gistfile1.js

var file = "/Sample Data/SDF/borken.sdf";
iterator = cdk.createMoleculeIterator(file);
var i = 0;
js.print("\n");
var numberOff = cdk.numberOfEntriesInSDF(file);
var molecules = cdk.createMoleculeList();

while ( iterator.hasNext() ) {
	m = iterator.next();
	i++;
	js.print("Read molecule" + i + " " + m.toString() + "\n");
	molecules.add(m);
}
js.print("Managed to parse " + i + " molecules out of " + numberOff 
         + " found by cdk.numberOfEntriesInSDF");

cdk.createSDFile("/Virtual/moleculesThatParse.sdf", molecules);