TestAtomIterator.java

package org.biojava.nbio.structure;

import static org.junit.Assert.*;

import java.io.IOException;
import java.util.NoSuchElementException;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.AtomIterator;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.StructureTools;
import org.junit.Test;

public class TestAtomIterator {
	@Test
	public void test5frf() throws IOException, StructureException {
		// 5frf: 10 models; residues -2-105, binds a ZN; 1615 atoms/model
		Structure s = StructureIO.getStructure("5frf");
		assertEquals("nrModels",10,s.nrModels());
		
		Atom[] allAtomArray = StructureTools.getAllAtomArray(s);
		assertEquals("getAllAtomArray length",16150, allAtomArray.length);
		
		int atoms=0;
		AtomIterator atomIt = new AtomIterator(s);
		while(atomIt.hasNext()) {
			atoms++;
			atomIt.next();
		}
		try {
			atomIt.next();
			fail("No more elements");
		} catch( NoSuchElementException e) {}
		assertEquals("AtomIterator full length",16150, atoms);
		
		atoms=0;
		atomIt = new AtomIterator(s,0);
		while(atomIt.hasNext()) {
			atoms++;
			atomIt.next();
		}
		try {
			atomIt.next();
			fail("No more elements");
		} catch( NoSuchElementException e) {}
		assertEquals("AtomIterator single model",1615, atoms);
	}
}