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

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);
		}
	}
 

/**
 * 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));
}
 

@Override
public void compute(final Vector3d v, final Quaterniondc q,
	final Vector3d vDot)
{
	vDot.set(v);
	vDot.rotate(q);
}
 

@Test
public void testAxisAngle() {
	final Vector3d xAxis = new Vector3d(1, 0, 0);
	final Vector3d in = new Vector3d(xAxis);
	final AxisAngle4d axisAngle = new AxisAngle4d(Math.PI / 2.0, 0, 0, 1);
	final Vector3d expected = xAxis.rotate(new Quaterniond(axisAngle));

	final Vector3d result = ops.linalg().rotate(in, axisAngle);

	assertEquals("Rotation is incorrect", expected, result);
}
 

@Test
public void testMutate() {
	final Vector3d xAxis = new Vector3d(1, 0, 0);
	final Vector3d in = new Vector3d(xAxis);
	final Quaterniond q = new Quaterniond(new AxisAngle4d(Math.PI / 2.0, 0, 0,
		1));
	final Vector3d expected = xAxis.rotate(q);

	final Vector3d result = ops.linalg().rotate1(in, q);

	assertSame("Mutate should operate on the input object", in, result);
	assertEquals("Rotation is incorrect", expected, result);
}
 

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);
		}
	}
 

@Override
public void mutate1(final Vector3d v, final Quaterniondc q) {
	v.rotate(q);
}