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);
}
}