/* (non-Javadoc)
* @see org.biojava.nbio.structure.quaternary.core.AxisAligner#getGeometicCenterTransformation()
*/
@Override
public Matrix4d getGeometicCenterTransformation() {
run();
Matrix4d geometricCentered = new Matrix4d(reverseTransformationMatrix);
geometricCentered.setTranslation(new Vector3d(getGeometricCenter()));
return geometricCentered;
}
public static void main(String[] args) {
double[] vertexCoords = {
1.0, 0.0, 0.0, 0.0, 1.0, 0.0, -1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0
};
int[][] faceIndices = {{0, 3, 2, 1}, {4, 0, 1}, {4, 1, 2}, {4, 2, 3}, {4, 3, 0}};
ConvexPolyhedron poly = new ConvexPolyhedron(vertexCoords, faceIndices);
PolyTree pyramid = new PolyTree("pyramid", poly);
PolyTree hourglass = new PolyTree("hourglass");
Matrix4d X = new Matrix4d();
X.setIdentity();
X.setTranslation(new Vector3d(0, 0, -1));
hourglass.addComponent("bottom", pyramid, X);
X.setTranslation(new Vector3d(0, 0, 1));
X.setRotation(new AxisAngle4d(1, 0, 0, Math.PI));
hourglass.addComponent("top", pyramid, X);
hourglass.buildBoundingHull(PolyTree.OBB_HULL);
}
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();
}
private static Matrix4d combineTransformation(
Matrix4d matrix, Vector3d translation, Vector3d rotation) {
Matrix4d gM = new Matrix4d(matrix);
Matrix4d m = new Matrix4d();
m.setIdentity();
m.setTranslation(translation);
gM.mul(m);
m.setIdentity();
m.rotZ(rotation.z);
gM.mul(m);
m.setIdentity();
m.rotY(rotation.y);
gM.mul(m);
m.setIdentity();
m.rotX(rotation.x);
gM.mul(m);
return gM;
}