code: public static int[][] aaBondInfo() {
  
          if (aminoAcids == null) {
              createAAs();
          }
  
          int[][] info = new int[153][4];
  
          int counter = 0;
          int total = 0;
          for (int aa = 0; aa < aminoAcids.length; aa++) {
              AminoAcid acid = aminoAcids[aa];
  
              LOGGER.debug("#bonds for ", acid.getProperty(RESIDUE_NAME).toString(), " = " + acid.getBondCount());
              total += acid.getBondCount();
              LOGGER.debug("total #bonds: ", total);
  
              Iterator<IBond> bonds = acid.bonds().iterator();
              while (bonds.hasNext()) {
                  IBond bond = (IBond) bonds.next();
                  info[counter][0] = counter;
                  info[counter][1] = acid.indexOf(bond.getBegin());
                  info[counter][2] = acid.indexOf(bond.getEnd());
                  info[counter][3] = bond.getOrder().numeric();
                  counter++;
              }
          }
  
          if (counter > 153) {
              LOGGER.error("Error while creating AA info! Bond count is too large: ", counter);
              return null;
          }
  
          return info;
      }
docs: Creates matrix with info about the bonds in the amino acids.
  0 = bond id, 1 = atom1 in bond, 2 = atom2 in bond, 3 = bond order.
  @return info