BioJava:CookBook:PDB:atoms

From BioJava

How can I access the atoms in a structure?

BioJava provides a flexible data structure for managing protein structural data. The Structure class is the main container.

A Structure has a hierarchy of sub-objects:

Structure
   |
   Model(s)
        |
        Chain(s)
            |
             Group(s)
                 |
                 Atom(s)

Different ways are provided how to access the data contained in a Structure. If you want to directly access an array of Atoms you can use the StructureTools

// get all Calpha atoms in the structure
Atom[] caAtoms = StructureTools.getAtomArray(structure,"CA");

Another possibility is to use one of the iterators to iterate over Atoms or Groups.

public static int getNrAtoms(Structure s){
       
        int nrAtoms = 0;
        
        Iterator iter = new GroupIterator(s);
        
        while ( iter.hasNext()){
            Group g = (Group) iter.next();
            nrAtoms += g.size();
        }
        
        return nrAtoms;
    }

AtomIterator iter = new AtomIterator(structure) ;
        while (iter.hasNext()) {
            Atom atom = (Atom) iter.next() ;
            Calc.rotate(atom,rotationmatrix);
        }

Next: BioJava:CookBook:PDB:atomsCalc - How to do calculations on atoms.