/**
* Generates a simple MultipleAlignment: 3 structures with the same Atoms but incorreclty aligned
* (offset of 1 position) without gaps.
*
* @return MultipleAlignment simple MSTA
* @throws StructureException
*/
private MultipleAlignment simpleMSTA() throws StructureException {
// Generate three identical Atom arrays
List<Atom[]> atomArrays = new ArrayList<Atom[]>(52);
for (int i = 0; i < 3; i++) atomArrays.add(makeDummyCA(52));
// Generate the incorrect alignment (0-1-2,1-2-3,etc)
List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
for (int str = 0; str < 3; str++) {
List<Integer> chain = new ArrayList<Integer>(50);
for (int res = 0; res < 50; res++) chain.add(res + str);
alnRes.add(chain);
}
// MultipleAlignment generation
MultipleAlignment msa = new MultipleAlignmentImpl();
msa.getEnsemble().setAtomArrays(atomArrays);
BlockSet bs = new BlockSetImpl(msa);
Block b = new BlockImpl(bs);
b.setAlignRes(alnRes);
// We want the identity transfromations to maintain the missalignment
Matrix4d ident = new Matrix4d();
ident.setIdentity();
msa.setTransformations(Arrays.asList(ident, ident, ident));
return msa;
}
public Point3d calcCenterOfRotation() {
List<Integer> line = getLongestLayerLine();
// can't determine center of rotation if there are only 2 points
// TODO does this ever happen??
if (line.size() < 3) {
return subunits.getCentroid();
}
Point3d centerOfRotation = new Point3d();
List<Point3d> centers = subunits.getOriginalCenters();
// calculate helix mid points for each set of 3 adjacent subunits
for (int i = 0; i < line.size() - 2; i++) {
Point3d p1 = new Point3d(centers.get(line.get(i)));
Point3d p2 = new Point3d(centers.get(line.get(i + 1)));
Point3d p3 = new Point3d(centers.get(line.get(i + 2)));
transformationMatrix.transform(p1);
transformationMatrix.transform(p2);
transformationMatrix.transform(p3);
centerOfRotation.add(getMidPoint(p1, p2, p3));
}
// average over all midpoints to find best center of rotation
centerOfRotation.scale(1 / (line.size() - 2));
// since helix is aligned along the y-axis, with an origin at y = 0, place the center of
// rotation there
centerOfRotation.y = 0;
// transform center of rotation to the original coordinate frame
reverseTransformationMatrix.transform(centerOfRotation);
// System.out.println("center of rotation: " + centerOfRotation);
return centerOfRotation;
}
/**
* Generates a simple MultipleAlignment: 3 structures with the same Atoms but incorreclty aligned
* with gaps.
*
* @return MultipleAlignment gapped MSTA
* @throws StructureException
*/
private MultipleAlignment gappedMSTA() throws StructureException {
// Generate three identical Atom arrays
List<Atom[]> atomArrays = new ArrayList<Atom[]>(30);
for (int i = 0; i < 3; i++) atomArrays.add(makeDummyCA(30));
// Generate alignment with nulls and some missalignments
List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
List<Integer> chain1 = Arrays.asList(1, 2, 3, 5, 8, 10, 12, 15, 17, 19, 22, null, 24, 27);
List<Integer> chain2 = Arrays.asList(1, null, 3, 6, 9, 11, 12, 15, null, 18, 22, 24, 26, 28);
List<Integer> chain3 = Arrays.asList(1, 2, 4, 7, 9, 10, null, 15, null, 17, 22, 24, 26, 28);
alnRes.add(chain1);
alnRes.add(chain2);
alnRes.add(chain3);
// MultipleAlignment generation
MultipleAlignment msa = new MultipleAlignmentImpl();
msa.getEnsemble().setAtomArrays(atomArrays);
BlockSet bs = new BlockSetImpl(msa);
Block b = new BlockImpl(bs);
b.setAlignRes(alnRes);
// We want the identity transfromations to mantain the missalignments
Matrix4d ident = new Matrix4d();
ident.setIdentity();
msa.setTransformations(Arrays.asList(ident, ident, ident));
return msa;
}
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;
}
private static Matrix4d flipZ() {
Matrix4d rot = new Matrix4d();
rot.m00 = -1;
rot.m11 = -1;
rot.m22 = 1;
rot.m33 = 1;
return rot;
}
/* (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;
}
/*
* 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);
}
}
/**
* Calculates the min and max boundaries of the structure after it has been transformed into its
* canonical orientation.
*/
private void calcBoundaries() {
minBoundary.x = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.y = Double.MAX_VALUE;
maxBoundary.x = Double.MIN_VALUE;
minBoundary.z = Double.MAX_VALUE;
maxBoundary.z = Double.MIN_VALUE;
xzRadiusMax = Double.MIN_VALUE;
Point3d probe = new Point3d();
for (Point3d[] list : subunits.getTraces()) {
for (Point3d p : list) {
probe.set(p);
transformationMatrix.transform(probe);
minBoundary.x = Math.min(minBoundary.x, probe.x);
maxBoundary.x = Math.max(maxBoundary.x, probe.x);
minBoundary.y = Math.min(minBoundary.y, probe.y);
maxBoundary.y = Math.max(maxBoundary.y, probe.y);
minBoundary.z = Math.min(minBoundary.z, probe.z);
maxBoundary.z = Math.max(maxBoundary.z, probe.z);
xzRadiusMax = Math.max(xzRadiusMax, Math.sqrt(probe.x * probe.x + probe.z * probe.z));
}
}
// System.out.println("MinBoundary: " + minBoundary);
// System.out.println("MaxBoundary: " + maxBoundary);
// System.out.println("zxRadius: " + xzRadiusMax);
}
/* (non-Javadoc)
* @see org.biojava.nbio.structure.quaternary.core.AxisAligner#getRotationMatrix()
*/
@Override
public Matrix3d getRotationMatrix() {
run();
Matrix3d m = new Matrix3d();
transformationMatrix.getRotationScale(m);
return m;
}
private Point3d[] transformPoints(final Matrix4d X, final Point3d[] pnts) {
final Point3d[] newpnts = new Point3d[pnts.length];
for (int i = 0; i < newpnts.length; i++) {
newpnts[i] = new Point3d(pnts[i]);
X.transform(newpnts[i]);
}
return newpnts;
}
public static void transformMesh(final TopLoc_Location loc, double[] src, float[] dst) {
double[] matrix = new double[16];
loc.transformation().getValues(matrix);
Matrix4d m4d = new Matrix4d(matrix);
Point3d p3d = new Point3d();
for (int i = 0; i < src.length; i += 3) {
p3d.x = src[i + 0];
p3d.y = src[i + 1];
p3d.z = src[i + 2];
m4d.transform(p3d);
dst[i + 0] = (float) p3d.x;
dst[i + 1] = (float) p3d.y;
dst[i + 2] = (float) p3d.z;
}
}
private static void writeMatrix(Matrix4d matrix, JsonGenerator jg) {
jg.writeStartArray("matrix");
for (int i = 0; i < 4; i++) {
for (int j = 0; j < 4; j++) {
jg.write(matrix.getElement(i, j));
}
}
jg.writeEnd();
}
public Matrix44 calculateTransformation(javax.vecmath.Matrix4d m, ReferenceFrame asSeenBy) {
ReferenceFrame vehicle = (ReferenceFrame) getParent();
if (asSeenBy == null) {
asSeenBy = vehicle;
}
if (asSeenBy == vehicle) {
return new Matrix44(m);
} else {
javax.vecmath.Matrix4d vehicleInverse;
if (vehicle != null) {
vehicleInverse = vehicle.getInverseAbsoluteTransformation();
} else {
vehicleInverse = new javax.vecmath.Matrix4d();
vehicleInverse.setIdentity();
}
return Matrix44.multiply(
m, Matrix44.multiply(asSeenBy.getAbsoluteTransformation(), vehicleInverse));
}
}
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();
}
@Override
public javax.vecmath.Matrix4d getInverseAbsoluteTransformation() {
synchronized (m_absoluteTransformationLock) {
if (m_inverseAbsoluteTransformation == null) {
m_inverseAbsoluteTransformation = getAbsoluteTransformation();
try {
m_inverseAbsoluteTransformation.invert();
} catch (javax.vecmath.SingularMatrixException sme) {
System.err.println("cannot invert: " + m_inverseAbsoluteTransformation);
throw sme;
}
}
return new javax.vecmath.Matrix4d(m_inverseAbsoluteTransformation);
}
}
private double[] getSubunitZDepth() {
int n = subunits.getSubunitCount();
double[] depth = new double[n];
Point3d probe = new Point3d();
// transform subunit centers into z-aligned position and calculate
// z-coordinates (depth) along the z-axis.
for (int i = 0; i < n; i++) {
Point3d p = subunits.getCenters().get(i);
probe.set(p);
transformationMatrix.transform(probe);
depth[i] = probe.z;
}
return depth;
}
/* (non-Javadoc)
* @see org.biojava.nbio.structure.quaternary.core.AxisAligner#getGeometricCenter()
*/
@Override
public Point3d getGeometricCenter() {
run();
Point3d geometricCenter = new Point3d();
Vector3d translation = new Vector3d();
// reverseTransformationMatrix.get(translation);
// TODO does this apply to the helic case?
// calculate adjustment around z-axis and transform adjustment to
// original coordinate frame with the reverse transformation
// Vector3d corr = new Vector3d(0,minBoundary.y+getDimension().y, 0);
// reverseTransformationMatrix.transform(corr);
// geometricCenter.set(corr);
reverseTransformationMatrix.transform(translation);
geometricCenter.add(translation);
return geometricCenter;
}
@Override
public void prologue(double t) {
beginEqualsEnd = false;
done = false;
subject = WalkToAnimation.this.subject.getTransformableValue();
m_asSeenBy = asSeenBy.getReferenceFrameValue();
edu.cmu.cs.stage3.math.Matrix44 asSeenByTrans =
m_asSeenBy.getTransformation(subject.getWorld());
((edu.cmu.cs.stage3.alice.core.Transformable) m_asSeenBy).standUpRightNow(subject.getWorld());
m_transformationBegin = subject.getTransformation(m_asSeenBy);
if (m_asSeenBy == null) {
throw new edu.cmu.cs.stage3.alice.core.SimulationPropertyException(
subject.name.getStringValue() + " needs something or someone to walk to.",
null,
asSeenBy);
}
if (subject == m_asSeenBy) {
throw new edu.cmu.cs.stage3.alice.core.SimulationPropertyException(
subject.name.getStringValue() + " can't walk to " + subject.name.getStringValue() + ".",
getCurrentStack(),
asSeenBy);
}
if (subject.isAncestorOf(m_asSeenBy)) {
throw new edu.cmu.cs.stage3.alice.core.SimulationPropertyException(
subject.name.getStringValue() + " can't walk to a part of itself",
getCurrentStack(),
asSeenBy);
}
// find end transformation
javax.vecmath.Vector3d posAbs = getPositionEnd();
javax.vecmath.Vector3d curPos = subject.getPosition();
subject.setPositionRightNow(posAbs, m_asSeenBy);
// javax.vecmath.Matrix3d paMatrix =
// subject.calculatePointAt(m_asSeenBy, null, new
// javax.vecmath.Vector3d(0,1,0), null, true);
javax.vecmath.Matrix3d paMatrix =
subject.calculatePointAt(
m_asSeenBy, null, new javax.vecmath.Vector3d(0, 1, 0), m_asSeenBy, true);
subject.setPositionRightNow(curPos);
javax.vecmath.Matrix4d pov = asSeenBy.getReferenceFrameValue().getPointOfView();
pov.set(paMatrix);
pov.setRow(3, posAbs.x, posAbs.y, posAbs.z, 1.0);
m_transformationEnd = new edu.cmu.cs.stage3.math.Matrix44(pov);
double dx = m_transformationBegin.m30 - m_transformationEnd.m30;
double dy = m_transformationBegin.m31 - m_transformationEnd.m31;
double dz = m_transformationBegin.m32 - m_transformationEnd.m32;
double distance = Math.sqrt(dx * dx + dy * dy + dz * dz);
double s = distance;
m_xHermite =
new edu.cmu.cs.stage3.math.HermiteCubic(
m_transformationBegin.m30,
m_transformationEnd.m30,
m_transformationBegin.m20 * s,
m_transformationEnd.m20 * s);
m_yHermite =
new edu.cmu.cs.stage3.math.HermiteCubic(
m_transformationBegin.m31,
m_transformationEnd.m31,
m_transformationBegin.m21 * s,
m_transformationEnd.m21 * s);
m_zHermite =
new edu.cmu.cs.stage3.math.HermiteCubic(
m_transformationBegin.m32,
m_transformationEnd.m32,
m_transformationBegin.m22 * s,
m_transformationEnd.m22 * s);
super.prologue(t);
getActualStepLength();
((edu.cmu.cs.stage3.alice.core.Transformable) m_asSeenBy)
.setTransformationRightNow(asSeenByTrans, subject.getWorld());
}
public Transformable() {
m_localTransformation = new javax.vecmath.Matrix4d();
m_localTransformation.setIdentity();
}
private static Element matrix4d2Transform(Matrix4d matrix4d) {
Element transform = new BaseElement("Transform");
Element m0 = new BaseElement("m0");
m0.addText(
matrix4d.getM00()
+ " "
+ matrix4d.getM01()
+ " "
+ matrix4d.getM02()
+ " "
+ matrix4d.getM03()
+ ".");
transform.add(m0);
Element m1 = new BaseElement("m1");
m1.addText(
matrix4d.getM10()
+ " "
+ matrix4d.getM11()
+ " "
+ matrix4d.getM12()
+ " "
+ matrix4d.getM13()
+ ".");
transform.add(m1);
Element m2 = new BaseElement("m2");
m2.addText(
matrix4d.getM20()
+ " "
+ matrix4d.getM21()
+ " "
+ matrix4d.getM22()
+ " "
+ matrix4d.getM23()
+ ".");
transform.add(m2);
Element m3 = new BaseElement("m3");
m3.addText(
matrix4d.getM30()
+ " "
+ matrix4d.getM31()
+ " "
+ matrix4d.getM32()
+ " "
+ matrix4d.getM33()
+ ".");
transform.add(m3);
return transform;
}
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;
}
/**
* 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);
}
private void calcTransformation() {
calcTransformationBySymmetryAxes();
// make sure this value is zero. On Linux this value is 0.
transformationMatrix.setElement(3, 3, 1.0);
}
/**
* 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;
}
private void calcReverseTransformation() {
reverseTransformationMatrix.invert(transformationMatrix);
}