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General.cpp
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// General.cpp: implementation of the CGeneral class.
//
//////////////////////////////////////////////////////////////////////
#include "stdafx.h"
#include "Surface.h"
#include "General.h"
#include "Grid.h"
#include "Receptor.h"
#include "Cell.h"
#include "SigMol.h"
#include "mersenne.cpp" // members of class TRandomMersenne
#include <cmath>
#ifdef _DEBUG
#undef THIS_FILE
static char THIS_FILE[]=__FILE__;
#define new DEBUG_NEW
#define message(x) printf(x"\n\n")
#endif
TRandomMersenne rg(0);
//int CGeneral::RecMSDResults[RECEPTOR_NUMBER];
int CGeneral::RecInRaft = 0;
int CGeneral::Glob_raft_ID;
CGrid CGeneral::grid;
std::vector<CReceptor> CGeneral::RArray;
std::vector<CReceptor> CGeneral::tmpRArray;
std::vector<CCell> CGeneral::CellArray;
std::vector<CSigMol> CGeneral::SMArray;
IndexStack CGeneral::delRecStack;
IndexStack CGeneral::delRaftStack;
IndexStack CGeneral::delSMStack;
SMprofileVector CGeneral::SMprofileVec;
RprofileVector CGeneral::RprofileVec;
std::vector<CPoint> CGeneral::MSDResultsArray;
std::vector<CPoint> CGeneral::Results_of_R_in_out_ratio_Array;
std::vector<CPoint> CGeneral::Results_of_R_SM_complex_in_out_ratio_Array;
ResultsVector CGeneral::R_SM_interaction_results_Array;
ResultsVector CGeneral::Protein_concentration_results_Array;
doublesVec CGeneral::R_SM_binding_durations_Vec;
std::queue<SM_Type> CGeneral::EndocytosedSMQueue;
ofstream CGeneral::out_singleCells_concentrations("Out_singleCells_concentrations.txt");
ofstream CGeneral::out_TS_concentrations("Out_TS_concentrations.txt");
ofstream CGeneral::out_singleCells_rates("Out_singleCells_rates.txt");
ofstream CGeneral::out_TS_rates("Out_TS_rates.txt");
ofstream CGeneral::out("Out.txt");
ofstream CGeneral::gillaspieLog("gillaspieLog.txt");
//int CGeneral::TIME_STEP_NUMBER = 26250000 ;
bool CGeneral::debug_version = false; //false;
bool CGeneral::stopProducingIFN_flag = false;
bool CGeneral::START_SIM = true; //false;
int CGeneral::step = 0;
int CGeneral::UpdateWindowVariable = 1;
int CGeneral::TimerInitialisator = 1;
bool CGeneral::DrawRecIndexes = false;
bool CGeneral::DrawReceptors = false;
bool CGeneral::DrawSigMol = true;
bool CGeneral::DrawSigMolNames = false;
bool CGeneral::DrawRecNames = false;
bool CGeneral::DrawSigMolInd = false;
bool CGeneral::DrawRaftIndexes = false;
bool CGeneral::DrawRafts = true;
bool CGeneral::DrawAgs = false;
bool CGeneral::DrawAgIndexes = false;
bool CGeneral::is_draw_finished = true;
bool CGeneral::is_simul_finished = true;
bool CGeneral::is_draw_rec_path = false;
bool CGeneral::is_delete_complexes = true;
int CGeneral::Simulation_Duration = 0;
int CGeneral::Recepter_Number = RECEPTOR_NUMBER;
double CGeneral::RAFT_SURFACE_COVERAGE_PERCENT = 1;//1;
double CGeneral::RAFT_DIFFUSION_COEFICIENT = 0;
double CGeneral::IFNb_D = 0.5/3;//1
//double CGeneral::IFNb_D = pow((TIME_STEP_LENGHT/UPPER_LIMIT_TIME_STEP_LENGHT),0.5) *1;//1
double CGeneral::UPPER_LIMIT_TIME_STEP_LENGHT = 9;//1
int CGeneral::TIME_STEP_LENGHT = 9;//1
//asserte(CGeneral::UPPER_LIMIT_TIME_STEP_LENGHT>CGeneral::TIME_STEP_LENGHT);
int CGeneral::SIMULATION_DURATION_IN_HOURS = 11;//1
double CGeneral::RAFT_DIFFUSION_COEFICIENT_OF_ACTIVE_RAFT = 0.0;//1
//int CGeneral::RAFT_NUMBER = 2*GRID_SIZE*GRID_SIZE/100/100;
//int CGeneral::RAFT_NUMBER = 1;
int CGeneral::RAFT_NUMBER = 20;
int CGeneral::MEAN_RAFT_SIZE = 90;
int CGeneral::CurRaftNum = 0;
double CGeneral::RAFT_PROBABILITY_TO_MERGE = 0.0; //
bool CGeneral::plusAB= false;//false;
bool CGeneral::TWmodel= true;//false;
double CGeneral::RIGI_prot_maxLevel = 400.1; //
double CGeneral::IFN_prot_maxLevel = 400; //
double CGeneral::RIGI_rna_maxLevel = 100.1; //
double CGeneral::IFN_rna_maxLevel = 100; //
double CGeneral::max_transcriptionRateC = 0.05;//*TIME_STEP_LENGHT; //
double CGeneral::max_translationRateC = 0.002;//*TIME_STEP_LENGHT; //
double CGeneral::typical_prot_degradationRateC = 0.0001;//*TIME_STEP_LENGHT; // 0.002
double CGeneral::typical_rna_degradationRateC = 0.0001;//*TIME_STEP_LENGHT;
double CGeneral::IFN_rna_activation_hillCoef = (TWmodel)?1.5:2;
double CGeneral::DDX58_rna_activation_hillCoef = (TWmodel)?3:2;
int CGeneral::IFN_protein_secretion_hillCoef = 1.0; //
double CGeneral::infectivityThreshould = .6; //
double CGeneral::Ppob_TypeR_Bind_IFNb = (plusAB)?1.25e-7*TIME_STEP_LENGHT*100*1 : 1.25e-7*TIME_STEP_LENGHT*100;
double CGeneral::Ppob_TypeR_Unbind_IFNb = 10e-4*TIME_STEP_LENGHT;
double CGeneral::Ppob_IFNb_die = (plusAB)?0.075:0.0;
int CGeneral::IFN_prot_secretion_Threshould = 10; //
int CGeneral::max_typeIRNumber = (plusAB)?RECEPTOR_NUMBER*0.6:RECEPTOR_NUMBER;
int CGeneral::CurSMNum = 0;
int CGeneral::raft_endoc_events_num = 0;
//void polygonFill(const POINT * mv, int count, short raftNum);
int noInterSec = 0;
double CGeneral::D_Stx = 0.00;
double CGeneral::D_SNAP25 = 1.1;
double CGeneral::D_Vamp = 0.1;
double CGeneral::D_NSF = 0.01;
int CGeneral::t_NSF_up = 10;
double CGeneral::Ptransloc_NSF = 0.01;
double CGeneral::D_ALPHA = 0.1;
int CGeneral::t_ALPHA_up = 100;
double CGeneral::Ptransloc_Alpha = 0.01;
double CGeneral::D_Stx_inRaft = 0.00;
double CGeneral::D_SNAP25_inRaft = 1.0;
double CGeneral::D_Vamp_inRaft = 0.00;
double CGeneral::Pin_Stx = 0.0;
double CGeneral::Pin_SNAP25 = 1.0;
double CGeneral::Pin_Vamp = 0.0;
double CGeneral::Pout_Stx = 0.0;
double CGeneral::Pout_SNAP25 = 1.0;
double CGeneral::Pout_Vamp = 0.0;
double CGeneral::Pin_SynSyn = 0.0;
double CGeneral::Pin_SynSynSyn = 0.01;
double CGeneral::Pin_SynSnap25 = 0.0;
double CGeneral::Pin_SynSnap25Vamp = 0.0;
double CGeneral::Pin_SynSnap25VampAlpha = 0.0;
double CGeneral::Pout_SynSyn = 0.0;
double CGeneral::Pout_SynSynSyn = 0.0;
double CGeneral::Pout_SynSnap25 = 0.0;
double CGeneral::Pout_SynSnap25Vamp = 0.0;
double CGeneral::Pout_SynSnap25VampAlpha = 0.0;
//int CGeneral::typeIRNumber = 0;
int CGeneral::initSntNumber = 0;
int CGeneral::initSntSntNumber = 00;
int CGeneral::initSntSntSntNumber = 00;
int CGeneral::initSNAP25Number = 1500;
int CGeneral::initNSFNumber = 00; //1%
int CGeneral::initAlphaNumber = 0; //1%
int CGeneral::initVampNumber = 0;
int CGeneral::initSynSnap25 = 0;
int CGeneral::initSynSnap25Vamp = 0;
int CGeneral::initSynSnap25VampAlpha = 0;
double CGeneral::Ppob_Syn_Bind_Syn = 0.0;
double CGeneral::Ppob_SynSyn_Bind_Syn = 0.0;
double CGeneral::Ppob_Syn_Bind_SNAP25 = 0.01;
//double CGeneral::Ppob_Syn_Bind_SNAP25 = 0.0000001;
double CGeneral::Ppob_SynSNAP25_BindVamp = 0.0;
double CGeneral::Ppob_SynSNAP25Vamp_BindAlpha = 1.0;
double CGeneral::Ppob_NSF_diss_SynSNAP25VampAlpha = 1.0;
double CGeneral::Ppob_SynSyn_Dissociation = 0.00;
double CGeneral::Ppob_SynSynSyn_Dissociation = 0.000;
double CGeneral::Ppob_SynSNAP25_Dissociation = 0.0000001;
double CGeneral::Ppob_SynSNAP25Vamp_Dissociation = 0.00000001;
double CGeneral::Ppob_SynSNAP25VampAlpha_Dissociation = 0.00000001;
double CGeneral::InitInRaftFractionSnt = 1.0;
double CGeneral::InitInRaftFractionSntSnt = 0.0;
double CGeneral::InitInRaftFractionSntSntSnt = 0.0;
double CGeneral::InitInRaftFractionSNAP25 = 0.0;
double CGeneral::InitInRaftFractionNSF = 0.0;
double CGeneral::InitInRaftFractionAlpha = 0.0;
double CGeneral::InitInRaftFractionVamp = 0.0;
double CGeneral::InitInRaftFractionSynSnap25 = 0;
double CGeneral::InitInRaftFractionSynSnap25Vamp = 0;
double CGeneral::InitInRaftFractionSynSnap25VampAlpha = 0;
int CGeneral::syn_snap25encounters=0;
int CGeneral::syn_syn_encounters=0;
int CGeneral::synSyn_syn_encounters=0;
int CGeneral::binary_Vamp_encounters=0;
int CGeneral::SNAR_SNAP_encounters=0;
int CGeneral::prodoctive_syn_snap25encounters=0;
int CGeneral::prodoctive_binary_Vamp_encounters=0;
int CGeneral::prodoctive_SNAR_SNAP_encounters=0;
int CGeneral::prodoctive_syn_syn_encounters=0;
int CGeneral::prodoctive_synSyn_syn_encounters=0;
int CGeneral::syn_snap25_diss=0;
int CGeneral::binary_Vamp_diss=0;
int CGeneral::SNAR_SNAP_diss=0;
int CGeneral::syn_syn_diss=0;
int CGeneral::syn_syn_syn_diss=0;
int CGeneral::lastSMindex = 0;
//////////////////////////////////////////////////////////////////////
// Construction/Destruction
//////////////////////////////////////////////////////////////////////
int CGeneral::TIME_STEP_NUMBER = SIMULATION_DURATION_IN_HOURS * 60*60/TIME_STEP_LENGHT;
///pow((TIME_STEP_LENGHT/UPPER_LIMIT_TIME_STEP_LENGHT),2);
//int CGeneral::GRID_SIZE = 60;
CGeneral::CGeneral()
{
}
CGeneral::~CGeneral()
{
}
void CGeneral::BindReceptorToGrid(CReceptor & rec)
{
/*
rec.SetUsage(true); //????
bool is_in_raft = false;
// int index_in_profileVec = GetId_in_R_ProfileVec(rec.GetName());
if( rg.Random() < RprofileVec[rec.GetType()].GetInitInRaftFraction() ) // is to put in raft
if(RAFT_NUMBER>0)
is_in_raft = true;
int attempt_count1 = 0;
while(1)
{
if(attempt_count1++ > 50000 )
{
CGeneral::START_SIM = false;
throw(-3);
}
rec.CurrentLocation.x = rec.InitLocation.x = rand()%GRID_SIZE;
rec.CurrentLocation.y = rec.InitLocation.y = rand()%GRID_SIZE;
if(grid.m_Grid[rec.InitLocation.y] [rec.InitLocation.x].array[Rec] == -1) //free place
{
int RaftNum = grid.m_Grid[rec.InitLocation.y] [rec.InitLocation.x].array[Raft];
if(RaftNum >= 0) // sm is inside the raft
{
if( is_in_raft )
{
CGeneral::RaftArray[RaftNum].SetRecIndex(rec.Get_R_index());
rec.GetInRaft(RaftNum);
break;
}//if inside raft is ok
}
else // SM is outside the raft
{
if( !is_in_raft )
{
break;
}//if outside raft is ok
}
}
}
grid.m_Grid[rec.InitLocation.y][rec.InitLocation.x].array[Rec] = rec.Get_R_index();
*/
}
void CGeneral::Fill_SM_Profile()
{
CSMprofile profile;
profile.SetDefaultD(D_NSF);
profile.Set_D_upon_Active(D_NSF);
profile.SetSpontaneousSMactivationRate(0.000);
profile.SetSpontaneousSMinactivationRate(000);
profile.SetIsCyto(true);
profile.SetInitNumber(initNSFNumber);
profile.SetLifeTime(t_NSF_up);
profile.SetPtransloc(Ptransloc_NSF);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionNSF);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SynSnap25);
SMprofileVec[NSF] = profile;
profile.SetDefaultD(D_ALPHA);
profile.Set_D_upon_Active(D_ALPHA);
profile.SetSpontaneousSMactivationRate(0.000);
profile.SetSpontaneousSMinactivationRate(000);
profile.SetIsCyto(true);
profile.SetInitNumber(initAlphaNumber);
profile.SetLifeTime(t_ALPHA_up);
profile.SetPtransloc(Ptransloc_Alpha);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionAlpha);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SynSnap25);
SMprofileVec[Alpha] = profile;
profile.SetDefaultD(D_SNAP25);
profile.Set_D_upon_Active(D_SNAP25);
profile.Set_D_inRaft(D_SNAP25_inRaft);
profile.SetDefault_P_enterRaft(Pin_SNAP25);
profile.SetP_enterRaft_upon_Active(Pin_SNAP25);
profile.SetDefault_P_leaveRaft(Pout_SNAP25);
profile.SetP_leaveRaft_upon_Active(Pout_SNAP25);
profile.SetSpontaneousSMactivationRate(0.0);
profile.SetSpontaneousSMinactivationRate(0);
profile.SetIsCyto(false);
profile.SetInitNumber(initSNAP25Number);
profile.SetInitActivePercent(0.0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionSNAP25);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SynSnap25);
SMprofileVec[SNAP25] = profile;
profile.SetDefaultD(D_Vamp);
profile.Set_D_upon_Active(D_Vamp);
profile.Set_D_inRaft(D_Vamp_inRaft);
profile.SetDefault_P_enterRaft(Pin_Vamp);
profile.SetP_enterRaft_upon_Active(Pin_Vamp);
profile.SetDefault_P_leaveRaft(Pout_Vamp);
profile.SetP_leaveRaft_upon_Active(Pout_Vamp);
profile.SetSpontaneousSMactivationRate(0.001);
profile.SetSpontaneousSMinactivationRate(1.E9);
profile.SetIsCyto(false);
profile.SetInitNumber(initVampNumber);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionVamp);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
SMprofileVec[Vamp] = profile;
}
void CGeneral::Fill_R_Profile()
{
CRProfile profile;
profile.SetDefaultD(D_Stx);
profile.Set_D_upon_Active(D_Stx);
profile.Set_D_inRaft(D_Stx_inRaft);
profile.SetDefault_P_enterRaft(Pin_Stx);
profile.SetP_enterRaft_upon_Active(Pin_Stx);
profile.SetDefault_P_leaveRaft(Pout_Stx);
profile.SetP_leaveRaft_upon_Active(Pout_Stx);
profile.SetSpontaneousSMactivationRate(0.000);
profile.SetSpontaneousSMinactivationRate(000);
// profile.SetInitNumber((GRID_SIZE*GRID_SIZE)/100);
profile.SetInitNumber(initSntNumber);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionSnt);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SynSnap25);
RprofileVec[Syn] = profile;
profile.SetDefaultD(RprofileVec[Syn].GetDefaultD()/sqrt(2));
profile.Set_D_upon_Active(RprofileVec[Syn].Get_D_upon_Active()/sqrt(2));
profile.SetDefault_P_enterRaft(Pin_SynSyn);
profile.SetP_enterRaft_upon_Active(Pin_SynSyn);
profile.SetDefault_P_leaveRaft(Pout_SynSyn);
profile.SetP_leaveRaft_upon_Active(Pout_SynSyn);
profile.SetSpontaneousSMactivationRate(0.000);
profile.SetSpontaneousSMinactivationRate(000);
// profile.SetInitNumber((GRID_SIZE*GRID_SIZE)/100);
profile.SetInitNumber(initSntSntNumber);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionSntSnt);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SynSnap25);
RprofileVec[SynSyn] = profile;
profile.SetDefaultD(RprofileVec[Syn].GetDefaultD()/sqrt(3));
profile.Set_D_upon_Active(RprofileVec[Syn].Get_D_upon_Active()/sqrt(3));
profile.SetDefault_P_enterRaft(Pin_SynSynSyn);
profile.SetP_enterRaft_upon_Active(Pin_SynSynSyn);
profile.SetDefault_P_leaveRaft(Pout_SynSynSyn);
profile.SetP_leaveRaft_upon_Active(Pout_SynSynSyn);
profile.SetSpontaneousSMactivationRate(0.000);
profile.SetSpontaneousSMinactivationRate(000);
// profile.SetInitNumber((GRID_SIZE*GRID_SIZE)/100);
profile.SetInitNumber(initSntSntSntNumber);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionSntSntSnt);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SynSnap25);
RprofileVec[SynSynSyn] = profile;
profile.SetDefaultD(RprofileVec[Syn].GetDefaultD()/sqrt(2));
profile.Set_D_upon_Active(RprofileVec[Syn].Get_D_upon_Active()/sqrt(2));
profile.SetDefault_P_enterRaft(Pin_SynSnap25);
profile.SetP_enterRaft_upon_Active(Pin_SynSnap25);
profile.SetDefault_P_leaveRaft(Pout_SynSnap25);
profile.SetP_leaveRaft_upon_Active(Pout_SynSnap25);
profile.SetSpontaneousSMactivationRate(0.000);
profile.SetSpontaneousSMinactivationRate(000);
profile.SetInitNumber(initSynSnap25);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionSynSnap25);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SNAP25);
RprofileVec[SynSnap25] = profile;
profile.SetDefaultD(RprofileVec[Syn].GetDefaultD()/sqrt(3));
profile.Set_D_upon_Active(RprofileVec[Syn].Get_D_upon_Active()/sqrt(3));
profile.SetDefault_P_enterRaft(Pin_SynSnap25Vamp);
profile.SetP_enterRaft_upon_Active(Pin_SynSnap25Vamp);
profile.SetDefault_P_leaveRaft(Pout_SynSnap25Vamp);
profile.SetP_leaveRaft_upon_Active(Pout_SynSnap25Vamp);
profile.SetSpontaneousSMactivationRate(0.001);
profile.SetSpontaneousSMinactivationRate(000);
profile.SetInitNumber(initSynSnap25Vamp);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionSynSnap25Vamp);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SNAP25);
RprofileVec[SynSnap25Vamp] = profile;
profile.SetDefaultD(RprofileVec[Syn].GetDefaultD()/sqrt(4));
profile.Set_D_upon_Active(RprofileVec[Syn].Get_D_upon_Active()/sqrt(4));
profile.SetDefault_P_enterRaft(Pin_SynSnap25VampAlpha);
profile.SetP_enterRaft_upon_Active(Pin_SynSnap25VampAlpha);
profile.SetDefault_P_leaveRaft(Pout_SynSnap25VampAlpha);
profile.SetP_leaveRaft_upon_Active(Pout_SynSnap25VampAlpha);
profile.SetSpontaneousSMactivationRate(0.001);
profile.SetSpontaneousSMinactivationRate(000);
profile.SetInitNumber(initSynSnap25VampAlpha);
profile.SetInitActivePercent(0);
profile.SetThresholdNumber(-1);
profile.SetInitInRaftFraction(InitInRaftFractionSynSnap25VampAlpha);
profile.SetAxisAttached(false);
profile.SetAxisName('n');
profile.SetSubstrateName(SNAP25);
RprofileVec[SynSnap25VampAlpha] = profile;
}
void CGeneral::BindSigMolToGrid(CSigMol & sm)
{
/*
sm.SetUsage(true);
bool is_in_raft = false;
if(rg.Random() < SMprofileVec[sm.GetType()].GetInitInRaftFraction()) // is to put in raft
if(RAFT_NUMBER>0)
is_in_raft = true;
int attempt_count1 = 0;
while(1)
{
if(attempt_count1++ > 300000 )
{
CGeneral::START_SIM = false;
throw(-3);
}
sm.Location.x = rand()%GRID_SIZE;
sm.Location.y = rand()%GRID_SIZE;
if(grid.m_Grid[sm.Location.y] [sm.Location.x].array[SM] == -1) //free place
{
int RaftNum = grid.m_Grid[sm.Location.y][sm.Location.x].array[Raft];
if(RaftNum >= 0) // sm is inside the raft
{
if( is_in_raft )
{
CGeneral::RaftArray[RaftNum].SetSMIndex(sm.GetIndex());
sm.GetInRaft(RaftNum);
break;
}//if inside raft is ok
}
else // SM is outside the raft
{
if( !is_in_raft )
{
break;
}//if outside raft is ok
}
}
}
grid.m_Grid[sm.Location.y][sm.Location.x].array[SM] = sm.GetIndex();
*/
}
bool CGeneral::LocateSMOnGrid(CSigMol & sm, CPoint location)
{
/*
bool valid_location = false;
////// looking for neihbor free place ///////////
int new_y = location.y;
int new_x = location.x;
POINT pts[8] = {-1,0, -1,-1, 0,-1, 1,-1, 1,0, 1,1, 0,1, -1,1};
for(int k=0; k<8; k++)
{
switch(k)
{
case 0:
// x - 1 = LEFT
if( (new_x = location.x + pts[k].x) < 0 ) new_x = GRID_SIZE - 1;
break;
case 1:
// x - 1, y - 1 = UP_LEFT
if( (new_x = location.x + pts[k].x) < 0 ) new_x = GRID_SIZE - 1;
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
case 2:
// y - 1 = UP
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
case 3 :
// x + 1, y - 1 = UP_RIGHT
if( (new_x = location.x + pts[k].x) >= GRID_SIZE ) new_x = 0;
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
case 4 :
// x + 1 = RIGHT
if( (new_x = location.x + pts[k].x) >= GRID_SIZE ) new_x = 0;
break;
case 5 :
// x + 1, y + 1 = DOWN_RIGHT
if( (new_x = location.x + pts[k].x) >= GRID_SIZE ) new_x = 0;
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
case 6:
// y + 1 = DOWN
if( (new_y = location.y + pts[k].y) >= GRID_SIZE ) new_y = 0;
break;
case 7 :
// x - 1, y + 1 = DOWN_LEFT
if( (new_x = location.x + pts[k].x) >= GRID_SIZE ) new_x = 0;
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
}
int smID = grid.m_Grid[new_y][new_x].array[SM];
// _ASSERTE(CGeneral::grid.m_Grid[new_y][new_x].GetCellIndex() >= 0);
if((smID == -1)) //pSM is absent
{
valid_location = true;
break;
}
}
//---------- finish looking for neihbor free place ---------------
sm.Location.y = new_y;
sm.Location.x = new_x;
if(!valid_location)
{
return false;
_ASSERTE(0);
}
sm.SetUsage(true);
grid.m_Grid[sm.Location.y][sm.Location.x].array[SM] = sm.GetIndex();// update grid with sm index
int RaftNum = grid.m_Grid[sm.Location.y][sm.Location.x].array[Raft];
if(RaftNum >= 0) // sm is inside the raft
{
CGeneral::RaftArray[RaftNum].SetSMIndex(sm.GetIndex());
sm.GetInRaft(RaftNum);
}
*/
return true;
}
bool CGeneral::LocateRecOnGrid(CReceptor & rec, CPoint location)
{
/*
bool valid_location = false;
////// looking for neihbor free place ///////////
int new_y = location.y;
int new_x = location.x;
POINT pts[8] = {-1,0, -1,-1, 0,-1, 1,-1, 1,0, 1,1, 0,1, -1,1};
for(int k=0; k<8; k++)
{
switch(k)
{
case 0:
// x - 1 = LEFT
if( (new_x = location.x + pts[k].x) < 0 ) new_x = GRID_SIZE - 1;
break;
case 1:
// x - 1, y - 1 = UP_LEFT
if( (new_x = location.x + pts[k].x) < 0 ) new_x = GRID_SIZE - 1;
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
case 2:
// y - 1 = UP
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
case 3 :
// x + 1, y - 1 = UP_RIGHT
if( (new_x = location.x + pts[k].x) >= GRID_SIZE ) new_x = 0;
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
case 4 :
// x + 1 = RIGHT
if( (new_x = location.x + pts[k].x) >= GRID_SIZE ) new_x = 0;
break;
case 5 :
// x + 1, y + 1 = DOWN_RIGHT
if( (new_x = location.x + pts[k].x) >= GRID_SIZE ) new_x = 0;
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
case 6:
// y + 1 = DOWN
if( (new_y = location.y + pts[k].y) >= GRID_SIZE ) new_y = 0;
break;
case 7 :
// x - 1, y + 1 = DOWN_LEFT
if( (new_x = location.x + pts[k].x) >= GRID_SIZE ) new_x = 0;
if( (new_y = location.y + pts[k].y) < 0 ) new_y = GRID_SIZE - 1;
break;
}
int recID = grid.m_Grid[new_y][new_x].array[Rec];
// _ASSERTE(CGeneral::grid.m_Grid[new_y][new_x].GetCellIndex() >= 0);
if((recID == -1)) //rec is absent
{
valid_location = true;
break;
}
}
//---------- finish looking for neihbor free place ---------------
rec.CurrentLocation.y = new_y;
rec.CurrentLocation.x = new_x;
if(!valid_location)
{
return false;
_ASSERTE(0);
}
rec.SetUsage(true);
grid.m_Grid[rec.CurrentLocation.y][rec.CurrentLocation.x].array[Rec] = rec.Get_R_index();// update grid with rec index
int RaftNum = grid.m_Grid[rec.CurrentLocation.y][rec.CurrentLocation.x].array[Raft];
if(RaftNum >= 0) // sm is inside the raft
{
CGeneral::RaftArray[RaftNum].SetRecIndex(rec.Get_R_index());
rec.GetInRaft(RaftNum);
}
*/
return true;
}
/*
void CGeneral::InitReceptors()
{
int Rindex = 0;
int rec_num = RprofileVec[Syn].GetInitNumber();
for(int index=0; index<rec_num; index++)
{
CReceptor r(Rindex++, Syn);
BindReceptorToGrid(r);
RArray.push_back(r);
}
}
void CGeneral::InitReceptors()
{
int Rindex = 0;
int r_amount;
std::vector<CRprofile> ::iterator iter = RprofileVec.begin();
for (; iter != R_ProfileVec.end(); iter++)
{
r_amount = iter->GetInitNumber();
for( int i =0 ; i<r_amount ; i++ )
{
CReceptor r(Rindex++, (R_Type)i);
BindReceptorToGrid(r);
RArray.push_back(r);
}
}
}
*/
void CGeneral::InitReceptors()
{
int index = 0;
int r_amount;
for (int r_type=0; r_type<R_TYPES_NUMBER; r_type++)
{
r_amount = RprofileVec[r_type].GetInitNumber();
for( int i =0 ; i<r_amount ; i++ )
{
CReceptor r_object(index++, (R_Type)r_type);
BindReceptorToGrid(r_object);
RArray.push_back(r_object);
}
}
}
void CGeneral::CreateReceptor() //create receptors during the run
{
while( ! delRecStack.empty() )
{
int tmp = delRecStack.top();
CReceptor & rec = CGeneral::RArray[tmp];
// _ASSERTE(rec.Get_R_index() >= 0 ); //
delRecStack.pop();
BindReceptorToGrid(rec);
// _ASSERTE(rec.Get_R_index() >= 0 ); //
if( is_create_sm_attached_rec )
{
} // if
_ASSERTE(rec.Get_R_index() >= 0 ); //
}
}
void CGeneral::InitSigMol()
{
int index = 0;
int sm_amount;
for (int sm_type=0; sm_type<SM_TYPES_NUMBER; sm_type++)
{
sm_amount = SMprofileVec[sm_type].GetInitNumber();
for( int i =0 ; i<sm_amount ; i++ )
{
MakeSigMol(index++,(SM_Type)sm_type, CPoint(-1,-1));// -1,-1 for arbitrLocation
}
}
lastSMindex = SMArray.size();
}
void CGeneral::MakeSigMol(int index, SM_Type sm_type, CPoint location)
{
if(index==-1) //new SM
{
index = lastSMindex;
}
CSigMol sm_object(index, (SM_Type)sm_type);
if(location == CPoint(-1,-1)){ BindSigMolToGrid(sm_object); }
else { LocateSMOnGrid(sm_object, location);}
if(SMprofileVec[sm_object.GetType()].GetIsCyto())
sm_object.SetUsage(false);
SMArray.push_back(sm_object);
lastSMindex = SMArray.size();
}
void CGeneral::CreateSigMol(SM_Type type)
{
int tmp = delSMStack.top();
CSigMol & sm = SMArray[tmp];
delSMStack.pop();
sm.SetType(type);
if( ! SMprofileVec[sm.GetType()].IsAxisAttached() ) //to create anywere
{
BindSigMolToGrid(sm);
}
else //to create near the axis
{
// BindSigMolToGrid(sm, SMprofileVec[sm.GetType()].GetAxisName());
}
}
void CGeneral::GenerateSigMol()
{
while( ! delSMStack.empty() )
{
if( !EndocytosedSMQueue.empty() )
{
CreateSigMol(EndocytosedSMQueue.front());
EndocytosedSMQueue.pop();
}
else //vremenno
{
_ASSERTE(0);
}
}
}
void CGeneral::CreateRaft(int in_index)
{
/*
int index;
if(in_index == -1)
{
while( ! delRaftStack.empty() )
{
index = delRaftStack.top();
delRaftStack.pop();
CRaft Raft_Object(index);
RaftArray[index] = Raft_Object;
polygonFill(Raft_Object.m_shape.GetPtVec() ,Raft_Object.m_shape.Count(), index );
} // while
}
else
{
index = in_index;
CRaft Raft_Object(index);
RaftArray.push_back(Raft_Object);
polygonFill(Raft_Object.m_shape.GetPtVec() ,Raft_Object.m_shape.Count(), index );
}
*/
}
void CGeneral::InitRafts(int raft_number)
{
for(int index=0; index < raft_number; index++)
{
CreateRaft(index);
}
}
int CGeneral::DimentionSquareDistrib()
{
return 15;
}
int CGeneral::BeginSimulation()
{
// bool flag_to_mesure_distance = false; //flag == true neans need to calculate the distanse
CGeneral::is_simul_finished = false;
if(step++ > TIME_STEP_NUMBER) return 0; //simulation is finished
///////////// start of calculations //////////////////////////////
// int calc_rule1 = (step<1000)?1:(step<10000)?10000:(step<100000)?100000:(step<1000000)?100000:1000000 ;
int calc_rule1 = 600/TIME_STEP_LENGHT;
// int calc_rule1 = 60*60/TIME_STEP_LENGHT;
if(step %calc_rule1 == 0 || step == 1)
// if(step %calc_rule1 == 0 || step == 1 || step == TIME_STEP_NUMBER)
{
// CalculateMSD(step);
// Calculate_R_in_out_ratio();
// Calculate_R_unbound_bound_ratio();
// Calculate_R_SM_complex_in_out_ratio();
// Calculate_R_SM_binding_duration();
// Calculate_endoc_results();
Calculate_protein_concentrations();
/*
int flg = 0;
if(flg) CalcResGridG();
else CalcResGrid();
*/
}
//------------- finish of calculations -----------------------//
///////////////// start of Rafts loop //////////////////////////////
// RaftsLoop();
CellsLoop();
//---------------finish of Rafts loop -----------------------//
///////////////// start of Ags loop //////////////////////////////
// AgsLoop();
//---------------finish of Ags loop -----------------------//
///////////////// start of SMs loop //////////////////////////////
SMsLoop();
//---------------finish of SMs loop -----------------------//
// CGeneral::Validation(Rec);
CGeneral::is_simul_finished = true;
return step;
}
int CGeneral::PtInRaft(CPoint & pt, int CurRaftNum)
{
/*
if(CurRaftNum >=0)
{
return (CGeneral::RaftArray[CurRaftNum].m_shape.PtInPolygon( pt)) ?
CurRaftNum : -1;
}
std::vector<CRaft>::iterator raft_iter = CGeneral::RaftArray.begin();
for(; raft_iter != CGeneral::RaftArray.end(); raft_iter++)
{
if(raft_iter->IsInUse() &&
raft_iter->m_shape.PtInPolygon( pt)) return raft_iter->Get_raft_index();
}
*/
return -1;
}
int CGeneral::PtInRaft(CPoint & pt, int & l, int CurRaftNum)
{
/*
_ASSERTE(!"Not in use");
if(CurRaftNum >=0)
{
l=0;
return (CGeneral::RaftArray[CurRaftNum].m_shape.PtInPolygon( pt)) ?
CurRaftNum : -1;
}
int l1=10000 ;
std::vector<CRaft>::iterator raft_iter = CGeneral::RaftArray.begin();
for(; raft_iter != CGeneral::RaftArray.end(); raft_iter++)
{
if(raft_iter->IsInUse() &&
raft_iter->m_shape.PtInPolygon( pt, l )) return raft_iter->Get_raft_index();
if(l < l1) l1 = l;
}
l = l1;
if(l > 0) noInterSec++;
//CGeneral::out << "Result l=" << l << "\n" ;
*/
return -1;
}
Kind_of_Move CGeneral::Select_move()
{
Kind_of_Move move;
// int choice = rand()%4;
int choice = rg.IRandom(0,3);
move = (Kind_of_Move)choice;
return move;
}
double CGeneral::My_rand(double min, double max)
{
return min + double(rg.IRandom(0, RAND_MAX)) / RAND_MAX * (max - min);
}
double CGeneral::My_rand0_1()
{
return rg.Random();
// return ( (double)rand() / (double)(RAND_MAX+1) );
}
void CGeneral::CalculateMSD(int time_step)
{
/*
int square_value = 0;
for(int index=0; index<RECEPTOR_NUMBER; index++)
{
// if(RecMSDResults[index] != -1) //to avoid calculating receptors that crossed the border
{
square_value += RecMSDResults[index];
}
}
int R_number = RECEPTOR_NUMBER;
int mean_square_value = square_value / R_number;
CPoint object(time_step, mean_square_value);
MSDResultsArray.push_back(object);
*/
}
void CGeneral::Calculate_protein_concentrations()
{
CResultsTemplate ResultsObject;
ResultsObject.step = step;