private void processAtomsBlock(int lineCount, IAtomContainer container) throws IOException {
   for (int i = 0; i < lineCount; i++) {
     String line = input.readLine();
     int atomicNumber = Integer.parseInt(line.substring(7, 10).trim());
     IAtom atom = container.getBuilder().newAtom();
     atom.setAtomicNumber(atomicNumber);
     atom.setSymbol(Symbols.byAtomicNumber[atomicNumber]);
     container.addAtom(atom);
   }
 }
 private void processBondsBlock(int lineCount, IAtomContainer container) throws IOException {
   for (int i = 0; i < lineCount; i++) {
     String line = input.readLine();
     int atom1 = Integer.parseInt(line.substring(10, 13).trim()) - 1;
     int atom2 = Integer.parseInt(line.substring(16, 19).trim()) - 1;
     if (container.getBond(container.getAtom(atom1), container.getAtom(atom2)) == null) {
       IBond bond =
           container.getBuilder().newBond(container.getAtom(atom1), container.getAtom(atom2));
       int order = Integer.parseInt(line.substring(23).trim());
       bond.setOrder(BondManipulator.createBondOrder((double) order));
       container.addBond(bond);
     } // else: bond already present; CTX store the bonds twice
   }
 }