//
public bool Create2newObjs(Object o1, Object o2, Object o, DSBs.DSBstruct dsb)
{
if (o1.FillObj(o1, o, dsb, PositionWithRespectToReferencePoint.downstream))
{
if (o2.FillObj(o2, o, dsb, PositionWithRespectToReferencePoint.upstream))
{
return(true);
}
else
{
return(false);
}
}
else
{
return(false);
}
}
//
public static bool ApplyRad2RWs(RadiationSchema rs, RandomWalk rw, DSBs DSBdata)
{
int ndsb = 0;
try
{
double dose;
double dose_total = 0.0;
for (int nb = 0; nb < rs.nBeams; nb++) // iterate over all beams
{
foreach (int j in rw.nmonomer)
{
dose = Dconst;
dose_total += Dconst;
try
{
for (int i = 0; i < amorphous_partile_tracks[nb].track_struct.ntracks; i++)
{
int x = amorphous_partile_tracks[nb].track_struct.X[i];
int y = amorphous_partile_tracks[nb].track_struct.Y[i];
int dist2 = (x - rw.LL[j].X) * (x - rw.LL[j].X) + (y - rw.LL[j].Y) * (y - rw.LL[j].Y);
if (dist2 < Convert.ToInt32((RadiationSchema.Pr / lattice_dim) * (RadiationSchema.Pr / lattice_dim)))
{
int t = Convert.ToInt32(MainForm.Particle.Tracks.grid * lattice_dim * Math.Sqrt(dist2) / RadiationSchema.Pr); // microns
dose += amorphous_partile_tracks[nb].track_struct.dose[t];
dose_total += amorphous_partile_tracks[nb].track_struct.dose[t];
}
}
}
catch { return(false); }
double Q = 0.812 * 35.0 / 25.0; // multiply by 35./25. for high/low LET; also 1e-5 is factored out
if (amorphous_partile_tracks[nb].p_t == MainForm.Radiation.p_type.photon)
{
Q = 0.812; // multiply by 35./25. for high LET
}
else
{
Q = 0.812 * 35.0 / 25.0; // multiply by 35./25. for high LET
}
Q *= 1.0e-5; // Q is determined from PFGE experiments
Random random = new Random();
try
{
if (SimpleRNG.GetUniform() < 1.0 - Math.Exp(-Q * dose))
{
ndsb++;
DSBs.DSBstruct new_dsb = new DSBs.DSBstruct
{
ndsb = ndsb,
L = rw.LL[j],
position = rw.nmonomer[j],
entry_time = rs.entryTime[nb],
exit_time = rs.exitTime[nb]
};
new_dsb.random_time = SimpleRNG.GetUniform() * (new_dsb.exit_time - new_dsb.entry_time) + new_dsb.entry_time; // a DSB is created sometime during the fractionation interval
double r = SimpleRNG.GetUniform();
if (r < DSBs.DSBcomplP[0])
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.simpleDSB;
}
else
{
if (r >= DSBs.DSBcomplP[0] && r < DSBs.DSBcomplP[1]) // zzz can a DSB appear more than 1 time at the same monomer
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.DSBplus;
}
else
{
new_dsb.DSBcmplx = DSBs.DSBstruct.DSBcomplexity.DSBplusplus;
}
}
DSBdata.listDSBs.Add(new_dsb);
}
}
catch { return(false); }
}
}
dose_total /= Convert.ToDouble(rw.nmonomer.Length); // total dose integrated over all monomers // zzz might wanna output somewhere
return(true);
}
catch { return(false); }
}
public bool FillObj(Object o_new, Object o, DSBs.DSBstruct dsb, PositionWithRespectToReferencePoint relative_location) // add attributes to an empty object
{
try
{
o_new.md = new MetaData
{
chromo_bands = new LinkedList <Band>()
};
if (relative_location == PositionWithRespectToReferencePoint.downstream) // downstream from the DSB
{
for (int i = 0; i < o.md.f_e.Count; i++)
{
if (o.md.f_e[i].Position <= dsb.position)
{
o_new.md.f_e.Add(new Free_end()
{
Position = o.md.f_e[i].Position,
FE_type = o.md.f_e[i].FE_type,
Reacting = o.md.f_e[i].Reacting,
L = o.md.f_e[i].L, // input X, Y, Z, location of a free end, only if it can interact with other free ends
Relative_position = PositionWithRespectToReferencePoint.not_known // since this is a new fragment, there is no point of reference yet for this reactive end; this var. is always for later use
});
foreach (Band b in o.md.chromo_bands)
{
if (!(b.Position_within_object <= dsb.position - o.md.f_e[i].Position && b.Position_within_object + b.Size >= dsb.position - o.md.f_e[i].Position))
{
var b1 = (Band)b.MemberwiseClone();
o_new.md.chromo_bands.AddLast(b1);
}
else
{
var b1 = (Band)b.MemberwiseClone();
o_new.md.chromo_bands.AddLast(b1);
o_new.md.chromo_bands.Last.Value.Size = dsb.position - o.md.f_e[i].Position - b.Position_within_object;
o_new.md.chromo_bands.Last.Value.Upstream_end_position = dsb.position;
break;
}
}
o_new.NumberOfBands = o_new.md.chromo_bands.Count;
o_new.Length = dsb.position - o.md.f_e[i].Position;
}
}
for (int i = 0; i < o.md.c_l.Count; i++)
{
if (o.md.c_l[i].Position < dsb.position)
{
o_new.md.c_l.Add(new Centromere()
{
Position = o.md.c_l[i].Position, Relative_position = PositionWithRespectToReferencePoint.not_known
});
}
}
o_new.md.f_e.Add(new Free_end()
{
Position = dsb.position,
FE_type = MetaData.FreeEndType.reactive,
Reacting = false,
L = dsb.L,
Relative_position = PositionWithRespectToReferencePoint.not_known // TBD later
// since this is a new fragment, there is no point of reference (like a new DSB) yet for this reactive end; this var. is always for later use
});
if (o_new.md.f_e[0].FE_type == MetaData.FreeEndType.reactive)
{
o_new.md.O_type = MetaData.ObjectType.open_fragement;
}
else
{
o_new.md.O_type = MetaData.ObjectType.frag_with_one_telomere;
}
}
else
{
for (int i = 0; i < o.md.f_e.Count; i++)
{
if (o.md.f_e[i].Position >= dsb.position)
{
o_new.md.f_e.Add(new Free_end()
{
Position = o.md.f_e[i].Position,
FE_type = o.md.f_e[i].FE_type,
Reacting = o.md.f_e[i].Reacting,
L = o.md.f_e[i].L,
Relative_position = PositionWithRespectToReferencePoint.not_known
// since this is a new fragment, there is no point of reference yet for this reactive end; this var. is always for later use
});
foreach (Band b in o.md.chromo_bands)
{
if (!(b.Position_within_object <= o.Length - (o.md.f_e[i].Position - dsb.position) && b.Position_within_object + b.Size >= o.Length - (o.md.f_e[i].Position - dsb.position)))
{
var b1 = (Band)b.MemberwiseClone();
o_new.md.chromo_bands.AddLast(b1);
o_new.md.chromo_bands.Last.Value.Position_within_object = b.Position_within_object - (o.Length - (o.md.f_e[i].Position - dsb.position));
}
else
{
var b1 = (Band)b.MemberwiseClone();
o_new.md.chromo_bands.AddFirst(b1); // first, add a band to the new obj., then adjust its size and position
o_new.md.chromo_bands.First.Value.Size = b.Size - ((o.Length - b.Position_within_object) - (o.md.f_e[i].Position - dsb.position));
o_new.md.chromo_bands.First.Value.Position_within_object = 0;
o_new.md.chromo_bands.First.Value.Downstream_end_position = dsb.position;
break;
}
}
o_new.NumberOfBands = o_new.md.chromo_bands.Count;
o_new.Length = -dsb.position + o.md.f_e[i].Position;
}
}
for (int i = 0; i < o.md.c_l.Count; i++)
{
if (o.md.c_l[i].Position >= dsb.position)
{
o_new.md.c_l.Add(new Centromere()
{
Position = o.md.c_l[i].Position, Relative_position = PositionWithRespectToReferencePoint.not_known
});
}
}
o_new.md.f_e.Add(new Free_end()
{
Position = dsb.position,
FE_type = MetaData.FreeEndType.reactive,
Reacting = false,
L = dsb.L,
Relative_position = PositionWithRespectToReferencePoint.not_known // TBD later
// since this is a new fragment, there is no point of reference (like a new DSB) yet for this reactive end; this var. is always for later use
});
if (o_new.md.f_e[0].FE_type == MetaData.FreeEndType.reactive)
{
o_new.md.O_type = MetaData.ObjectType.open_fragement;
}
else
{
o_new.md.O_type = MetaData.ObjectType.frag_with_one_telomere;
}
}
foreach (Band b in o_new.md.chromo_bands)
{
b.Size = b.Upstream_end_position - b.Downstream_end_position;
}
int bsize = 0;
foreach (Band b in o_new.md.chromo_bands)
{
b.Position_within_object += bsize;
bsize = b.Size;
}
if (o_new.md.f_e.Count == 2)
{
return(true);
}
else
{
return(false); // >= and <= should be for all conditions related to a DSB, and >= and < for a centromere
}
}
catch
{
return(false);
}
}
