import numpy
from MMTK import *


file_list=["correlations/3CH0_all_correlation_matrix.dat"]
filename2 = "3CH0_all_modes_residuebondlengths.txt"

def calc_residue_dist(residue_one, residue_two) :
    """Returns the C-alpha distance between two residues"""
    diff_vector  = residue_one["CA"].coord - residue_two["CA"].coord
    return numpy.sqrt(numpy.sum(diff_vector * diff_vector))

filename in file_list:
	corrs = open(filename,"r")
	corrs = corrs.readlines()
	dist = open(filename2,"r")
	dist = dist.readlines()
	index = corrs[0]
	index=index.split()
	#print index
	for i in xrange(1,len(index)):
#		print i	
		new_line=corrs[i].split()
#		del new_line[0:i]
	#	print len(new_line)
	#	print len(new_line[0])
		for j in xrange(1,len(new_line)):	
#			print j
			#if float(new_line[j]) == 1:
			#	print "yes!"	
			if float(new_line[j]) > 0.0 or float(new_line[j]) < -0.0:
				if float(new_line[j]) != 1.0:
				#	if dist[j].split()[1] > 3.00 and dist[j].split()[0] == j:
				#		print i-1, j-1
					if float(dist[i-1].split()[1])> 3.9:
					#	print dist[i-1]
						print i-1, j-1