BioJava utilizes the Chem. Comp. Dictionary to achieve a chemically correct representation of each group. To make it clear how this can work, let's take a look at how [Selenomethionine](http://en.wikipedia.org/wiki/Selenomethionine) and water is dealt with:

Structure structure = StructureIO.getStructure("1A62");

for (Chain chain : structure.getChains()){

}

}

}

This will give this output:

You can enable the first behaviour by doing using the [FileParsingParameters](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/FileParsingParameters.html) class:

AtomCache cache = new AtomCache();

// by default all files are stored at a temporary location.

StructureIO.setAtomCache(cache);

Structure structure = StructureIO.getStructure(...);

If you want to enable the second behaviour (slow loading of all chem comps at startup, but no further small delays later on) you can use the same code but change the behaviour by switching the [ChemCompProvider](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/ChemCompProvider.html) implementation in the [ChemCompGroupFactory](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/ChemCompGroupFactory.html)

ChemCompGroupFactory.setChemCompProvider(new AllChemCompProvider());