Different ways are provided how to access the data contained in a [Structure](http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html).

If you want to directly access an array of [Atoms](http://www.biojava.org/docs/api/org/biojava/bio/structure/Atom.html) you can use the utility class called [StructureTools](http://www.biojava.org/docs/api/org/biojava/bio/structure/StructureTools.html)

// get all C-alpha atoms in the structure

Atom[] caAtoms = StructureTools.getAtomCAArray(structure);

Alternatively you can access atoms also by their parent-group.

Here an example that loops over the whole data model and prints out the HEM groups of hemoglobin:

Structure structure = StructureIO.getStructure("4hhb");

List<Chain> chains = structure.getChains();

}

}

}

In order to get all amino acids that have been observed in a PDB chain, you can use the following utility method:

Chain chain = s.getChainByPDB("A");

List<Group> groups = chain.getAtomGroups("amino");

for (Group group : groups) {

// do something amino acid specific, e.g. print the secondary structure assignment

System.out.println(aa + " " + aa.getSecStruc());

}

In a similar way you can access all nucleotide groups by

chain.getAtomGroups("nucleotide");

The Hetatom groups are access in a similar fashion:

chain.getAtomGroups("hetatm");

Since all 3 types of groups are implementing the Group interface, you can also iterate over all groups and check for the instance type:

List<Group> allgroups = chain.getAtomGroups();

for (Group group : groups) {

if ( group instanceof AminoAcid) {

AminoAcid aa = (AminoAcid) group;

System.out.println(aa.getSecStruc());

}

}

built up out of four chains.

This prints all the compounds/entities in a structure

Structure structure = StructureIO.getStructure("4hhb");

System.out.println(structure);

for ( Compound entity: structure.getCompounds()) {

System.out.println(" " + entity);

}