Esempio n. 1
0
  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;
  }
Esempio n. 2
0
  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();
  }
Esempio n. 3
0
 /* (non-Javadoc)
  * @see org.biojava.nbio.structure.quaternary.core.AxisAligner#getCentroid()
  */
 @Override
 public Point3d getCentroid() {
   return new Point3d(subunits.getCentroid());
 }