public void addResidue(String name, String chain, String loc) {
Variable var;
if (titratableResNames.contains(name)) {
String[] labels = resToTaut.get(name);
// for (int i=0; i<labels.length; i++){
// labels[i] = labels[i]+"_"+chain+"_"+loc;
// }
var = new Variable(name + "_" + chain + "_" + loc, labels);
for (String l : labels) {
Instance vl = var.getInstance(l);
if (tRes.contains(l)) {
vl.setEnergy(modPka.get(l));
} else {
vl.setEnergy(0);
}
}
} else {
nonTitratableResNames.add(name);
String[] label = {name};
var = new Variable(name + "_" + chain + "_" + loc, label);
Instance vl = var.getInstance(label[0]);
vl.setEnergy(0);
}
addResidue(var);
}
public void printProtein() {
System.out.println();
System.out.println("*****************");
System.out.println("* PROTEIN *");
System.out.println("*****************");
for (Variable v : residues) {
System.out.println(v.toString());
for (Instance i : v.getInstances()) {
System.out.println(" " + i.toString() + " with energy " + i.getEnergy());
}
}
System.out.println();
}
public void printEnergy() {
System.out.println();
System.out.println("*****************");
System.out.println("* ENERGY *");
System.out.println("*****************");
for (Variable v1 : residues) {
for (Instance i1 : v1.getInstances()) {
for (Variable v2 : residues) {
if (v1.equals(v2)) {
continue;
}
for (Instance i2 : v2.getInstances()) {
System.out.println(i1.toString() + ", " + i2.toString() + " " + bi.get(i1, i2));
}
}
}
}
}
public Instance getInstance(String name, String chain, String loc) {
String chainLoc = chain + "_" + loc;
int endLength = chainLoc.length();
for (Variable v : residues) {
String nm = v.getName();
if (chainLoc.equals(nm.substring(nm.length() - endLength))) {
for (Instance i : v.getInstances()) {
if (i.getLabel().equals(name)) {
return i;
}
}
}
}
return null;
// String[] tauts;
// if (titratableResNames.contains(name)){
// tauts = resToTaut.get(name);
//
// }else{
// tauts = new String[1];
// tauts[0] = name;
// }
// for (Variable r: residues){
// for (int j=0; j<tauts.length; j++){
// if (r.getName().equals(tauts[j]+"_"+chain+"_"+loc)){
// for (Instance i: r.getInstances()){
// if (i.getLabel().equals(name)){
// return i;
// }
// }
// }
// }
// }
// return null;
}
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);
}
}
public void simplify() {
Vector<Variable> toRemove = new Vector<Variable>();
Vector<Vector<Instance>> toRemoveFromBi = new Vector<Vector<Instance>>();
for (Variable v : residues) {
// Instances within variable v
Vector<Instance> vis = v.getInstances();
if (vis.size() == 1) {
// if there is only one instance we must
// (a) remove it
toRemove.add(v);
// (b) add its energy to the constant
con += vis.get(0).getEnergy() * 0.5;
for (Variable w : residues) {
if (v.equals(w)) continue;
// (c) add its interaction energy with other instances
// either to the constant or to the unary energy
// of the other instances
Vector<Instance> wis = w.getInstances();
if (wis.size() == 1) {
// if the other variable has only one instance then
// we add the binary energy between the two instances
// to the constant and we mark the other variable
// for removal
toRemove.add(w);
con += bi.get(vis.get(0), wis.get(0)) * 0.5;
Vector<Instance> temp = new Vector<Instance>(2);
temp.add(0, vis.get(0));
temp.add(1, wis.get(0));
toRemoveFromBi.add(temp);
} else {
// if w has multiple instances then we add the
// binary energy to the unary energy of the
// instance of w
for (Instance wi : wis) {
wi.setEnergy(wi.getEnergy() + bi.get(vis.get(0), wi) * 0.5);
Vector<Instance> temp = new Vector<Instance>(2);
temp.add(0, vis.get(0));
temp.add(1, wi);
toRemoveFromBi.add(temp);
}
}
}
} else {
// if there are multiple instances of v then we look at other instances
// to update the energy of v if needed
for (Variable w : residues) {
if (v.equals(w)) continue;
Vector<Instance> wis = w.getInstances();
if (wis.size() == 1) {
toRemove.add(w);
for (Instance vi : vis) {
vi.setEnergy(vi.getEnergy() + bi.get(vi, wis.get(0)) * 0.5);
Vector<Instance> temp = new Vector<Instance>(2);
temp.add(0, vi);
temp.add(1, wis.get(0));
toRemoveFromBi.add(temp);
}
} else {
// both v and w have multiple instances so we do nothing
}
}
}
}
residues.removeAll(toRemove);
bi.removeAll(toRemoveFromBi);
}