public Point3d calcCenterOfRotation() {
List<Integer> line = getLongestLayerLine();
// can't determine center of rotation if there are only 2 points
// TODO does this ever happen??
if (line.size() < 3) {
return subunits.getCentroid();
}
Point3d centerOfRotation = new Point3d();
List<Point3d> centers = subunits.getOriginalCenters();
// calculate helix mid points for each set of 3 adjacent subunits
for (int i = 0; i < line.size() - 2; i++) {
Point3d p1 = new Point3d(centers.get(line.get(i)));
Point3d p2 = new Point3d(centers.get(line.get(i + 1)));
Point3d p3 = new Point3d(centers.get(line.get(i + 2)));
transformationMatrix.transform(p1);
transformationMatrix.transform(p2);
transformationMatrix.transform(p3);
centerOfRotation.add(getMidPoint(p1, p2, p3));
}
// average over all midpoints to find best center of rotation
centerOfRotation.scale(1 / (line.size() - 2));
// since helix is aligned along the y-axis, with an origin at y = 0, place the center of
// rotation there
centerOfRotation.y = 0;
// transform center of rotation to the original coordinate frame
reverseTransformationMatrix.transform(centerOfRotation);
// System.out.println("center of rotation: " + centerOfRotation);
return centerOfRotation;
}
private double[] getSubunitZDepth() {
int n = subunits.getSubunitCount();
double[] depth = new double[n];
Point3d probe = new Point3d();
// transform subunit centers into z-aligned position and calculate
// z-coordinates (depth) along the z-axis.
for (int i = 0; i < n; i++) {
Point3d p = subunits.getCenters().get(i);
probe.set(p);
transformationMatrix.transform(probe);
depth[i] = probe.z;
}
return depth;
}
/**
* Calculates the min and max boundaries of the structure after it has been transformed into its
* canonical orientation.
*/
private void calcBoundaries() {
minBoundary.x = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.y = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.z = Double.MAX_VALUE;
maxBoundary.z = Double.MIN_VALUE;
xzRadiusMax = Double.MIN_VALUE;
Point3d probe = new Point3d();
for (Point3d[] list : subunits.getTraces()) {
for (Point3d p : list) {
probe.set(p);
transformationMatrix.transform(probe);
minBoundary.x = Math.min(minBoundary.x, probe.x);
maxBoundary.x = Math.max(maxBoundary.x, probe.x);
minBoundary.y = Math.min(minBoundary.y, probe.y);
maxBoundary.y = Math.max(maxBoundary.y, probe.y);
minBoundary.z = Math.min(minBoundary.z, probe.z);
maxBoundary.z = Math.max(maxBoundary.z, probe.z);
xzRadiusMax = Math.max(xzRadiusMax, Math.sqrt(probe.x * probe.x + probe.z * probe.z));
}
}
// System.out.println("MinBoundary: " + minBoundary);
// System.out.println("MaxBoundary: " + maxBoundary);
// System.out.println("zxRadius: " + xzRadiusMax);
}
/**
* Returns a list of list of subunit ids that form an "orbit", i.e. they are transformed into each
* other during a rotation around the principal symmetry axis (z-axis)
*
* @return
*/
private List<List<Integer>> calcOrbits() {
int n = subunits.getSubunitCount();
List<List<Integer>> orbits = new ArrayList<List<Integer>>();
for (int i = 0; i < n; i++) {
orbits.add(Collections.singletonList(i));
}
return orbits;
}
private void calcPrincipalAxes() {
MomentsOfInertia moi = new MomentsOfInertia();
for (Point3d[] list : subunits.getTraces()) {
for (Point3d p : list) {
moi.addPoint(p, 1.0);
}
}
principalAxesOfInertia = moi.getPrincipalAxes();
}
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 void calcTransformationBySymmetryAxes() {
Vector3d[] axisVectors = new Vector3d[2];
axisVectors[0] = new Vector3d(principalRotationVector);
axisVectors[1] = new Vector3d(referenceVector);
// y,z axis centered at the centroid of the subunits
Vector3d[] referenceVectors = new Vector3d[2];
referenceVectors[0] = new Vector3d(Z_AXIS);
referenceVectors[1] = new Vector3d(Y_AXIS);
transformationMatrix = alignAxes(axisVectors, referenceVectors);
// combine with translation
Matrix4d combined = new Matrix4d();
combined.setIdentity();
Vector3d trans = new Vector3d(subunits.getCentroid());
trans.negate();
combined.setTranslation(trans);
transformationMatrix.mul(combined);
// for helical geometry, set a canonical view for the Z direction
calcZDirection();
}
/* (non-Javadoc)
* @see org.biojava.nbio.structure.quaternary.core.AxisAligner#getCentroid()
*/
@Override
public Point3d getCentroid() {
return new Point3d(subunits.getCentroid());
}