Esempio n. 1
0
  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);
  }
Esempio n. 2
0
 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();
 }
Esempio n. 3
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 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));
         }
       }
     }
   }
 }
Esempio n. 4
0
  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);
    }
  }
Esempio n. 6
0
  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);
  }