filtering.js

var FILTERING = "Filtering";
var FILTERED = "Filtered";
if ( structuredb.allDatabaseNames().contains(FILTERING) ) {
	structuredb.deleteDatabase(FILTERING);
}
structuredb.createDatabase(FILTERING);
structuredb.addMoleculesFromSDF(FILTERING, "/Sample Data/SDF/Fragments2.sdf");

var iterator = structuredb.allStructuresIterator( FILTERING );
var filteredAnnotation = structuredb.createTextAnnotation( FILTERING, "label", FILTERED );
while ( iterator.hasNext() ) {
	var molecule = iterator.next();
	if ( cdk.calculateSMILES(molecule).contains( "Cl" ) ) {
		molecule.addAnnotation(filteredAnnotation);
		structuredb.updateMolecule(FILTERING, molecule);
	}
}