looping over the whole data model

andreasprlic · andreasprlic · commit e3b8dd65538d · 2013-09-18T22:01:27.000-07:00
diff --git a/structure/structure-data-model.md b/structure/structure-data-model.md
@@ -47,10 +47,47 @@ If you want to directly access an array of [Atoms](http://www.biojava.org/docs/a
 
 Alternatively you can access atoms also by their parent-group.
 
-## Loop over all the data
+## Compounds (Entities) and Chains
 
 //TODO
 
+## Loop over all the data
+
+Here an example that loops over the whole data model and prints out the HEM groups of hemoglobin:
+
+<pre>
+			Structure structure = StructureIO.getStructure("4hhb");			
+
+			System.out.println(" # of compounds (entities) " + structure.getCompounds().size());
+
+			for ( Compound entity: structure.getCompounds()) {
+				System.out.println("   " + entity);
+			}
+			List<Chain> chains = structure.getChains();
+
+			System.out.println(" # chains: " + chains.size());
+
+			for (Chain c : chains) {
+				System.out.println("   Chain: " + c.getChainID());
+				for (Group g: c.getAtomGroups()){
+
+					if ( g.getPDBName().equalsIgnoreCase("HEM")) {
+
+						System.out.println(g);
+
+						for (Atom a: g.getAtoms()) {
+
+							System.out.println(a);
+
+						}
+
+					}
+
+				}
+			}
+</pre>
+
+
 ## Working with groups
 
 The [Group](http://www.biojava.org/docs/api/org/biojava/bio/structure/Group.html) interface defines all methods common to a group of atoms. There are 3 types of Groups:
