/**
* 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;
}
public HelixAxisAligner(QuatSymmetryResults results) {
this.subunits = results.getSubunits();
this.helixLayers = results.getHelixLayers();
if (subunits == null) {
throw new IllegalArgumentException("HelixAxisTransformation: Subunits are null");
} else if (helixLayers == null) {
throw new IllegalArgumentException("HelixAxisTransformation: HelixLayers is null");
} else if (subunits.getSubunitCount() == 0) {
throw new IllegalArgumentException("HelixAxisTransformation: Subunits is empty");
} else if (helixLayers.size() == 0) {
throw new IllegalArgumentException("HelixAxisTransformation: HelixLayers is empty");
}
}
private List<Integer> getLongestLayerLine() {
int len = 0;
int index = 0;
Helix helix = helixLayers.getByLargestContacts();
List<List<Integer>> layerLines = helix.getLayerLines();
for (int i = 0; i < layerLines.size(); i++) {
if (layerLines.get(i).size() > len) {
len = layerLines.get(i).size();
index = i;
}
}
return layerLines.get(index);
}
/**
* Returns a vector along the principal rotation axis for the alignment of structures along the
* z-axis
*
* @return principal rotation vector
*/
private void calcPrincipalRotationVector() {
// AxisAngle4d axisAngle = helixLayers.getByLowestAngle().getAxisAngle();
AxisAngle4d axisAngle = helixLayers.getByLargestContacts().getAxisAngle();
principalRotationVector = new Vector3d(axisAngle.x, axisAngle.y, axisAngle.z);
}