예제 #1
0
 private Vector3d orthogonalize(Vector3d vector1, Vector3d vector2) {
   double dot = vector1.dot(vector2);
   Vector3d ref = new Vector3d(vector2);
   //		System.out.println("p.r: " + dot);
   //		System.out.println("Orig refVector: " + referenceVector);
   if (dot < 0) {
     vector2.negate();
   }
   if (Math.abs(dot) < 0.00001) {
     System.out.println("HelixAxisAligner: Warning: reference axis parallel");
   }
   vector2.cross(vector1, vector2);
   //		System.out.println("Intermed. refVector: " + vector2);
   vector2.normalize();
   //		referenceVector.cross(referenceVector, principalRotationVector);
   vector2.cross(vector1, vector2);
   vector2.normalize();
   if (ref.dot(vector2) < 0) {
     vector2.negate();
   }
   //		System.out.println("Mod. refVector: " + vector2);
   return vector2;
 }
예제 #2
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;
  }