Examples of javax.vecmath.Vector3f.normalize()

javax.vecmath.Vector3f.normalize()

     * 
     */
    Vector3f ecc = new Vector3f(info.x, info.y, info.z);
    float c = (scale > 0 ? scale : info.w < 0 ? 1f : ecc.length());
    float fab_c = Math.abs(info.w);
    ecc.normalize();
    Vector3f z = new Vector3f(0, 0, 1);
    ecc.add(z);
    ecc.normalize();
    if (Float.isNaN(ecc.x)) // was exactly {0 0 -1} -- just rotate about x
      ecc.set(1, 0, 0);

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      return;
    int nx = voxelCounts[0];
    int ny = voxelCounts[1];
    int nz = voxelCounts[2];
    Vector3f normal = new Vector3f(plane.x, plane.y, plane.z);
    normal.normalize();
    float f = 1f;
    for (int x = 0; x < nx; x++)
      for (int y = 0; y < ny; y++)
        for (int z = 0; z < nz; z++) {
          float value = voxelData[x][y][z] - cutoff;

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        vA.cross(vB, vC);
    }
    Vector3f vBprime = new Vector3f();
    vBprime.cross(vC, vA);
    vA.normalize();
    vBprime.normalize();
    vC.normalize();
    Matrix3f mat = new Matrix3f();
    mat.setColumn(0, vA);
    mat.setColumn(1, vBprime);
    mat.setColumn(2, vC);

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  private static Vector3f getRawNormal(Quaternion q) {
    Vector3f v = new Vector3f(q.q1, q.q2, q.q3);
    if (v.length() == 0)
      return new Vector3f(0, 0, 1);
    v.normalize();
    return v;
  }


  /**
   *

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      offsetVertices[i] = new Point3f(vertices[i]);
    Vector3f normal = null;
    float val = 0;
    if (scale3d != 0 && vertexValues != null && thePlane != null) {
        normal = new Vector3f(thePlane.x, thePlane.y, thePlane.z);
        normal.normalize();
        normal.scale(scale3d);
    }
    for (int i = 0; i < vertexCount; i++) {
      if (vertexValues != null && Float.isNaN(val = vertexValues[i]))
        continue;

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      return;
    matrixRotate = new Matrix3f();
    Vector3f v = new Vector3f();
    // rows in Sygress/CAChe and Spartan become columns here
    v.set(x1, y1, z1);
    v.normalize();
    matrixRotate.setColumn(0, v);
    v.set(x2, y2, z2);
    v.normalize();
    matrixRotate.setColumn(1, v);
    v.set(x3, y3, z3);

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    // rows in Sygress/CAChe and Spartan become columns here
    v.set(x1, y1, z1);
    v.normalize();
    matrixRotate.setColumn(0, v);
    v.set(x2, y2, z2);
    v.normalize();
    matrixRotate.setColumn(1, v);
    v.set(x3, y3, z3);
    v.normalize();
    matrixRotate.setColumn(2, v);
    atomSetCollection.setAtomSetCollectionAuxiliaryInfo(

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    matrixRotate.setColumn(0, v);
    v.set(x2, y2, z2);
    v.normalize();
    matrixRotate.setColumn(1, v);
    v.set(x3, y3, z3);
    v.normalize();
    matrixRotate.setColumn(2, v);
    atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
        "defaultOrientationMatrix", new Matrix3f(matrixRotate));
    // first two matrix column vectors define quaternion X and XY plane
    Quaternion q = new Quaternion(matrixRotate);

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      */
      vNH.sub(nitrogenPoint, getLeadAtom());
      vNH.normalize();
      Vector3f v = new Vector3f();
      v.sub(nitrogenPoint, prev.getCarbonylCarbonAtom());
      v.normalize();
      vNH.add(v);
    } else {
      // Rasmol def -- just use C=O vector, so this does not account for cis-amino acids
      // but I guess if those are just proline...
      Point3f oxygen = prev.getCarbonylOxygenAtom();

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    if (nAttached >= 3) {
      if (x.angle(v[1]) < almost180)
        vTemp.cross(x, v[1]);
      else
        vTemp.cross(x, v[2]);
      vTemp.normalize();
      Vector3f vTemp2 = new Vector3f();
      if (v[1].angle(v[2]) < almost180)
        vTemp2.cross(v[1], v[2]);
      else
        vTemp2.cross(x, v[2]);

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