Examples of IAtom

    IAtomContainer removed = selected.getBuilder().newInstance(IAtomContainer.class);
    if(rGroupHandler!=null && !rGroupHandler.checkRGroupOkayForDelete(selected, this))
      return removed;
    
    for (int i = 0; i < selected.getAtomCount(); i++) {
      IAtom atom = selected.getAtom(i);
      removed.addAtom(atom);
      Iterator<IBond> it = ChemModelManipulator.getRelevantAtomContainer(
          chemModel, atom).getConnectedBondsList(atom).iterator();
      IAtomContainer ac = selected.getBuilder().newInstance(IAtomContainer.class);
      while (it.hasNext()) {

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Examples of org.openscience.cdk.interfaces.IAtom