Java Code Examples for org.joml.Vector3d#sub()

The following examples show how to use org.joml.Vector3d#sub() . You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source File: TranslationRotation.java    From OSPREY3 with GNU General Public License v2.0 6 votes vote down vote up 
private void apply() {

		Vector3d pos = new Vector3d();
		Quaterniond qPsi = new Quaterniond().rotationX(dofPsi.value);
		Quaterniond qTheta = new Quaterniond().rotationY(dofTheta.value);
		Quaterniond qPhi = new Quaterniond().rotationZ(dofPhi.value);
		Vector3d t = new Vector3d(dofX.value, dofY.value, dofZ.value);

		// transform each atom
		for (int atomi : atomIndices) {
			originalCoords.get(atomi, pos);
			pos.sub(desc.centroid);
			pos.rotate(qPsi);
			pos.rotate(qTheta);
			pos.rotate(qPhi);
			pos.add(desc.centroid);
			pos.add(t);
			coords.coords.set(atomi, pos);
		}
	}
Example 2
Source File: DihedralAngle.java    From OSPREY3 with GNU General Public License v2.0 6 votes vote down vote up 
/**
 * Measures the dihedral angle in radians, using the usual a,b,c,d atom position convention.
 *
 * WARNING: this implementation overwrites the values of a, c, and d,
 * but it doesn't do any heap allocations.
 */
private static double measureAngleRadians(Vector3d a, Vector3d b, Vector3d c, Vector3d d) {

	// translate so b is at the origin
	a.sub(b);
	c.sub(b);
	d.sub(b);

	// rotate into a coordinate system where:
	//   b->c is along the -z axis
	//   b->a is in the yz plane
	Quaterniond q = new Quaterniond()
		.lookAlong(c, a);
	d.rotate(q);

	return Protractor.normalizeMinusPiToPi(Math.PI/2 - Math.atan2(d.y, d.x));
}
Example 3
Source File: GraphPruning.java    From AnalyzeSkeleton with GNU General Public License v3.0 5 votes vote down vote up 
/**
 * Sets the length of the {@link Edge} to the calibrated euclidean distance
 * between its endpoints.
 *
 * @param e an edge of a graph.
 * @param voxelSize [x, y, z] voxel size in the skeleton image from which the
 *          graph was created.
 */
private static void euclideanDistance(final Edge e,
	final double[] voxelSize)
{
	final Vector3d centre = PointUtils.centroid(e.getV1().getPoints());
	final Vector3d centre2 = PointUtils.centroid(e.getV2().getPoints());
	centre.sub(centre2);
	final double l = length(centre, voxelSize);
	e.setLength(l);
}
Example 4
Source File: VertexUtils.java    From AnalyzeSkeleton with GNU General Public License v3.0 5 votes vote down vote up 
private static Vector3d getOppositeCentroid(final Vertex vertex,
	final Vector3d centroid, final Edge edge)
{
	final List<Point> points = edge.getOppositeVertex(vertex).getPoints();
	final Vector3d endPoint = PointUtils.centroid(points);
	return endPoint.sub(centroid);
}
Example 5
Source File: DihedralAngle.java    From OSPREY3 with GNU General Public License v2.0 4 votes vote down vote up 
public void setAngle(double angleRadians) {

		// TODO: profile and optimize this

		Vector3d temp = new Vector3d();
		Quaterniond qIn = new Quaterniond();
		Quaterniond qZ = new Quaterniond();
		Quaterniond qOut = new Quaterniond();

		Vector3d a = new Vector3d();
		Vector3d b = new Vector3d();
		Vector3d c = new Vector3d();
		Vector3d d = new Vector3d();

		// copy our a,b,c,d from the coords array
		coords.coords.get(ai, a);
		coords.coords.get(bi, b);
		coords.coords.get(ci, c);
		coords.coords.get(di, d);

		// translate so b is at the origin
		a.sub(b);
		c.sub(b);
		d.sub(b);

		// rotate into a coordinate system where:
		//   b->c is along the -z axis
		//   b->a is in the yz plane
		qIn.lookAlong(c, a);
		d.rotate(qIn);

		// rotate about z to set the desired dihedral angle
		qZ.rotationZ(Math.PI/2 - angleRadians - Math.atan2(d.y, d.x));

		// rotate back into the world frame
		qOut.set(qIn)
			.conjugate();

		// transform all the rotated atoms
		for (int i : ri) {
			coords.coords.get(i, temp);
			temp.sub(b);
			temp.rotate(qIn);
			temp.rotate(qZ);
			temp.rotate(qOut);
			temp.add(b);
			coords.coords.set(i, temp);
		}
	}