// ## configuration RMG::RMG public static void main(String[] args) { File funcGroups = new File("FunctionalGroups.txt"); try { BufferedReader reader = new BufferedReader(new FileReader(funcGroups)); String line = ChemParser.readMeaningfulLine(reader, true); String fgname1 = line; Graph fgGraph1 = null; try { fgGraph1 = ChemParser.readFGGraph(reader); } catch (InvalidGraphFormatException e) { throw new InvalidFunctionalGroupException(fgname1 + ": " + e.getMessage()); } FunctionalGroup fg1 = FunctionalGroup.make(fgname1, fgGraph1); line = ChemParser.readMeaningfulLine(reader, true); String fgname2 = line; Graph fgGraph2 = null; try { fgGraph2 = ChemParser.readFGGraph(reader); } catch (InvalidGraphFormatException e) { throw new InvalidFunctionalGroupException(fgname2 + ": " + e.getMessage()); } FunctionalGroup fg2 = FunctionalGroup.make(fgname2, fgGraph2); boolean isSub = fg2.isSubAtCentralNodes(fg1); // boolean isSub = fg2.isSub(fg1); System.out.println("fg2 is a sub of fg1: " + isSub); } catch (IOException e) { System.out.println(e.toString()); } }