var file = "/workspace/tmp/input.sdf"; mols = cdk.createMoleculeIterator(file); molecules = cdk.createMoleculeList(); var ids = ["AI-555/32919017","AA-516/12432317"] while ( mols.hasNext() ) { m = mols.next(); id= cdk.getProperty(m,"cdk:Title"); for (i=0;i < ids.length;i++) { if (ids[i]==id) { molecules.add(m); } } } ui.open(molecules); // cdk.createSDFile("/workspace/tmp/found.sdf", molecules);