Examples of BondIterator

      bsOrderSet.or(bsSelected);
      return;
    }
    if (bsSizeSet == null)
      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);
    }
  }

Examples of org.jmol.modelset.BondIterator


    if ("bondOrder" == propertyName) {
      if (bsOrderSet == null)
        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) {
      if (bsColixSet == null)
        bsColixSet = new BitSet();
      short colix = Graphics3D.getColix(value);
      byte pid = JmolConstants.pidOf(value);
      if (pid == JmolConstants.PALETTE_TYPE || pid == JmolConstants.PALETTE_ENERGY) {
        //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 {
            bond.setColix(Graphics3D.getColix(JmolConstants.getArgbHbondType(bond.getOrder())));
          }
        }
        return;
      }
      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));
      }
      return;
    }
    if ("translucency" == propertyName) {
      if (bsColixSet == null)
        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;
    }
    
    if ("deleteModelAtoms" == propertyName) {

Examples of org.jmol.modelset.BondIterator

  }


  private void setColixDipole(short colix, int bondTypeMask, BitSet bs) {
    if (colix == Graphics3D.USE_PALETTE)
      return; // not implemented
    BondIterator iter = modelSet.getBondIterator(bondTypeMask, bs);
    while (iter.hasNext()) {
      Dipole d = findBondDipole(iter.next());
      if (d != null)
        d.colix = colix;
    }
  }