//
public double MisrejoiningProb(Free_end fe1, Free_end fe2)
{
double dist2 = (fe1.L.X - fe2.L.X) * (fe1.L.X - fe2.L.X) + (fe1.L.Y - fe2.L.Y) * (fe1.L.Y - fe2.L.Y) + (fe1.L.Z - fe2.L.Z) * (fe1.L.Z - fe2.L.Z); // Eucld. distance between free ends
double dtemp = 0.08 * (1.0 / Z) * Math.Exp(-dist2 / sigma2); // the probability to misrejoin or create a ring
return(dtemp);
}
//
public bool RestitutionKinetics(List <Object> listObjs)
{
// the class FreeEnds is derived from DSBs class and is based on DSBdata
// Free_end class is for Objects (which are fragments that can have free ends)
Random random = new Random();
try
{
for (int i = 0; i < Convert.ToInt32(expTime / tau); i++) // number of elementary time steps
{
if (!SplitObjects(listObjs, i * tau, (i + 1) * tau))
{
return(false); // split only using DSBs avaibale in time interval timeIncrement / tau
}
int availableFreeEnds = 0;
foreach (Object o in listObjs)
{
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.reactive)
{
availableFreeEnds++;
}
}
}
if (availableFreeEnds != 0)
{
for (int j = 0; j < availableFreeEnds / 2; j++) // cycle through all pairs of Free Ends in one elementary time step
{
int availableFreeEnds1 = 0;
foreach (Object o in listObjs)
{
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.reactive)
{
availableFreeEnds1++; // determine the number of free ends, which are still reactive
}
}
}
int end1, end2;
while (true)
{
end1 = random.Next(0, availableFreeEnds1);
end2 = random.Next(0, availableFreeEnds1);
if (end1 != end2)
{
break;
}
}
int itemp = 0;
Free_end freeend1 = null, freeend2 = null;
foreach (Object o in listObjs)
{
bool b = false;
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.reactive)
{
if (itemp == end1)
{
fe.Reacting = true;
freeend1 = fe;
b = true;
break;
}
itemp++;
}
}
if (b)
{
break;
}
}
itemp = 0;
foreach (Object o in listObjs)
{
bool b = false;
foreach (Free_end fe in o.md.f_e)
{
if (fe.FE_type == MetaData.FreeEndType.reactive)
{
if (itemp == end2)
{
fe.Reacting = true; // this marks a free end for rejoining/misrejoining
freeend2 = fe;
b = true;
break;
}
itemp++;
}
}
if (b)
{
break;
}
}
if (freeend1 != null && freeend2 != null)
{
if (freeend1.Position == freeend2.Position) // proper ends
{
if (SimpleRNG.GetUniform() < P)
{
Object o_new = new Object();
if (CreateMergedObj(o_new, listObjs)) // merge the chosen reactive ends in the chosen objects and remove the objs with this pair of free ends
{
listObjs.Add(o_new);
// renumber bands in the whole genome
int[] b_index = new int[46];
foreach (Object o in listObjs)
{
foreach (Band b in o.md.chromo_bands)
{
b_index[b.Chromo_num]++;
b.Ordinal_number = b_index[b.Chromo_num];
}
}
}
else
{
o_new = null; // this happens when one if the members of listObjs becomes a ring
}
}
}
else
{
if (SimpleRNG.GetUniform() < MisrejoiningProb(freeend1, freeend2))
{
Object o_new = new Object();
if (CreateMergedObj(o_new, listObjs)) // merge the chosen reactive ends in the chosen objects
{
listObjs.Add(o_new);
// renumber bands in the whole genome
int[] b_index = new int[46];
foreach (Object o in listObjs)
{
foreach (Band b in o.md.chromo_bands)
{
b_index[b.Chromo_num]++;
b.Ordinal_number = b_index[b.Chromo_num];
}
}
}
else
{
o_new = null; // this happens when one if the members of listObjs becomes a ring
}
}
}
// if nothing happens de-activate free ends
foreach (Object o in listObjs)
{
foreach (Free_end fe in o.md.f_e)
{
if (fe.Reacting)
{
fe.Reacting = false;
}
}
}
}
}
}
}
if (CheckDSBlist(DSBdata) && CheckObjList(listObjs))
{
return(true);
}
else
{
return(false);
}
}
catch
{ // merge failure
Detailed_checkObjList(listObjs);
Detailed_checkDSBlist(DSBdata);
return(false);
}
}