Current/Proposed SMILES parsing

current.java

IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
SmilesParser       parser  = new SmilesParser(builder);

IAtomContainer sodiumChloride = parser.parseSmiles("[Na+].[Cl-]");
IAtomContainer adenine        = parser.parseSmiles("n1c(c2c(nc1)ncn2)N");

// if you want the separate parts
// import static org.openscience.cdk.graph.ConnectivityChecker.partitionIntoMolecules;
IAtomContainerSet  sodiumChlorideSet = partitionIntoMolecules(sodiumChloride);
IAtomContainerSet  adenineSet        = partitionIntoMolecules(adenine);

proposed.java

IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
SmilesParser       parser  = new SmilesParser(builder);

IAtomContainerSet  sodiumChlorideSet = builder.newInstance(IAtomContainerSet.class);
IAtomContainerSet  adenineSet        = builder.newInstance(IAtomContainerSet.class);

sodiumChlorideSet.addAtomContainer(parser.parseSmiles("[Na+].[Cl-]"));
while (parser.hasMoreMolecules()){
    sodiumChlorideSet.addAtomContainer(parser.getNextMolecule());
}
adenineSet.addAtomContainer(parser.parseSmiles("n1c(c2c(nc1)ncn2)N"));
while (parser.hasMoreMolecules()){
    adenineSet.addAtomContainer(parser.getNextMolecule());
}

// merge sets into single atom containers
IAtomContainer sodimChloride = builder.newInstance(IAtomContainer.class);
IAtomContainer adenin         = builder.newInstance(IAtomContainer.class);

for(IAtomContainer part : sodiumChlorideSet.atomContainers()) {
    sodimChloride.add(part);
}
for(IAtomContainer part : adenineSet.atomContainers()) {
   adenin.add(part);
}