/* (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;
}
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();
}