From BioJava

Align two protein structures

This source code is run in the example that calculates the structure alignment of Myoglobin and Hemoglobin. See BioJava:CookBook:PDB:align for more information on how to calculate protein structure alignments.

Structure s1 = getStructureFromFile(fileName1);
Structure s2 = getStructureFromFile(fileName2);
			
StructurePairAligner aligner = new StructurePairAligner();
 
aligner.align(s1, s2);