import sys

pdbfile = sys.argv[1]
#pdbfile = "3CH0"
#atompairs=open("correlated_atompairs_3CH0_0.35.txt","r")
#atompairs = open("3ch0_0_3.9_correlated.txt", "r")
atompairs = open(pdbfile+"_atompairs_0.3_2.39-2.8_30.txt","r")

atompairs=atompairs.readlines()

output=open("visualise_"+pdbfile+"_all_atom_0.3_2.39-2.8_30.pml","w")
i=0
for line in atompairs:
	i+=1
	a="obj_"+str(i)
	line=line.split()
	first=int(line[0])+1
	second=int(line[1].rstrip())+1
	output.write("create "+a+", struct and (id "+str(first)+" or id "+str(second)+")\n")
        output.write("bond ("+a+" and id "+str(first)+"), ("+a+" and id "+str(second)+")\n" )
        output.write("show sticks, "+a+"\n") 
        output.write("set stick_radius,0.3,"+a+"\n")
        output.write("color purple,"+a+"\n")
	output.write("\n")