#!/bin/bash

file=$1
atom=$2
btom=$3
ctom=$4

((offset=8))

scale=`sed -n 2p $file`
X1=`sed -n 3p $file | awk '{ print $1 }'`
X2=`sed -n 3p $file | awk '{ print $2 }'`
X3=`sed -n 3p $file | awk '{ print $3 }'`
Y1=`sed -n 4p $file | awk '{ print $1 }'`
Y2=`sed -n 4p $file | awk '{ print $2 }'`
Y3=`sed -n 4p $file | awk '{ print $3 }'`
Z1=`sed -n 5p $file | awk '{ print $1 }'`
Z2=`sed -n 5p $file | awk '{ print $2 }'`
Z3=`sed -n 5p $file | awk '{ print $3 }'`
export X1 X2 X3
export Y1 Y2 Y3
export Z1 Z2 Z3

((line1=atom+offset))
((line2=btom+offset))
((line3=ctom+offset))

temp="`sed -n ${line1}p $1`"
xa=`echo $temp | awk '{ print $1 }'`
ya=`echo $temp | awk '{ print $2 }'`
za=`echo $temp | awk '{ print $3 }'`

temp="`sed -n ${line2}p $1`"
xb=`echo $temp | awk '{ print $1 }'`
yb=`echo $temp | awk '{ print $2 }'`
zb=`echo $temp | awk '{ print $3 }'`

temp="`sed -n ${line3}p $1`"
xc=`echo $temp | awk '{ print $1 }'`
yc=`echo $temp | awk '{ print $2 }'`
zc=`echo $temp | awk '{ print $3 }'`

echo -en "angle: "
foo=`echo "$xa $ya $za $xb $yb $zb $xc $yc $zc $scale" | \
	awk ' \
	BEGIN {
		X1=ENVIRON["X1"]; X2=ENVIRON["X2"]; X3=ENVIRON["X3"]
		Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"]
		Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"]
		pi=3.14159265
	}	
	{
		X=sqrt(X1^2+X2^2+X3^2)
		Y=sqrt(Y1^2+Y2^2+Y3^2)
		Z=sqrt(Z1^2+Z2^2+Z3^2)
		dx=$1-$4
		dy=$2-$5
		dz=$3-$6
		if(dx>1/2)
			dx-=1
		if(dx<-1/2)
			dx+=1
		if(dy>1/2)
			dy-=1
		if(dy<-1/2)
			dy+=1
		if(dz>1/2)
			dz-=1
		if(dz<-1/2)
			dz+=1
		Dx=$1-$7
		Dy=$2-$8
		Dz=$3-$9
		if(Dx>1/2)
			Dx-=1
		if(Dx<-1/2)
			Dx+=1
		if(Dy>1/2)
			Dy-=1
		if(Dy<-1/2)
			Dy+=1
		if(Dz>1/2)
			Dz-=1
		if(Dz<-1/2)
			Dz+=1
		dxt=dx*X1+dy*Y1+dz*Z1
		dyt=dx*X2+dy*Y2+dz*Z2
		dzt=dx*X3+dy*Y3+dz*Z3
		Dxt=Dx*X1+Dy*Y1+Dz*Z1
		Dyt=Dx*X2+Dy*Y2+Dz*Z2
		Dzt=Dx*X3+Dy*Y3+Dz*Z3
		sp=dxt*Dxt+dyt*Dyt+dzt*Dzt
		d=sqrt(dxt^2+dyt^2+dzt^2)
		D=sqrt(Dxt^2+Dyt^2+Dzt^2)
		print sp/(d*D)
	}'`

./acos $foo

echo