Calculate the RMS deviation between the values in 2 distance matrices computed by Gaussian and parsed by matrixparse.

matrixRMS

#!/usr/bin/env python

import argparse, sys, csv, math

def calcRMS(reader1, reader2):

    def makeList(reader):
        l = []
        for row in reader:
            for val in row:
                if val != '':
                    l.append(float(val.strip()))
        return l
    
    dist1 = makeList(reader1)
    dist2 = makeList(reader2)

    if len(dist1) != len(dist2):
        return 'File dimensions are incompatible'

    else:
        gen = zip([el for el in dist1], [el for el in dist2])
        diffs = [a - b for a, b in gen]
        squares = [a*a for a in diffs]
        return math.sqrt(sum(squares)/len(squares))
    

def main(args):
    parser = argparse.ArgumentParser(description = 'Calculate the RMS deviation of one Gaussian distance matrix from another.')
    parser.add_argument('File1', type=str)
    parser.add_argument('File2', type=str)

    args = parser.parse_args(args)

    try:
        file1 = open(args.File1, 'r')
        file1reader = csv.reader(file1)
    except:
        print('{} is not a valid file'.format(file1))
        return 2
    try:
        file2 = open(args.File2, 'r')
        file2reader = csv.reader(file2)
    except:
        print('{} is not a valid file'.format(file2))
        return 2

    print(calcRMS(file1reader,file2reader))
        
if __name__ == '__main__':
    sys.exit(main(sys.argv[1:]))