Examples of javax.vecmath.Point3f

javax.vecmath.Point3f

     */


    int n = centerAndPoints[0].length - 1;
    if (doReport)
      for (int i = 1; i <= n; i++) {
        Point3f aij = centerAndPoints[0][i];
        Point3f bij = centerAndPoints[1][i];
        if (aij instanceof Atom)
          Logger.info(" atom 1 " + ((Atom) aij).getInfo() + "\tatom 2 "
              + ((Atom) bij).getInfo());
        else
          break;
      }


    if (n < 2)
      return q;


    double Sxx = 0, Sxy = 0, Sxz = 0, Syx = 0, Syy = 0, Syz = 0, Szx = 0, Szy = 0, Szz = 0;
    for (int i = n + 1; --i >= 1;) {
      Point3f aij = centerAndPoints[0][i];
      Point3f bij = centerAndPoints[1][i];
      Point3f ptA = new Point3f(aij);
      ptA.sub(centerAndPoints[0][0]);
      Point3f ptB = new Point3f(bij);
      ptB.sub(centerAndPoints[0][1]);
      Sxx += (double) ptA.x * (double) ptB.x;
      Sxy += (double) ptA.x * (double) ptB.y;
      Sxz += (double) ptA.x * (double) ptB.z;
      Syx += (double) ptA.y * (double) ptB.x;
      Syy += (double) ptA.y * (double) ptB.y;

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  public static float getRmsd(Point3f[][] centerAndPoints, Quaternion q) {
    double sum = 0;
    double sum2 = 0;
    int n = centerAndPoints[0].length - 1;
    Point3f ptAnew = new Point3f();
    for (int i = n + 1; --i >= 1;) {
      ptAnew.set(centerAndPoints[0][i]);
      ptAnew.sub(centerAndPoints[0][0]);
      q.transform(ptAnew, ptAnew);
      ptAnew.add(centerAndPoints[1][0]);
      double d = ptAnew.distance(centerAndPoints[1][i]);
      sum += d;
      sum2 += d * d;
    }
    return (float) Math.sqrt((sum2 - sum * sum / n) / (n - 1));
  }

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  }


  public static List transformPoints(List vPts, Matrix4f m4, Point3f center) {
    List v = new ArrayList();
    for (int i = 0; i < vPts.size(); i++) {
      Point3f pt = new Point3f((Point3f)vPts.get(i));
      pt.sub(center);
      m4.transform(pt, pt);
      pt.add(center);
      v.add(pt);
    }
    return v;
  }

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    }
    return Shade3D.rgb((int) x, (int) y, (int) z);
  }


  public final static Point3f colorPointFromInt2(int color) {
    return new Point3f((color >> 16) & 0xFF, (color >> 8) & 0xFF, color & 0xFF);
  }

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    Colix3D.flushShades();
    Sphere3D.flushSphereCache();
  }


  public static Point3f getLightSource() {
    return new Point3f(Shade3D.xLight, Shade3D.yLight, Shade3D.zLight);
  }

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     * UNfortunately, omega is defined for residue 1 (page 294)
     * such that the residue having unusual omega is not the
     * proline itself but the one prior to it.
     * 
     */
    Point3f nitrogen1 = residue1.getNitrogenAtom();
    Point3f alphacarbon1 = residue1.getLeadAtom();
    Point3f carbon1 = residue1.getCarbonylCarbonAtom();
    Point3f nitrogen2 = residue2.getNitrogenAtom();
    Point3f alphacarbon2 = residue2.getLeadAtom();
    Point3f carbon2 = residue2.getCarbonylCarbonAtom();


    residue2.setGroupParameter(Token.phi, Measure.computeTorsion(carbon1,
        nitrogen2, alphacarbon2, carbon2, true));
    residue1.setGroupParameter(Token.psi, Measure.computeTorsion(nitrogen1,
        alphacarbon1, carbon1, nitrogen2, true));

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                                      boolean dsspIgnoreHydrogens) {
    if (polymer == null)
      polymer = this;
    if (!(polymer instanceof AminoPolymer))
      return;
    Point3f pt = new Point3f();
    Vector3f vNH = new Vector3f();
    AminoMonomer source;
    int[][] min1 = (min == null ? new int[2][3] : null);
    for (int i = 1; i < monomerCount; ++i) { //not first N
      if (min == null) {

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  private void checkRasmolHydrogenBond(AminoMonomer source, Polymer polymer,
                                       int indexDonor, Point3f hydrogenPoint,
                                       BitSet bsB, List vHBonds,
                                       int[][] min, boolean checkDistances) {
    Point3f sourceAlphaPoint = source.getLeadAtom();
    Point3f sourceNitrogenPoint = source.getNitrogenAtom();
    Atom nitrogen = source.getNitrogenAtom();
    int[] m;
    for (int i = polymer.monomerCount; --i >= 0;) {
      if (polymer == this && (i == indexDonor || i + 1 == indexDonor 
          /* || i - 1 == indexDonor*/ ))
        continue; 
      // 3mn5 GLY36->ARG37 is an example where we can have i-1 be the donor  
      AminoMonomer target = (AminoMonomer) ((BioPolymer) polymer).monomers[i];
      Atom oxygen = target.getCarbonylOxygenAtom();
      if (oxygen == null || bsB != null && !bsB.get(oxygen.index))
        continue;
      Point3f targetAlphaPoint = target.getLeadAtom();
      float dist2 = sourceAlphaPoint.distanceSquared(targetAlphaPoint);
      if (dist2 >= maxHbondAlphaDistance2)
        continue;
      int energy = calcHbondEnergy(sourceNitrogenPoint, hydrogenPoint, target,
          checkDistances);

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   * @param checkDistances
   * @return               energy in cal/mol or 0 (none)
   */
  private int calcHbondEnergy(Point3f nitrogenPoint, Point3f hydrogenPoint,
                              AminoMonomer target, boolean checkDistances) {
    Point3f targetOxygenPoint = target.getCarbonylOxygenAtom();


    if (targetOxygenPoint == null)
      return 0;
    float distON2 = targetOxygenPoint.distanceSquared(nitrogenPoint);
    if (distON2 < minimumHbondDistance2)
      return 0;


    float distOH2 = targetOxygenPoint.distanceSquared(hydrogenPoint);
    if (distOH2 < minimumHbondDistance2)
      return 0;


    Point3f targetCarbonPoint = target.getCarbonylCarbonAtom();
    float distCH2 = targetCarbonPoint.distanceSquared(hydrogenPoint);
    if (distCH2 < minimumHbondDistance2)
      return 0;


    float distCN2 = targetCarbonPoint.distanceSquared(nitrogenPoint);
    if (distCN2 < minimumHbondDistance2)
      return 0;


    double distOH = Math.sqrt(distOH2);
    double distCH = Math.sqrt(distCH2);

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    //vA = ptP(i+1) - ptP
    //vB = ptP(i-1) - ptP
    int i = monomerIndex;
    if (i == 0 || i >= bioPolymer.monomerCount - 1)
      return null;
    Point3f ptP = bioPolymer.monomers[i].getAtomFromOffsetIndex(P);
    Point3f ptA, ptB;
    ptA = bioPolymer.monomers[i + 1].getAtomFromOffsetIndex(P);
    ptB = bioPolymer.monomers[i - 1].getAtomFromOffsetIndex(P);
    if (ptP == null || ptA == null || ptB == null)
      return null;
    Vector3f vA = new Vector3f();

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