/**
* Return a midpoint of a helix, calculated from three positions of three adjacent subunit
* centers.
*
* @param p1 center of first subunit
* @param p2 center of second subunit
* @param p3 center of third subunit
* @return midpoint of helix
*/
private Point3d getMidPoint(Point3d p1, Point3d p2, Point3d p3) {
Vector3d v1 = new Vector3d();
v1.sub(p1, p2);
Vector3d v2 = new Vector3d();
v2.sub(p3, p2);
Vector3d v3 = new Vector3d();
v3.add(v1);
v3.add(v2);
v3.normalize();
// calculat the total distance between to subunits
double dTotal = v1.length();
// calculate the rise along the y-axis. The helix axis is aligned with y-axis,
// therfore, the rise between subunits is the y-distance
double rise = p2.y - p1.y;
// use phythagorean theoremm to calculate chord length between two subunit centers
double chord = Math.sqrt(dTotal * dTotal - rise * rise);
// System.out.println("Chord d: " + dTotal + " rise: " + rise + "chord: " + chord);
double angle = helixLayers.getByLargestContacts().getAxisAngle().angle;
// using the axis angle and the chord length, we can calculate the radius of the helix
// http://en.wikipedia.org/wiki/Chord_%28geometry%29
double radius = chord / Math.sin(angle / 2) / 2; // can this go to zero?
// System.out.println("Radius: " + radius);
// project the radius onto the vector that points toward the helix axis
v3.scale(radius);
v3.add(p2);
// System.out.println("Angle: " +
// Math.toDegrees(helixLayers.getByLowestAngle().getAxisAngle().angle));
Point3d cor = new Point3d(v3);
return cor;
}
/* (non-Javadoc)
* @see org.biojava.nbio.structure.quaternary.core.AxisAligner#getDimension()
*/
@Override
public Vector3d getDimension() {
run();
Vector3d dimension = new Vector3d();
dimension.sub(maxBoundary, minBoundary);
dimension.scale(0.5);
return dimension;
}
protected void computeCircle() {
Vector3d center = new Vector3d((Vector3d) get(0));
Vector3d p2 = new Vector3d((Vector3d) get(1));
p2.sub(center);
double radius = p2.length();
removeAllElements();
double angle = 0;
double incAngle = 2 * Math.PI / sides;
for (int i = 0; i < sides; i++) {
super.add(
new Vector3d(
center.x + radius * Math.cos(angle), center.y + radius * Math.sin(angle), 0));
angle += incAngle;
}
super.add(new Vector3d(center.x + radius, center.y, 0));
}