public void makeBiGr() {
   if (!checkBinary()) {
     System.out.println("Can't do binary graph cut, Systm isn't binary.");
   } else {
     sys.makeNF();
     sysBiGr = new BinaryGraph(sys, false);
   }
 }
  public void makeBiGr(WriteFile wr) {
    if (!checkBinary()) {
      System.out.println("Can't do binary graph cut, Systm isn't binary.");
    } else {
      sys.makeNF();

      wr.writeln("REGULAR ENERGIES");
      // binary
      for (Variable var1 : sys.getVars()) {
        for (Instance inst1 : var1.getInstances()) {
          for (Variable var2 : sys.getVars()) {
            if (var1.equals(var2)) continue;
            for (Instance inst2 : var2.getInstances()) {
              if (inst1.getLabel().equals("PROT") && inst2.getLabel().equals("PROT")) {
                wr.writeln(
                    "("
                        + inst1.getName()
                        + "_PROTONATED, "
                        + inst2.getName()
                        + "_PROTONATED) "
                        + Math.round(sys.getBinary().get(inst1, inst2) * 10000.0) / 10000.0);
              } else if (inst1.getLabel().equals("PROT") && inst2.getLabel().equals("DEPROT")) {
                wr.writeln(
                    "("
                        + inst1.getName()
                        + "_PROTONATED, "
                        + inst2.getName()
                        + "_DEPROTONATED) "
                        + Math.round(sys.getBinary().get(inst1, inst2) * 10000.0) / 10000.0);
              } else if (inst1.getLabel().equals("DEPROT") && inst2.getLabel().equals("PROT")) {
                wr.writeln(
                    "("
                        + inst1.getName()
                        + "_DEPROTONATED, "
                        + inst2.getName()
                        + "_PROTONATED) "
                        + Math.round(sys.getBinary().get(inst1, inst2) * 10000.0) / 10000.0);
              } else if (inst1.getLabel().equals("DEPROT") && inst2.getLabel().equals("DEPROT")) {
                wr.writeln(
                    "("
                        + inst1.getName()
                        + "_DEPROTONATED, "
                        + inst2.getName()
                        + "_DEPROTONATED) "
                        + Math.round(sys.getBinary().get(inst1, inst2) * 10000.0) / 10000.0);
              }
            }
          }
        }
      }

      //			Set<Vector<Instance>> keys = sys.getBinary().keySet();
      //			for (Vector<Instance> key : keys){
      //				Instance key1 = key.get(0);
      //				Instance key2 = key.get(1);
      //				if (key1.getLabel().equals("PROT") && key2.getLabel().equals("PROT")){
      //					wr.writeln("("+key1.getName()+"_PROTONATED, "+key2.getName()+"_PROTONATED)
      // "+Math.round(sys.getBinary().get(key1, key2)*10000.0)/10000.0);
      //				}else if (key1.getLabel().equals("PROT") && key2.getLabel().equals("DEPROT")){
      //					wr.writeln("("+key1.getName()+"_PROTONATED, "+key2.getName()+"_DEPROTONATED)
      // "+Math.round(sys.getBinary().get(key1, key2)*10000.0)/10000.0);
      //				}else if (key1.getLabel().equals("DEPROT") && key2.getLabel().equals("PROT")){
      //					wr.writeln("("+key1.getName()+"_DEPROTONATED, "+key2.getName()+"_PROTONATED)
      // "+Math.round(sys.getBinary().get(key1, key2)*10000.0)/10000.0);
      //				}else{
      //					wr.writeln("("+key1.getName()+"_DEPROTONATED, "+key2.getName()+"_DEPROTONATED)
      // "+Math.round(sys.getBinary().get(key1, key2)*10000.0)/10000.0);
      //				}
      //			}
      // unary
      for (Variable var : sys.getVars()) {
        for (Instance inst : var.getInstances()) {
          if (inst.getLabel().equals("PROT")) {
            wr.writeln(
                inst.getName() + "_PROTONATED " + Math.round(inst.getEnergy() * 10000.0) / 10000.0);
          } else if (inst.getLabel().equals("DEPROT")) {
            wr.writeln(
                inst.getName()
                    + "_DEPROTONATED "
                    + Math.round(inst.getEnergy() * 10000.0) / 10000.0);
          } else {
            wr.writeln(
                inst.toString() + "_OTHER " + Math.round(inst.getEnergy() * 10000.0) / 10000.0);
          }
        }
      }
      wr.writeln();

      wr.writeln("NORMAL FORM ENERGIES");
      // binary

      for (Variable var1 : sys.getVars()) {
        for (Instance inst1 : var1.getInstances()) {
          for (Variable var2 : sys.getVars()) {
            if (var1.equals(var2)) continue;
            for (Instance inst2 : var2.getInstances()) {
              if (inst1.getLabel().equals("PROT") && inst2.getLabel().equals("PROT")) {
                wr.writeln(
                    "("
                        + inst1.getName()
                        + "_PROTONATED, "
                        + inst2.getName()
                        + "_PROTONATED) "
                        + Math.round(sys.getBinaryNF().get(inst1, inst2) * 10000.0) / 10000.0);
              } else if (inst1.getLabel().equals("PROT") && inst2.getLabel().equals("DEPROT")) {
                wr.writeln(
                    "("
                        + inst1.getName()
                        + "_PROTONATED, "
                        + inst2.getName()
                        + "_DEPROTONATED) "
                        + Math.round(sys.getBinaryNF().get(inst1, inst2) * 10000.0) / 10000.0);
              } else if (inst1.getLabel().equals("DEPROT") && inst2.getLabel().equals("PROT")) {
                wr.writeln(
                    "("
                        + inst1.getName()
                        + "_DEPROTONATED, "
                        + inst2.getName()
                        + "_PROTONATED) "
                        + Math.round(sys.getBinaryNF().get(inst1, inst2) * 10000.0) / 10000.0);
              } else if (inst1.getLabel().equals("DEPROT") && inst2.getLabel().equals("DEPROT")) {
                wr.writeln(
                    "("
                        + inst1.getName()
                        + "_DEPROTONATED, "
                        + inst2.getName()
                        + "_DEPROTONATED) "
                        + Math.round(sys.getBinaryNF().get(inst1, inst2) * 10000.0) / 10000.0);
              }
            }
          }
        }
      }

      //			Set<Vector<Instance>> keysNF = sys.getBinaryNF().keySet();
      //			for (Vector<Instance> key : keysNF){
      //				Instance key1 = key.get(0);
      //				Instance key2 = key.get(1);
      //				if (key1.getLabel().equals("PROT") && key2.getLabel().equals("PROT")){
      //					wr.writeln("("+key1.getName()+"_PROTONATED, "+key2.getName()+"_PROTONATED)
      // "+Math.round(sys.getBinaryNF().get(key1, key2)*10000.0)/10000.0);
      //				}else if (key1.getLabel().equals("PROT") && key2.getLabel().equals("DEPROT")){
      //					wr.writeln("("+key1.getName()+"_PROTONATED, "+key2.getName()+"_DEPROTONATED)
      // "+Math.round(sys.getBinaryNF().get(key1, key2)*10000.0)/10000.0);
      //				}else if (key1.getLabel().equals("DEPROT") && key2.getLabel().equals("PROT")){
      //					wr.writeln("("+key1.getName()+"_DEPROTONATED, "+key2.getName()+"_PROTONATED)
      // "+Math.round(sys.getBinaryNF().get(key1, key2)*10000.0)/10000.0);
      //				}else{
      //					wr.writeln("("+key1.getName()+"_DEPROTONATED, "+key2.getName()+"_DEPROTONATED)
      // "+Math.round(sys.getBinaryNF().get(key1, key2)*10000.0)/10000.0);
      //				}
      //			}
      // unary
      for (Variable var : sys.getVars()) {
        for (Instance inst : var.getInstances()) {
          if (inst.getLabel().equals("PROT")) {
            wr.writeln(
                inst.getName()
                    + "_PROTONATED "
                    + Math.round(inst.getEnergyNF() * 10000.0) / 10000.0);
          } else if (inst.getLabel().equals("DEPROT")) {
            wr.writeln(
                inst.getName()
                    + "_DEPROTONATED "
                    + Math.round(inst.getEnergyNF() * 10000.0) / 10000.0);
          } else {
            wr.writeln(
                inst.toString() + "_OTHER " + Math.round(inst.getEnergyNF() * 10000.0) / 10000.0);
          }
        }
      }
      // constant
      wr.writeln(
          "Normalized constant energy: " + Math.round(sys.getConstantNF() * 10000.0) / 10000.0);

      sysBiGr = new BinaryGraph(sys, false, wr);
    }
  }