private Matrix4d reorientHelix(int index) {
Matrix4d matrix = new Matrix4d();
matrix.setIdentity();
matrix.setRotation(new AxisAngle4d(1, 0, 0, Math.PI / 2 * (index + 1)));
matrix.mul(transformationMatrix);
return matrix;
}
/*
* Modifies the rotation part of the transformation axis for
* a Cn symmetric complex, so that the narrower end faces the
* viewer, and the wider end faces away from the viewer. Example: 3LSV
*/
private void calcZDirection() {
calcBoundaries();
// if the longer part of the structure faces towards the back (-z direction),
// rotate around y-axis so the longer part faces the viewer (+z direction)
if (Math.abs(minBoundary.z) > Math.abs(maxBoundary.z)) {
Matrix4d rot = flipY();
rot.mul(transformationMatrix);
transformationMatrix.set(rot);
}
}
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();
}
/**
* Returns a transformation matrix that rotates refPoints to match coordPoints
*
* @param refPoints the points to be aligned
* @param referenceVectors
* @return
*/
private Matrix4d alignAxes(Vector3d[] axisVectors, Vector3d[] referenceVectors) {
Matrix4d m1 = new Matrix4d();
AxisAngle4d a = new AxisAngle4d();
Vector3d axis = new Vector3d();
// calculate rotation matrix to rotate refPoints[0] into coordPoints[0]
Vector3d v1 = new Vector3d(axisVectors[0]);
Vector3d v2 = new Vector3d(referenceVectors[0]);
double dot = v1.dot(v2);
if (Math.abs(dot) < 0.999) {
axis.cross(v1, v2);
axis.normalize();
a.set(axis, v1.angle(v2));
m1.set(a);
// make sure matrix element m33 is 1.0. It's 0 on Linux.
m1.setElement(3, 3, 1.0);
} else if (dot > 0) {
// parallel axis, nothing to do -> identity matrix
m1.setIdentity();
} else if (dot < 0) {
// anti-parallel axis, flip around x-axis
m1.set(flipX());
}
// apply transformation matrix to all refPoints
m1.transform(axisVectors[0]);
m1.transform(axisVectors[1]);
// calculate rotation matrix to rotate refPoints[1] into coordPoints[1]
v1 = new Vector3d(axisVectors[1]);
v2 = new Vector3d(referenceVectors[1]);
Matrix4d m2 = new Matrix4d();
dot = v1.dot(v2);
if (Math.abs(dot) < 0.999) {
axis.cross(v1, v2);
axis.normalize();
a.set(axis, v1.angle(v2));
m2.set(a);
// make sure matrix element m33 is 1.0. It's 0 on Linux.
m2.setElement(3, 3, 1.0);
} else if (dot > 0) {
// parallel axis, nothing to do -> identity matrix
m2.setIdentity();
} else if (dot < 0) {
// anti-parallel axis, flip around z-axis
m2.set(flipZ());
}
// apply transformation matrix to all refPoints
m2.transform(axisVectors[0]);
m2.transform(axisVectors[1]);
// combine the two rotation matrices
m2.mul(m1);
// the RMSD should be close to zero
Point3d[] axes = new Point3d[2];
axes[0] = new Point3d(axisVectors[0]);
axes[1] = new Point3d(axisVectors[1]);
Point3d[] ref = new Point3d[2];
ref[0] = new Point3d(referenceVectors[0]);
ref[1] = new Point3d(referenceVectors[1]);
if (SuperPosition.rmsd(axes, ref) > 0.1) {
System.out.println(
"Warning: AxisTransformation: axes alignment is off. RMSD: "
+ SuperPosition.rmsd(axes, ref));
}
return m2;
}
/**
* Computes the new transform for this interpolator for a given alpha value.
*
* @param alphaValue alpha value between 0.0 and 1.0
* @param transform object that receives the computed transform for the specified alpha value
* @since Java 3D 1.3
*/
public void computeTransform(float alphaValue, Transform3D transform) {
// compute the current value of u from alpha and the
// determine lower and upper knot points
computePathInterpolation(alphaValue);
// Determine the segment within which we will be interpolating
currentSegmentIndex = this.lowerKnot - 1;
// if we are at the start of the curve
if (currentSegmentIndex == 0 && currentU == 0f) {
iHeading = keyFrames[1].heading;
iPitch = keyFrames[1].pitch;
iBank = keyFrames[1].bank;
iPos.set(keyFrames[1].position);
iScale.set(keyFrames[1].scale);
// if we are at the end of the curve
} else if (currentSegmentIndex == (numSegments - 1) && currentU == 1.0) {
iHeading = keyFrames[upperKnot].heading;
iPitch = keyFrames[upperKnot].pitch;
iBank = keyFrames[upperKnot].bank;
iPos.set(keyFrames[upperKnot].position);
iScale.set(keyFrames[upperKnot].scale);
// if we are somewhere in between the curve
} else {
// Get a reference to the current spline segment i.e. the
// one bounded by lowerKnot and upperKnot
currentSegment = cubicSplineCurve.getSegment(currentSegmentIndex);
// interpolate quaternions
iHeading = currentSegment.getInterpolatedHeading(currentU);
iPitch = currentSegment.getInterpolatedPitch(currentU);
iBank = currentSegment.getInterpolatedBank(currentU);
// interpolate position
currentSegment.getInterpolatedPositionVector(currentU, iPos);
// interpolate position
currentSegment.getInterpolatedScale(currentU, iScale);
// System.out.println("Pos :" + iPos);
}
// Modification by ReubenDB
if (colorRampingInterpolate == true) {
float[] curPos = new float[3];
iPos.get(curPos);
myColorRamp.getColor(curPos[1], histColor);
// System.out.println("SETING COLOR:" + histColor + " CurPos: " + curPos[0] + ", " + curPos[1]
// + ", " + curPos[2]);
objectCA.setColor(histColor);
// System.out.println("CurrentAlpha = " + myAlpha.value());
}
if (timeDisplayInterpolate == true) {
myTimeDisplay.updateDisplayFromAlpha(myAlpha.value());
// System.out.println(myAlpha.value());
}
// Generate a transformation matrix in tMat using interpolated
// heading, pitch and bank
pitchMat.setIdentity();
pitchMat.rotX(-iPitch);
bankMat.setIdentity();
bankMat.rotZ(iBank);
tMat.setIdentity();
tMat.rotY(-iHeading);
tMat.mul(pitchMat);
tMat.mul(bankMat);
// TODO: Vijay - Handle Non-Uniform scale
// Currently this interpolator does not handle non uniform scale
// We cheat by just taking the x scale component
// Scale the transformation matrix
sMat.set((double) iScale.x);
tMat.mul(sMat);
// Set the translation components.
tMat.m03 = iPos.x;
tMat.m13 = iPos.y;
tMat.m23 = iPos.z;
rotation.set(tMat);
// construct a Transform3D from: axis * rotation * axisInverse
transform.mul(axis, rotation);
transform.mul(transform, axisInverse);
}
