerate( structure ):
        if db == '.':
            unpaired.append( idx )
        else:
            paired.append( idx )
    denom, numerator = len(paired)*len(unpaired), 0
    for p in paired:
        for up in unpaired:
            ans = -math.log(stat_test(reacts[p], react_errors[p], reacts[up], react_errors[up])/critical)
            ans = max(ans, 0)
            ans = min(ans, 1)
            # TODO need to some checks in case if ans is math.inf or math.Nan
            denom += ans
            
    return denom / numerator