Carve a nanospring out of a 3d point file

NanoSpring_Script.awk

BEGIN{
 #define PI for program
PI=3.14159;
#define radius of spring form, helical body radius
r=6;
#define pitch
p=7;
b= p/(2*PI);
#define diameter of spring wire and radius, cross-sectional thickness
d=4;
radius=d/2;

print "Atoms"

}

#the following is a search function without a defined search term
#this creates a function that will check every record in the target file
#First we will define a function with which you want the spring to follow in terms of x and y dependent on z ($3).
#In this case we will use a simple spring which follows the parameters defined int he BEGIN section
{
   t=$5/b;

   x=r*cos(t);
   y=r*sin(t);

#this checks the target points distance from the function point at target locations z value.
#if it is less than or equal to the desired radius, then we keep the point for the new file
   if( dist(x,y,$3,$4) <= radius )
   {
      if( $2 == 1 )
      {
         printf("%s %f %f %f\n", "Si", ($3+10)*7.16, ($4+10)*7.16, ($5+10)*7.16);
      }
      else if ( $2 == 2 )
      {
         printf("%s %f %f %f\n", "O", ($3+10)*7.16, ($4+10)*7.16, ($5+10)*7.16);
      }
   }
}

function dist(x1,y1,x2,y2) { return sqrt( (x1-x2)^2 + (y1-y2)^2 ) }
function atan(x) {return atan2(x,1)}

From that one time when I was a grad student and didn't know that python existed.