void fire()
{
if( theLastTime < 0.0 )
{
return;
}
Real aCurrentTime( getStepper()->getCurrentTime() );
Real aNextTime( theLastTime + Interval );
if( aNextTime >= Duration )
{
theLastTime = -1;
P0.setValue( 1e-20 * getSuperSystem()->getSizeN_A() );
return;
}
Real aTimeDifference( aCurrentTime - theLastTime );
Real aDecay( aTimeDifference * DecayFactor / Interval );
P0.setValue( Impulse * getSuperSystem()->getSizeN_A()
/ ( aDecay + 1 ) );
if( aTimeDifference >= Interval )
{
theLastTime += Interval;
}
}
Variable* createVariable(String anID)
{
String anEntityType("Variable");
SystemPath aSystemPath(getSuperSystem()->getSystemPath());
aSystemPath.push_back(getSuperSystem()->getID());
FullID aFullID(anEntityType, aSystemPath, anID);
Variable* aVariable(reinterpret_cast<Variable*>(
getModel()->createEntity("Variable", aFullID)));
aVariable->setValue(0);
return aVariable;
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real VGPA_maxr = VGPA_maxf->getValue() * KGPA_GLYb * KGPA_iG1P / KGPA_iGLYf / KGPA_Pi / KGPA_eq;
Real GPA_a= VGPA_maxf->getValue() * (GLY->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / KGPA_iGLYf / KGPA_Pi ) - VGPA_maxr * (GLY->getMolarConc()*1000.0 * G1P->getMolarConc()*1000.0 / KGPA_GLYb / KGPA_iG1P);
Real GPA_b= 1.0 + GLY->getMolarConc()*1000.0 / KGPA_iGLYf + Pi->getMolarConc()*1000.0 / KGPA_iPi + GLY->getMolarConc()*1000.0 / KGPA_iGLYb + G1P->getMolarConc()*1000.0 / KGPA_iG1P + GLY->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / (KGPA_GLYf * KGPA_iPi) + GLY->getMolarConc()*1000.0 * G1P->getMolarConc()*1000.0 /(KGPA_GLYb * KGPA_iG1P) ;
Real V_GPA = GPA_a / GPA_b;
Real VGPB_maxr = VGPB_maxf->getValue() * KGPB_iGLYb * KGPB_G1P / KGPB_iGLYf / KGPB_Pi / KGPB_eq;
Real GPB_a = (pow(AMP->getMolarConc()*1000.0, nH_GPB)/ KGPB_AMP) * (VGPB_maxf->getValue() * (GLY->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 /(KGPB_iGLYf * KGPB_Pi)) - VGPB_maxr * (GLY->getMolarConc()*1000.0 * G1P->getMolarConc()*1000.0/(KGPB_iGLYb * KGPB_G1P)));
Real GPB_b = (1.0 + pow(AMP->getMolarConc()*1000.0, nH_GPB)/ KGPB_AMP) * ( 1.0 + GLY->getMolarConc()*1000.0 / KGPB_iGLYf + Pi->getMolarConc()*1000.0 / KGPB_iPi + GLY->getMolarConc()*1000.0 / KGPB_iGLYb + G1P->getMolarConc()*1000.0 / KGPB_iG1P + GLY->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / (KGPB_iGLYf * KGPB_Pi) + GLY->getMolarConc()*1000.0 * G1P->getMolarConc()*1000.0 /(KGPB_iGLYb * KGPB_G1P) );
Real V_GPB = GPB_a / GPB_b;
setFlux( GX->getValue() * _SizeN_A * ( V_GPA * frac_a->getValue() + V_GPB * frac_b->getValue()) / 60000.0 / 1000.0);
// setFlux( V_GPA * frac_a->getValue() + V_GPB * frac_b->getValue());
// setFlux(GPB_a / GPB_b );
// setFlux(GPA_a / GPA_b );
//V_GPA.setValue(GPA_a / GPA_b / unit);
// ducky
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void fire()
{
Real hkrd =
( 1 + ( S1.getMolarConc() / KiMgATP ) +
( (S0.getMolarConc() * 7 / 3) / KiGlc ) +
( ( S1.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KiGlc * KmMgATP ) ) +
( P1.getMolarConc() / KiMgADP ) +
( P0.getMolarConc() / KiGlc6P ) +
( ( P1.getMolarConc() * P0.getMolarConc() ) / ( KiGlc6P * KmMgADP ) ) +
( ( E1.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KdiB23PG * KiGlc ) ) +
( ( E2.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KdiGlc16P2 * KiGlc ) ) +
( ( P0.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KdiGlc6P * KiGlc ) ) +
( ( E3.getMolarConc() * (S0.getMolarConc() * 7 / 3) ) / ( KdiGSH * KiGlc ) ) );
// fix me: * voli?
Real GG = E3.getMolarConc()/E4.getMolarConc();
Real velocity =
(GG/(K_GSSG + GG)) * ( HK / hkrd *
( ( theKcatf * (S0.getMolarConc() * 7 / 3) * S1.getMolarConc() ) /
( KiGlc * KmMgATP ) -
( theKcatr * P0.getMolarConc() * P1.getMolarConc() ) /
( KiGlc6P * KmMgADP ) ) );
//velocity = velocity * getSuperSystem()->getSize() * N_A * ( 20.0 / 7.0 );
velocity = velocity * getSuperSystem()->getSize() * N_A;
setFlux( velocity );
}
unsigned int MicrotubuleProcess::getLatticeResizeCoord(unsigned int aStartCoord)
{
theComp = theSpatiocyteStepper->system2Comp(getSuperSystem());
theVacantSpecies->resetFixedAdjoins();
theVacantSpecies->setMoleculeRadius(DimerPitch*VoxelDiameter/2);
theMinusSpecies->resetFixedAdjoins();
theMinusSpecies->setMoleculeRadius(DimerPitch*VoxelDiameter/2);
thePlusSpecies->resetFixedAdjoins();
thePlusSpecies->setMoleculeRadius(DimerPitch*VoxelDiameter/2);
tempID = theSpecies.size();
C = theComp->centerPoint;
C.x += OriginX*theComp->lengthX/2;
C.y += OriginY*theComp->lengthY/2;
C.z += OriginZ*theComp->lengthZ/2;
for(unsigned int i(0); i != theKinesinSpecies.size(); ++i)
{
theKinesinSpecies[i]->setIsOffLattice();
theKinesinSpecies[i]->setDimension(1);
theKinesinSpecies[i]->setVacantSpecies(theVacantSpecies);
theKinesinSpecies[i]->setMoleculeRadius(DimerPitch*VoxelDiameter/2);
}
offLatticeRadius = DimerPitch/2;
latticeRadius = 0.5;
theDimerSize = (unsigned int)rint(Length/DimerPitch);
startCoord = aStartCoord;
endCoord = startCoord+Protofilaments*theDimerSize;
return endCoord-startCoord;
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real delta1 = (1.0 + F6P->getMolarConc()*1000.0 / KPFK_F6P) * (1.0 + ATP->getMolarConc()*1000.0 / KPFK_ATP)+ ADP->getMolarConc()*1000.0 / KPFK_ADP + FBP->getMolarConc()*1000.0 / KPFK_FBP * (1.0 + ADP->getMolarConc()*1000.0 / KPFK_ADP);
Real delta2 = (1.0 + F6P->getMolarConc()*1000.0 / KPFK_F6P2) * (1.0 + ATP->getMolarConc()*1000.0 / KPFK_ATP2)+ ADP->getMolarConc()*1000.0 / KPFK_ADP2 + FBP->getMolarConc()*1000.0 / KPFK_FBP2 * (1.0 + ADP->getMolarConc()*1000.0 / KPFK_ADP2);
Real alpha = KPFK_F6P * KPFK_ATP / KPFK_F6P2 / KPFK_ATP2;
Real L = Lo_PFK * pow(((1.0+ATP->getMolarConc()*1000.0/KPFK_iATP) / (1.0 + d_PFK * ATP->getMolarConc()*1000.0/KPFK_iATP)) * ((1.0 + e_PFK * AMP->getMolarConc()*1000.0/KPFK_aAMP) / (1.0 + AMP->getMolarConc()*1000.0/KPFK_aAMP)), 4);
Real VPFK_maxr = VPFK_maxf->getValue() * KPFK_ADP * KPFK_FBP / KPFK_ATP / KPFK_F6P / KPFK_eq;
Real PFK_a = (1.0 + alpha * L * pow(delta2/delta1, 3))*(VPFK_maxf->getValue() * ATP->getMolarConc()*1000.0 * F6P->getMolarConc()*1000.0 /(KPFK_ATP * KPFK_F6P) - VPFK_maxr * ADP->getMolarConc()*1000.0 * FBP->getMolarConc()*1000.0 /(KPFK_ADP * KPFK_FBP));
Real PFK_b = delta1 * (1.0 + L * pow(delta2/delta1, 4));
setFlux( GX->getValue() * _SizeN_A * PFK_a / PFK_b / 60000.0 /1000.0);
// setFlux(PFK_a / PFK_b );
//V_PFK.setValue(PFK_a / PFK_b / unit);
// ducky
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
System*
System::getSystem( String const& anID ) const
{
if ( anID[0] == '.' )
{
const String::size_type anIDSize( anID.size() );
if ( anIDSize == 1 ) // == "."
{
return const_cast<System*>( this );
}
else if ( anID[1] == '.' && anIDSize == 2 ) // == ".."
{
if ( isRootSystem() )
{
THROW_EXCEPTION_INSIDE( NotFound,
asString() + ": the root system has no super "
"systems" );
}
return getSuperSystem();
}
}
SystemMap::const_iterator i( theSystemMap.find( anID ) );
if ( i == theSystemMap.end() )
{
THROW_EXCEPTION_INSIDE( NotFound,
asString() + ": System [" + anID +
"] not found in this System" );
}
return i->second;
}
virtual void initialize()
{
Process::initialize();
declareUnidirectional();
theSpatiocyteStepper =
dynamic_cast<SpatiocyteStepper*>(getSuperSystem()->getStepper());
}
virtual void fire()
{
Real L = ( pow( pow( 10, -1 * E0.getValue() ) / Ka, n ) *
pow( 1 + E1.getMolarConc() / KTATP, 4 ) *
pow( 1 + E2.getMolarConc() / KTMg, 4 ) *
pow( 1 + E3.getMolarConc() / KTB23PG, 4 ) ) /
( pow( 1 + ( S0.getMolarConc() / KmFru6P ) + ( P0.getMolarConc() / KmFru16P2 ), 4 ) *
pow( 1 + E4.getMolarConc() / KRAMP, 4 ) *
pow( 1 + E5.getMolarConc() / KRPhos, 4 ) *
pow( 1 + E6.getMolarConc() / KRGlc16P2, 4 ) );
Real pfkrd = 1 + ( S0.getMolarConc() / KmFru6P ) +
( S1.getMolarConc() / KmMgATP ) +
( ( S0.getMolarConc() * S1.getMolarConc() ) / ( KmFru6P * KmMgATP ) ) +
( P0.getMolarConc() / KmFru16P2 ) +
( P1.getMolarConc() / KmMgADP ) +
( ( P0.getMolarConc() * P1.getMolarConc() ) / ( KmFru16P2 * KmMgADP ) );
Real velocity = ( C0.getMolarConc() / ( ( 1 + L ) * pfkrd ) ) *
( ( kcatf * S0.getMolarConc() * S1.getMolarConc() ) / ( KmFru6P * KmMgATP ) -
//note: use book model.
( kcatf * P0.getMolarConc() * P1.getMolarConc() ) / ( KmFru16P2 * KmMgADP ) );
velocity = velocity * getSuperSystem()->getSize() * N_A * E7.getValue()/1000;
Real GG = E8.getMolarConc()/E9.getMolarConc();
velocity *= GG/(K_GSSG + GG);
setFlux( velocity );
}
virtual void fire()
{
Real velocity = k8* S0.getMolarConc() - k9 * P0.getMolarConc();
velocity = velocity * getSuperSystem()->getSize() * N_A;
setFlux( velocity );
}
virtual void fire()
{
Real velocity = theK1 * S0.getMolarConc() * S1.getMolarConc() - k2 * P0.getMolarConc();
velocity = velocity * getSuperSystem()->getSize() * N_A;
velocity = velocity * E1.getValue() / 1000;
setFlux( velocity );
}
virtual void fire()
{
Real velocity = Kma * S0.getMolarConc() -
Kmd * P0.getMolarConc();
velocity = velocity * getSuperSystem()->getSize() * N_A;
velocity = velocity * E0.getValue() / 1000;
setFlux( velocity );
}
virtual void fire()
{
Real velocity = k * S0.getMolarConc();
velocity = velocity * getSuperSystem()->getSize() * N_A;
if(velocity < 0)
{
velocity = 0;
}
setFlux( velocity );
}
virtual void fire()
{
Real pgmrd = 1 + ( S0.getMolarConc() / KmP3GA ) +
( P0.getMolarConc() / KmP2GA );
Real velocity = ( PGM / pgmrd ) *
( ( ( kcatf * S0.getMolarConc() ) / KmP3GA ) -
( ( kcatr * P0.getMolarConc() ) / KmP2GA ) );
velocity = velocity * getSuperSystem()->getSize() * N_A;
setFlux( velocity );
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real VPGLM_maxr = VPGLM_maxf->getValue() * KPGLM_G6P / KPGLM_G1P / KPGLM_eq;
Real PGLM_a = VPGLM_maxf->getValue() * G1P->getMolarConc()*1000.0 / KPGLM_G1P - VPGLM_maxr * G6P->getMolarConc()*1000.0 / KPGLM_G6P;
Real PGLM_b = 1.0 + G1P->getMolarConc()*1000.0 / KPGLM_G1P + G6P->getMolarConc()*1000.0 / KPGLM_G6P;
setFlux( GX->getValue() * _SizeN_A * PGLM_a / PGLM_b / 60000.0 /1000.0);
// setFlux(PGLM_a / PGLM_b );
//V_PGLM.setValue(PGLM_a / PGLM_b / unit);
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void fire()
{
double currTime(getStepper()->getCurrentTime());
//std::cout << theVariableReferenceVector[0].getVariable()->getID() << std::endl;
if(currTime > 1000)
{
double currValue(theVariableReferenceVector[0].getValue());
double diffValue(currValue-prevValue);
if(diffValue*diffValue >=
theVariableReferenceVector[0].getCoefficient()*
theVariableReferenceVector[0].getCoefficient()
&& currValue != prevValue)
{
double interval(currTime-prevTime);
totalInterval += interval;
++intervalCnt;
std::cout << currTime << " " << getID() << " averageInterval:"
<< totalInterval/intervalCnt << std::endl;
prevTime = currTime;
prevValue = currValue;
}
}
else
{
prevTime = currTime;
}
Real velocity( k * N_A );
velocity *= getSuperSystem()->getSize();
for( VariableReferenceVector::const_iterator s(
theVariableReferenceVector.begin() );
s != theZeroVariableReferenceIterator; ++s )
{
VariableReference const& aVariableReference( *s );
Integer aCoefficient( aVariableReference.getCoefficient() );
do
{
++aCoefficient;
velocity *= aVariableReference.getVariable()->getMolarConc();
}
while( aCoefficient != 0 );
}
setFlux(velocity);
}
SystemPath Entity::getSystemPath() const
{
System* aSystem( getSuperSystem() );
if ( !aSystem )
{
THROW_EXCEPTION( IllegalOperation, "no system is associated" );
}
if ( aSystem == this )
{
return SystemPath();
}
SystemPath aSystemPath( aSystem->getSystemPath() );
aSystemPath.push_back( aSystem->getID() );
return aSystemPath;
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
// Real VPGI_maxf = VPGI_maxr * KPGI_G6P * KPGI_eq / KPGI_F6P;
Real VPGI_maxf = VPGI_maxr->getValue() * KPGI_G6P * KPGI_eq / KPGI_F6P;
// Real PGI_a = VPGI_maxf * G6P->getValue() / KPGI_G6P - VPGI_maxr * F6P->getValue() / KPGI_F6P;
Real PGI_a = VPGI_maxf * G6P->getMolarConc()*1000.0 / KPGI_G6P - VPGI_maxr->getValue() * F6P->getMolarConc()*1000.0 / KPGI_F6P;
Real PGI_b = 1.0 + G6P->getMolarConc()*1000.0 / KPGI_G6P + F6P->getMolarConc()*1000.0 / KPGI_F6P;
setFlux( GX->getValue() * _SizeN_A * PGI_a / PGI_b / 60000.0 / 1000.0);
// setFlux(PGI_a / PGI_b );
//V_PGI.setValue(PGI_a / PGI_b / unit);
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real VGAPDH_maxr = VGAPDH_maxf->getValue() * KGAPDH_13BPG * KGAPDH_NADH / KGAPDH_GAP / KGAPDH_NAD / KGAPDH_Pi / KGAPDH_eq;
Real GAPDH_a = VGAPDH_maxf->getValue() * GAP->getMolarConc()*1000.0 * NAD->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / (KGAPDH_GAP * KGAPDH_NAD * KGAPDH_Pi) - VGAPDH_maxr * BPG13->getMolarConc()*1000.0 * NADH->getMolarConc()*1000.0 / (KGAPDH_13BPG * KGAPDH_NADH);
Real GAPDH_b = 1.0 + GAP->getMolarConc()*1000.0 / KGAPDH_GAP + NAD->getMolarConc()*1000.0 / KGAPDH_NAD + Pi->getMolarConc()*1000.0 / KGAPDH_Pi + GAP->getMolarConc()*1000.0 * NAD->getMolarConc()*1000.0 / (KGAPDH_GAP * KGAPDH_NAD) + GAP->getMolarConc()*1000.0 * NAD->getMolarConc()*1000.0 * Pi->getMolarConc()*1000.0 / (KGAPDH_GAP * KGAPDH_NAD * KGAPDH_Pi) + BPG13->getMolarConc()*1000.0 / KGAPDH_13BPG + NADH->getMolarConc()*1000.0 / KGAPDH_NADH + BPG13->getMolarConc()*1000.0 * NADH->getMolarConc()*1000.0/(KGAPDH_13BPG * KGAPDH_NADH);
setFlux( GX->getValue() * _SizeN_A * GAPDH_a / GAPDH_b / 60000.0 /1000.0);
// setFlux(GAPDH_a / GAPDH_b );
//V_GAPDH.setValue(GAPDH_a / GAPDH_b / unit);
// ducky
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
void GillespieProcess::fire()
{
Real velocity( getk() * N_A );
velocity *= getSuperSystem()->getSize();
for( VariableReferenceVector::const_iterator
s( theVariableReferenceVector.begin() );
s != theZeroVariableReferenceIterator; ++s )
{
VariableReference aVariableReference( *s );
Integer aCoefficient( aVariableReference.getCoefficient() );
do
{
++aCoefficient;
velocity *= aVariableReference.getVariable()->getMolarConc();
}
while( aCoefficient != 0 );
}
setActivity( velocity );
}
virtual void fire()
{
Real velocity( k * N_A );
velocity *= getSuperSystem()->getSize();
for( VariableReferenceVector::const_iterator
s( theVariableReferenceVector.begin() );
s != theZeroVariableReferenceIterator; ++s )
{
VariableReference aVariableReference( *s );
Integer aCoefficient( aVariableReference.getCoefficient() );
do {
++aCoefficient;
velocity *= aVariableReference.getMolarConc();
} while( aCoefficient != 0 );
}
setFlux(velocity);
}
virtual void fire()
{
Real _SizeN_A = getSuperSystem()->getSizeN_A();
Real VCK_maxf = VCK_maxr->getValue() / KCK_iATP / KCK_Cr / KCK_eq * KCK_iADP * KCK_PCr;
// Real VCK_maxf = VCK_maxr->getValue() * KCK_iATP * KCK_Cr * KCK_eq / KCK_iADP / KCK_PCr; ducky 140414
Real CK_a = VCK_maxr->getValue() * ATP->getMolarConc()*1000.0 * Cr->getMolarConc()*1000.0 / (KCK_iATP * KCK_Cr) - VCK_maxf * ADP->getMolarConc()*1000.0 * PCr->getMolarConc()*1000.0 / (KCK_iADP * KCK_PCr);
Real CK_b = 1.0 + ADP->getMolarConc()*1000.0 / KCK_iADP + PCr->getMolarConc()*1000.0 / KCK_iPCr + ADP->getMolarConc()*1000.0 * PCr->getMolarConc()*1000.0 / (KCK_iADP * KCK_PCr) + ATP->getMolarConc()*1000.0 / KCK_iATP + Cr->getMolarConc()*1000.0 / KCK_Cr + ATP->getMolarConc()*1000.0 * Cr->getMolarConc()*1000.0 / (KCK_iATP * KCK_Cr);
setFlux(GX->getValue() * _SizeN_A * CK_a / CK_b / 60000.0 /1000.0);
// Real V_CK = 16.05 * PCr->getMolarConc()*1000.0 * ADP->getMolarConc()*1000.0 - 9.67e-6 * ATP->getMolarConc()*1000.0 * Cr->getMolarConc()*1000.0;
// setFlux(V_CK * _SizeN_A / 60000.0 / 1000.0);
// setFlux(CK_a / CK_b );
//V_CK.setValue(CK_a / CK_b / unit);
// ducky
// T->setValue( Tt->getValue() - TCa->getValue() - TCaCB->getValue() - TCB->getValue() );
}
virtual void initializeThird()
{
theComp = theSpatiocyteStepper->system2Comp(getSuperSystem());
theStepInterval = 1;
}
/**
Check if this is a root System.
@return true if this is a Root System, false otherwise.
*/
bool isRootSystem() const
{
return ( getSuperSystem() == this );
}
Variable* createVariable(String anID)
{
return createVariable(anID, getSuperSystem());
}
virtual void fire(){
Real deoxyHbcomp = S0.getVariable()->getMolarConc();
Real oxyHbcomp = P0.getVariable()->getMolarConc();
Real pHi = E0.getVariable()->getValue();
Real T = E1.getVariable()->getValue();
Real PO2 = E2.getVariable()->getValue();
Real PCO2 = E3.getVariable()->getValue();
Real BPG = E4.getVariable()->getMolarConc();
Real H = pow(10, -1*pHi); //H+(M)
Real aO2 = (1.37 - 0.0137*(T-37)+ 0.00058*(T-37)*(T-37))*0.000001/Wpl;
Real aCO2 = (3.07 - 0.057*(T-37)+ 0.002*(T-37)*(T-37))*0.00001/Wpl;
Real O2 = Wrbc * aO2 * PO2;//O2 concentration(M)
Real CO2 = Wrbc * aCO2 * PCO2;//CO2 concentration(M)
/*
Real n1 = -6.775 + 2.0372 * pHi - 0.1235 * pHi * pHi;
Real n2 = -0.008765 + 0.00086 * PCO2 + 6.3 * 0.0000001 * PCO2 * PCO2;
Real n3 = 0.2583 + 28.6978 * BPG - 917.69 * BPG * BPG;
Real n4 = 1.6914 + 0.06186 * T + 0.00048 * T * T;
Real K2d = K2/K2dd;
Real K3d = K3/K3dd;
Real nO2 = pow(O2,n);
Real K4dn1 = K4dd * pow((57.5*0.000000001/H),n1);
Real K4d = K4dn1 * pow((0.85*0.001/CO2),n2) * pow((4.65*0.001/BPG),n3) * pow((37/T),n4);
Real KHbO2 = K4d * (K3d*CO2*(1+K3dd/H)+(1+H/K6dd))/(K2d*CO2*(1+K2dd/H)+(1+H/K5dd));
Real kO2 = KHbO2 * nO2;
setKHbO2_c( KHbO2 ); // ducky 090616
*/
//Real SHbO2 = kO2 / (1 + kO2);
O2 = PO2;
// ducky 090715
Real SHbO2_num = O2/k1;
SHbO2_num += 3.0*pow(O2,2.0)/(k1*k2);
SHbO2_num += 3.0*pow(O2,3.0)/(k1*k2*k3);
SHbO2_num += pow(O2,4.0)/(k1*k2*k3*k4);
Real SHbO2_deno = 1.0;
SHbO2_deno += 4.0*O2/k1;
SHbO2_deno += 6.0*pow(O2,2.0)/(k1*k2);
SHbO2_deno += 4.0*pow(O2,3.0)/(k1*k2*k3);
SHbO2_deno += pow(O2,4.0)/(k1*k2*k3*k4);
Real SHbO2 = SHbO2_num / SHbO2_deno;
setSHb_O2_c( SHbO2 ); // ducky 090616
// std::cout << "PO2: " << PO2 << std::endl;
// std::cout << "SHbO2: " << SHbO2 << std::endl;
Real Ka;
Real Keq;
Keq = SHbO2 / (1 - SHbO2);
Ka = Keq * Kd;
// std::cout << "Keq: " << Keq << std::endl;
// std::cout << "Ka: " << Ka << std::endl;
// std::cout << "Kd: " << Kd << std::endl;
// Real velocity = deoxyHbcomp * Ka - oxyHbcomp * Kd;
// velocity = velocity * getSuperSystem()->getSize() * N_A;
Real oxyHb1 = E5.getVariable()->getMolarConc();//oxyHbMgATP
Real oxyHb2 = E6.getVariable()->getMolarConc();//oxyHbATP
Real oxyHb3 = E7.getVariable()->getMolarConc();//oxyHbADP
Real oxyHb4 = E8.getVariable()->getMolarConc();//oxyHb23DPG
Real oxyHb5 = E9.getVariable()->getMolarConc();//oxyHb13DPG
Real oxyHb6 = E10.getVariable()->getMolarConc();//band3oxyHbMgATP
Real oxyHb7 = E11.getVariable()->getMolarConc();//band3oxyHbATP
Real oxyHb8 = E12.getVariable()->getMolarConc();//band3oxyHbADP
Real oxyHb9 = E13.getVariable()->getMolarConc();//band3oxyHb23DPG
Real oxyHb10 = E14.getVariable()->getMolarConc();//band3oxyHb13DPG
Real oxyHb11 = E15.getVariable()->getMolarConc();//band3oxyHb
Real oxyHb12 = E16.getVariable()->getMolarConc();//oxyHb
Real toxyHb = oxyHb1 + oxyHb2 + oxyHb3 + oxyHb4 + oxyHb5 + oxyHb6 + oxyHb7 + oxyHb8 + oxyHb9 + oxyHb10 + oxyHb11 + oxyHb12;
Real velocity = (0.007-toxyHb) * Ka - toxyHb * Kd;
velocity = velocity * getSuperSystem()->getSize() * N_A;
setFlux(velocity);
}
void Process::resolveVariableReferences()
{
if ( !getSuperSystem() )
{
THROW_EXCEPTION_INSIDE( IllegalOperation,
asString() + ": process is not associated to "
"any system" );
}
Integer anEllipsisNumber( 0 );
for ( VariableReferenceVector::iterator
i( theVariableReferenceVector.begin() ),
e( theVariableReferenceVector.end() );
i != e; ++i )
{
VariableReference& aVarRef( *i );
if( aVarRef.isDefaultName() )
{
aVarRef.setName( VariableReference::ELLIPSIS_PREFIX +
( boost::format( "%03d" ) % anEllipsisNumber ).str() );
anEllipsisNumber++;
}
if ( !aVarRef.getVariable() )
{
// relative search; allow relative systempath
FullID const& aFullID( aVarRef.getFullID() );
if ( aFullID.isValid() )
{
System* aSystem( 0 );
try
{
aSystem = getSuperSystem()->getSystem( aFullID.getSystemPath() );
}
catch ( BadSystemPath const& )
{
}
if ( !aSystem )
{
THROW_EXCEPTION_INSIDE( IllegalOperation,
asString() + ": system path ["
+ aFullID.getSystemPath().asString()
+ "] could not be resolved" );
}
aVarRef.setVariable( aSystem->getVariable( aFullID.getID() ) );
}
else
{
THROW_EXCEPTION_INSIDE( IllegalOperation,
asString() + ": variable reference #"
+ boost::lexical_cast<std::string>( aVarRef.getSerial() )
+ " could not be resolved" );
}
}
else
{
aVarRef.setFullID( aVarRef.getVariable()->getFullID() );
}
}
}
void GillespieProcess::calculateOrder()
{
theOrder = 0;
for( VariableReferenceVector::const_iterator i(
theVariableReferenceVector.begin() );
i != theVariableReferenceVector.end() ; ++i )
{
libecs::VariableReference const& aVariableReference( *i );
const libecs::Integer aCoefficient( aVariableReference.getCoefficient() );
// here assume aCoefficient != 0
if( aCoefficient == 0 )
{
THROW_EXCEPTION_INSIDE( libecs::InitializationFailed,
asString()
+ ": zero stoichiometry is not allowed" );
}
if( aCoefficient < 0 )
{
// sum the coefficient to get the order of this reaction.
theOrder -= aCoefficient;
}
}
// set theGetPropensityMethodPtr and theGetMinValueMethodPtr
if( theOrder == 0 ) // no substrate
{
theGetPropensityMethodPtr =
RealMethodProxy::createConst<&GillespieProcess::getZero>();
theGetMinValueMethodPtr =
RealMethodProxy::createConst<&GillespieProcess::getZero>();
theGetPDMethodPtr = &GillespieProcess::getPD_Zero;
}
else if( theOrder == 1 ) // one substrate, first order.
{
theGetPropensityMethodPtr =
RealMethodProxy::createConst<&GillespieProcess::getPropensity_FirstOrder>();
theGetMinValueMethodPtr =
RealMethodProxy::createConst<&GillespieProcess::getMinValue_FirstOrder>();
theGetPDMethodPtr = &GillespieProcess::getPD_FirstOrder;
}
else if( theOrder == 2 )
{
if( getZeroVariableReferenceOffset() == 2 ) // 2 substrates, 2nd order
{
theGetPropensityMethodPtr = RealMethodProxy::createConst<
&GillespieProcess::getPropensity_SecondOrder_TwoSubstrates > ();
theGetMinValueMethodPtr = RealMethodProxy::createConst<
&GillespieProcess::getMinValue_SecondOrder_TwoSubstrates >();
theGetPDMethodPtr =
&GillespieProcess::getPD_SecondOrder_TwoSubstrates;
}
else // one substrate, second order (coeff == -2)
{
theGetPropensityMethodPtr = RealMethodProxy::createConst<
&GillespieProcess::getPropensity_SecondOrder_OneSubstrate>();
theGetMinValueMethodPtr = RealMethodProxy::createConst<
&GillespieProcess::getMinValue_SecondOrder_OneSubstrate>();
theGetPDMethodPtr =
&GillespieProcess::getPD_SecondOrder_OneSubstrate;
}
}
else
{
//FIXME: generic functions should come here.
theGetPropensityMethodPtr = RealMethodProxy::createConst<
&GillespieProcess::getZero>();
theGetPropensityMethodPtr = RealMethodProxy::createConst<
&GillespieProcess::getZero>();
theGetPDMethodPtr = &GillespieProcess::getPD_Zero;
}
//
if ( theOrder == 1 )
{
c = k;
}
else if ( theOrder == 2 && getZeroVariableReferenceOffset() == 1 )
{
c = k * 2.0 / ( libecs::N_A * getSuperSystem()->getSize() );
}
else if ( theOrder == 2 && getZeroVariableReferenceOffset() == 2 )
{
c = k / ( libecs::N_A * getSuperSystem()->getSize() );
}
else
{
THROW_EXCEPTION_INSIDE( InitializationFailed,
asString() + ": only first or second order "
"scheme is allowed" );
}
}
