molfilter.js

var iter = cdk.createMoleculeIterator("/tmp/C10H16_filtered.sdf");
var substructure = cdk.fromSMILES("C1CCCCC1");
var filepath = "/tmp/matches.sdf";
var molList = cdk.createMoleculeList();

while (iter.hasNext()) {
	var mol = cdk.create(iter.next());
	if (cdk.subStructureMatches(mol, substructure)) {
		molList.add(mol);
	}
}

cdk.createSDFile(filepath, molList);