How can I do calculations with Atoms?

The Calc class provides a set of methods that can be used for calculations.

public double getPhi(Group a, Group b)

   throws StructureException  
       if ( ! Calc.isConnected(a,b)){  
           throw new StructureException("can not calc Phi - AminoAcids are not connected!") ;  
       Atom a_C  = a.getAtom("C");  
       Atom b_N  = b.getAtom("N");  
       Atom b_CA = b.getAtom("CA");  
       Atom b_C  = b.getAtom("C");  
       double phi = Calc.torsionAngle(a_C,b_N,b_CA,b_C);  
       return phi ;  

BioJava contains a protein structure superimposition algorithm that is implemented using the BioJava structure API. To learn more about aligning protein structures go to <BioJava:CookBook:PDB:align>

Next: <BioJava:CookBook:PDB:groups> - How to work with Groups (AminoAcids,Nucleotides, Hetatom)