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RMSD.py
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RMSD.py
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#!/usr/bin/env python3
#https://github.com/LeahKuhn/BCH5884
import sys, math
from decimal import Decimal
def readfiles(file1, file2):
"""
loop that takes first file and reads out the input then repeats with
second file
"""
global tmplist1, tmplist2
# Open file1.pdb from user input
#filetmp=file1
f=open(file1,'r')
lines=f.readlines()
# Save rows of pdb file to lists
tmplist1=[]
for line in lines:
words=line.split()
words[1]=(int(words[1]))
words[5]=(int(words[5]))
for i in range (6, (len(words)-1)):
words[i] = Decimal(words[i])
tmplist1.append(words)
f.close()
# open file2.pdb and put into lists
f=open(file2,'r')
lines=f.readlines()
# Save rows of pdb file to lists
tmplist2=[]
for line in lines:
words=line.split()
if len(words) != 12:
pass
else:
words[1]=(int(words[1]))
words[5]=(int(words[5]))
for i in range (6, (len(words)-1)):
words[i] = Decimal(words[i])
tmplist2.append(words)
f.close()
#sys.exit()
def rmsd(data1, data2):
"""*************************************************
Determines the root-mean-square deviation for two
.pdb files that are being stored in lists and prints
out the root-mean-square deviation value
*************************************************"""
sum_coor = 0
for x in range(0, len(data1)):
# find difference then square for x, y, and z coordinates
x_diff_sqr = (data1[x][6] - data2[x][6])**2
y_diff_sqr = (data1[x][7] - data2[x][7])**2
z_diff_sqr = (data1[x][8] - data2[x][8])**2
sum_coor = sum_coor + x_diff_sqr + y_diff_sqr + z_diff_sqr
# Determine root-mean-square using sum from above and the length of the list
rmsd_value = math.sqrt(sum_coor/len(data1))
print("Root-mean-square deviation:", rmsd_value)
if __name__ == "__main__":
readfiles(sys.argv[1], sys.argv[2])
rmsd(tmplist1, tmplist2)