Package org.jmol.atomdata

Examples of org.jmol.atomdata.RadiusData

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  public Point3f[] calculateSurface(BitSet bsSelected, float envelopeRadius) {
    if (envelopeRadius < 0)
      envelopeRadius = EnvelopeCalculation.SURFACE_DISTANCE_FOR_CALCULATION;
    EnvelopeCalculation ec = new EnvelopeCalculation(viewer, atomCount, null, viewer.getTestFlag2());
    ec.calculate(new RadiusData(envelopeRadius, RadiusData.TYPE_ABSOLUTE, 0),
        Float.MAX_VALUE,
        bsSelected, BitSetUtil.copyInvert(bsSelected, atomCount),
        false, false, false, true);
    Point3f[] points = ec.getPoints();
    surfaceDistanceMax = 0;
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      }
      atomData.atomicNumber[i] = atom.getElementNumber();
      atomData.lastModelIndex = atom.modelIndex;
      if (includeRadii) {
        float r = 0;
        RadiusData rd = atomData.radiusData;
        switch (rd.type) {
        case RadiusData.TYPE_ABSOLUTE:
          r = rd.value;
          break;
        case RadiusData.TYPE_FACTOR:
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  protected void setSize(int size, BitSet bsSelected) {
    if (size == 0)
      setSize(null, bsSelected);
    else
      setSize(new RadiusData(size, RadiusData.TYPE_SCREEN, 0), bsSelected);
  }
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  private Point3f[] currentPoints;
 
  public Point3f[] getPoints() {
    if (dotsConvexMaps == null) {
      calculate(new RadiusData(SURFACE_DISTANCE_FOR_CALCULATION, RadiusData.TYPE_ABSOLUTE, 0),
          Float.MAX_VALUE, bsMySelected, null, false, false, false, false);
    }
    if (currentPoints != null)
      return currentPoints;
    int nPoints = 0;
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Related Classes of org.jmol.atomdata.RadiusData

  • org.jmol.geodesic.EnvelopeCalculation
  • org.jmol.jvxl.readers.AtomDataReader
  • org.jmol.modelset.AtomCollection
  • org.jmol.modelset.ModelLoader
  • org.jmol.modelset.ModelSet
  • org.jmol.script.ScriptEvaluator
  • org.jmol.shape.AtomShape
  • org.jmol.shapespecial.Dots
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