Package org.jmol.modelset

Examples of org.jmol.modelset.BondIterator.nextIndex()

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      bsSizeSet = new BitSet();
    BondIterator iter = (selectedBonds != null ? modelSet.getBondIterator(selectedBonds)
        : modelSet.getBondIterator(myMask, bsSelected));
    short mad = (short) size;
    while (iter.hasNext()) {
      bsSizeSet.set(iter.nextIndex());
      iter.next().setMad(mad);
    }
  }

  public void setProperty(String propertyName, Object value, BitSet bs) {
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        bsOrderSet = new BitSet();
      int order = ((Integer) value).shortValue();
      BondIterator iter = (selectedBonds != null ? modelSet.getBondIterator(selectedBonds)
          : modelSet.getBondIterator(JmolEdge.BOND_ORDER_ANY, bs));
      while (iter.hasNext()) {
        bsOrderSet.set(iter.nextIndex());
        iter.next().setOrder(order);
      }
      return;
    }
    if ("color" == propertyName) {
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        //only for hydrogen bonds
        boolean isEnergy = (pid == JmolConstants.PALETTE_ENERGY);
        BondIterator iter = (selectedBonds != null ? modelSet.getBondIterator(selectedBonds)
            : modelSet.getBondIterator(myMask, bs));
        while (iter.hasNext()) {
          bsColixSet.set(iter.nextIndex());
          Bond bond = iter.next();
          if (isEnergy) {
              bond.setColix(setColix(colix, pid, bond));
              bond.setPaletteID(pid);
          } else {
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      if (colix == Graphics3D.USE_PALETTE && pid != JmolConstants.PALETTE_CPK)
        return; //palettes not implemented for bonds
      BondIterator iter = (selectedBonds != null ? modelSet.getBondIterator(selectedBonds)
          : modelSet.getBondIterator(myMask, bs));
      while (iter.hasNext()) {
        int iBond = iter.nextIndex();
        Bond bond = iter.next();
        bond.setColix(colix);
        bsColixSet.set(iBond, (colix != Graphics3D.INHERIT_ALL
            && colix != Graphics3D.USE_PALETTE));
      }
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        bsColixSet = new BitSet();
      boolean isTranslucent = (((String) value).equals("translucent"));
      BondIterator iter = (selectedBonds != null ? modelSet.getBondIterator(selectedBonds)
          : modelSet.getBondIterator(myMask, bs));
      while (iter.hasNext()) {
        bsColixSet.set(iter.nextIndex());
        iter.next().setTranslucent(isTranslucent, translucentLevel);
      }
      return;
    }
   
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