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 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());
}
