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 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);
}
