virtual void initialize()
{
Process::initialize();
S0 = getVariableReference( "S0" );
P0 = getVariableReference( "P0" );
}
virtual void initialize()
{
Process::initialize();
VPGLM_maxf = getVariableReference( "VPGLM_maxf" ).getVariable();
G1P = getVariableReference( "G1P" ).getVariable();
G6P = getVariableReference( "G6P" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
}
virtual void initialize()
{
Process::initialize();
VPGI_maxr = getVariableReference( "VPGI_maxr" ).getVariable();
G6P = getVariableReference( "G6P" ).getVariable();
F6P = getVariableReference( "F6P" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
}
virtual void initialize(){
Process::initialize();
E0 = getVariableReference( "E0" );
E1 = getVariableReference( "E1" );
count = 0;
}
virtual void initialize()
{
Process::initialize();
AS1 = getVariableReference( "AS" ).getVariable(); ;
Fum2 = getVariableReference( "Fum" ).getVariable(); ;
Arg3 = getVariableReference( "Arg" ).getVariable(); ;
ASL4 = getVariableReference( "ASL" ).getVariable(); ;
//velocity=N_A/60;
}
virtual void initialize()
{
Process::initialize();
KmSP = KmS * KmP;
S0 = getVariableReference( "S0" );
P0 = getVariableReference( "P0" );
C0 = getVariableReference( "C0" );
}
virtual void initialize()
{
Process::initialize();
S0 = getVariableReference( "S0" );
S1 = getVariableReference( "S1" );
P0 = getVariableReference( "P0" );
P1 = getVariableReference( "P1" );
E0 = getVariableReference( "E0" );
E1 = getVariableReference( "E1" );
E2 = getVariableReference( "E2" );
E3 = getVariableReference( "E3" );
E4 = getVariableReference( "E4" );
theKcatf =
( kcatf * 1.662 ) /
( 1 + ( pow( 10, -1.0 * E0.getValue() ) / pow( 10, -7.02 ) ) +
( pow( 10, -9.55 ) / pow( 10, -1.0 * E0.getValue() ) ) );
theKcatr =
( kcatr * 1.662 ) /
( 1 + ( pow( 10, -1.0 * E0.getValue() ) / pow( 10, -7.02 ) ) +
( pow( 10, -9.55 ) / pow( 10, -1.0 * E0.getValue() ) ) );
}
virtual void initialize()
{
ContinuousProcess::initialize();
S0 = getVariableReference( "S0" );
S1 = getVariableReference( "S1" );
P0 = getVariableReference( "P0" );
P1 = getVariableReference( "P1" );
C0 = getVariableReference( "C0" );
KcF_Keq_Inv = KcF / Keq;
}
virtual void initialize()
{
Process::initialize();
target = getVariableReference( "target" ).getVariable();
flag = getVariableReference( "flag" ).getVariable();
_rockOn = false;
_nextFire = 0.0;
_lastValue = target->getValue();
}
virtual void initialize()
{
Process::initialize();
Cm = getVariableReference( "Cm" ).getVariable();
CFCl = getVariableReference( "CFCl" ).getVariable();
I = getVariableReference( "I" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
_I = permeabilityCl * pOpen;
}
virtual void initialize()
{
Process::initialize();
Ca_i_f = getVariableReference("Ca_i_f").getVariable();
Ca_nsr = getVariableReference("Ca_nsr").getVariable();
I = getVariableReference( "I" ).getVariable();
SR_factor = getVariableReference("SR_f").getVariable();
GX = getVariableReference( "GX" ).getVariable();
}
virtual void initialize()
{
Process::initialize();
S0 = getVariableReference( "S0" );
S1 = getVariableReference( "S1" );
P0 = getVariableReference( "P0" );
E0 = getVariableReference( "E0" );
E1 = getVariableReference( "E1" );
theK1 = k1 * ( ( 1 + pow( 10, -6.8 ) / pow( 10, -7.20 ) ) /
( 1 + pow( 10, -6.8 ) / pow( 10, -1 * E0.getValue() ) ) );
}
virtual void initialize()
{
Process::initialize();
i = getVariableReference( "i" ).getVariable();
A_cap = getVariableReference( "A_cap" ).getVariable();
N_A = getVariableReference( "N_A" ).getVariable();
F = getVariableReference( "F" ).getVariable();
z = getVariableReference( "z" ).getVariable();
_pA2J = 1.0e-9 * A_cap->getValue() * N_A->getValue() / z->getValue() / F->getValue(); //1.0e-6, if J is in per sec. probably...
//_pA2J = 1.0e-15 * N_A->getValue() / z->getValue() / F->getValue();
}
virtual void fire(){
E0 = getVariableReference( "E0" );
Real PO2 = E0.getVariable()->getValue();
// theCurrentTime = getStepper()->getCurrentTime();
Real i = trunc( getStepper()->getCurrentTime() / 5.5 );
theCalcTime = getStepper()->getCurrentTime() - 5.5 * i;
if (0 < theCalcTime <=0.36)
PO2 = 186.1111 * theCalcTime + 30;
else if(theCalcTime <= 2.55)
PO2 = 97;
else if(theCalcTime < 5.5)
PO2 = 60 - 32 * (theCalcTime - 2.57)/(0.15 + (theCalcTime - 2.57));
// else if(theCalcTime == 5.5)
// {
//// theCalcTime = 0;
// i= i+1;
// }
// std::cout << "i: " << i << std::endl;
// std::cout << "theCalcTime: " << theCalcTime << std::endl;
E0.getVariable()->setValue( PO2 );
}
virtual void initialize()
{
Process::initialize();
VGPA_maxf = getVariableReference( "VGPA_maxf" ).getVariable();
VGPB_maxf = getVariableReference( "VGPB_maxf" ).getVariable();
frac_a = getVariableReference( "frac_a" ).getVariable();
frac_b = getVariableReference( "frac_b" ).getVariable();
GLY = getVariableReference( "GLY" ).getVariable();
Pi = getVariableReference( "Pi" ).getVariable();
AMP = getVariableReference( "AMP" ).getVariable();
G1P = getVariableReference( "G1P" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
}
virtual void initialize()
{
Process::initialize();
Cao = getVariableReference( "Cao" ).getVariable();
Cai = getVariableReference( "Cai" ).getVariable();
PLBphos = getVariableReference( "PLBphos" ).getVariable();
dE = getVariableReference( "dE" ).getVariable();
y = getVariableReference( "y" ).getVariable();
ATP = getVariableReference( "ATP" ).getVariable();
I = getVariableReference( "I" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
Cm = getVariableReference( "Cm" ).getVariable();
}
virtual void initialize(){
Process::initialize();
S0 = getVariableReference( "S0" );
S1 = getVariableReference( "S1" );
P0 = getVariableReference( "P0" );
P1 = getVariableReference( "P1" );
C0 = getVariableReference( "C0" );
E0 = getVariableReference( "E0" );
E1 = getVariableReference( "E1" );
E2 = getVariableReference( "E2" );
E3 = getVariableReference( "E3" );
E4 = getVariableReference( "E4" );
ConstAct = E0.getCoefficient();
}
virtual void initialize()
{
Process::initialize();
VGAPDH_maxf = getVariableReference( "VGAPDH_maxf" ).getVariable();
GAP = getVariableReference( "GAP" ).getVariable();
NAD = getVariableReference( "NAD" ).getVariable();
Pi = getVariableReference( "Pi" ).getVariable();
BPG13 = getVariableReference( "BPG13" ).getVariable();
NADH = getVariableReference( "NADH" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
}
virtual void initialize()
{
Process::initialize();
VPFK_maxf = getVariableReference( "VPFK_maxf" ).getVariable();
F6P = getVariableReference( "F6P" ).getVariable();
ATP = getVariableReference( "ATP" ).getVariable();
ADP = getVariableReference( "ADP" ).getVariable();
AMP = getVariableReference( "AMP" ).getVariable();
FBP = getVariableReference( "FBP" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
}
virtual void initialize()
{
Process::initialize();
Cm = getVariableReference( "Cm" ).getVariable();
cNa = getVariableReference( "cNa" ).getVariable();
CFNa = getVariableReference( "CFNa" ).getVariable();
cK = getVariableReference( "cK" ).getVariable();
CFK = getVariableReference( "CFK" ).getVariable();
I = getVariableReference( "I" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
}
virtual void fire()
{
if ( theTriggerFlag == false && theFireFlag == false )
{
if ( theTriggerProcessor.execute() != 0.0 )
{
theFireTime = getModel()->getCurrentTime() +
theDelayProcessor.execute();
theTriggerFlag = true;
}
}
if ( theFireTime <= getModel()->getCurrentTime() && theTriggerFlag == true )
{
theFireFlag = true;
theTriggerFlag = false;
for( EANameVector::const_iterator aName = theEANameVector.begin();
aName != theEANameVector.end(); ++aName )
{
getVariableReference( *aName ).getVariable()->setValue( getVariableReference( *aName ).getCoefficient() * theEventAssignmentMap[ *aName ].execute() );
}
}
}
virtual void initialize(){
Process::initialize();
S0 = getVariableReference( "S0" );
S1 = getVariableReference( "S1" );
P0 = getVariableReference( "P0" );
P1 = getVariableReference( "P1" );
C0 = getVariableReference( "C0" );
E0 = getVariableReference( "E0" );
E1 = getVariableReference( "E1" );
}
void *
R_getNativeReference(SEXP arg, const char *type, const char *tag)
{
SEXP el, elTag;
void *ans;
el = GET_SLOT(arg, Rf_install("ref"));
if(R_isVariableReference(arg)) {
void *tmp;
tmp = getVariableReference(arg, el, type, tag);
if(!tmp) {
PROBLEM "Got null value for variable reference %s", type
ERROR;
}
return(tmp);
}
/* XXX added allow through if the TAG is null on the object. Just for now. */
if(tag && tag[0] && (elTag = R_ExternalPtrTag(el)) && elTag != Rf_install(tag)) {
/* So not a direct match. Now see if it is from a derived class
by comparing the value in the object to the name of each of the
ancestor classes.
*/
SEXP ancestors = GET_SLOT(arg, Rf_install("classes"));
int n, i;
n = Rf_length(ancestors);
for(i = 0; i < n ; i ++) {
if(strcmp(CHAR(STRING_ELT(ancestors, i)), tag) == 0)
break;
}
#ifndef R_REF_NO_CLASS_MATCH_ERROR
if(i == n) {
PROBLEM "Looking for %s, got %s",
tag, elTag != R_NilValue ? CHAR(PRINTNAME(elTag)) : "NULL"
ERROR;
}
#endif
}
ans = R_ExternalPtrAddr(el);
if(!ans) {
PROBLEM "NULL value passed to R_getNativeReference. This may not be an error, but it could be.\n Have you loaded an object from a previous R session?"
ERROR;
}
return(ans);
}
virtual void initialize()
{
Process::initialize();
I = getVariableReference( "I" ).getVariable();
Cai = getVariableReference( "Cai" ).getVariable();
Cao = getVariableReference( "Cao" ).getVariable();
SR_f = getVariableReference( "SR_f" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
Cm = getVariableReference( "Cm" ).getVariable();
}
virtual void initialize()
{
Process::initialize();
VCK_maxr = getVariableReference( "VCK_maxr" ).getVariable();
PCr = getVariableReference( "PCr" ).getVariable();
ADP = getVariableReference( "ADP" ).getVariable();
Cr = getVariableReference( "Cr" ).getVariable();
ATP = getVariableReference( "ATP" ).getVariable();
GX = getVariableReference( "GX" ).getVariable();
}
virtual void initialize()
{
Process::initialize();
Gln_o1 = getVariableReference( "Gln_o" ).getVariable();
Gln_i2 = getVariableReference( "Gln_i" ).getVariable();
Na_o3 = getVariableReference( "Na_o" ).getVariable();
Na_i4 = getVariableReference( "Na_i" ).getVariable();
His_o5 = getVariableReference( "His_o" ).getVariable();
His_i6 = getVariableReference( "His_i" ).getVariable();
//velocity=N_A/60;
}
virtual void initialize(){
Process::initialize();
S0 = getVariableReference( "S0" );
S1 = getVariableReference( "S1" );
P0 = getVariableReference( "P0" );
P1 = getVariableReference( "P1" );
P2 = getVariableReference( "P2" );
C0 = getVariableReference( "C0" );
E0 = getVariableReference( "E0" );
ConstAct = E0.getCoefficient();
D1 = k2 * k9 * k11 * ( k4 * k6 + k4 * k7 + k5 * k7 );
D2 = k1 * k9 * k11 * ( k4 * k6 + k4 * k7 + k5 * k7 );
D3 = k3 * k5 * k7 * k9 * k11;
D4 = k2 * k4 * k6 * k8 * k11;
D5 = k2 * k9 * k12 * ( k4 * k6 + k4 * k7 + k5 * k7 );
D6 = k1 * k3 * ( k5 * k9 * k11 + k6 * k9 * k11 + k7 * k9 * k11
+ k5 * k7 * k9 + k5 * k7 * k11 );
D7 = k1 * k4 * k6 * k8 * k11;
D8 = k3 * k5 * k7 * k9 * k12;
D9 = k2 * k4 * k6 * k8 * k10;
D10 = k2 * k4 * k6 * k8 * k12;
D11 = k2 * k10 * k12 * ( k4 * k6 + k4 * k7 + k5 * k7 );
D12 =k1 * k3 * k8 * k11 * ( k5 + k6 );
D13 = k1 * k3 * k5 * k7 * k10;
D14 = k1 * k4 * k6 * k8 * k10;
D15 = k3 * k5 * k7 * k10 * k12;
D16 = k8 * k10 * k12 * ( k2 * k4 + k2 * k5 + k2 * k6 + k4 * k6 );
D17 =k1 * k3 * k8 * k10 * ( k5 + k6 );
D18 =k3 * k8 * k10 * k12 * ( k5 + k6 );
N1 = k1 * k3 * k5 * k7 * k9 * k11;
N2 = k2 * k4 * k6 * k8 * k10 * k12;
}
virtual void initialize()
{
Process::initialize();
S0 = getVariableReference( "S0" );
S1 = getVariableReference( "S1" );
P0 = getVariableReference( "P0" );
E0 = getVariableReference( "E0" );
E1 = getVariableReference( "E1" );
E2 = getVariableReference( "E2" );
Real mgfphf = 8.3 * 0.001 *
( Kmgfru16p2 + pow( 10, -1 * E0.getValue() ) * Khf * Kmghf ) /
( 1 + ( pow( 10, -1 * E0.getValue() ) * Khf ) +
( pow( 10, -2 * E0.getValue() ) * Khf * Kh2f ) +
( E1.getMolarConc() * Kkf ) +
( E1.getMolarConc() * pow( 10, -1 * E0.getValue() ) * Khf * Kkhf ) );
theKmgf16p2a = kmgf16p2a * mgfphf;
}
virtual void initialize()
{
Process::initialize();
S0 = getVariableReference( "S0" );
S1 = getVariableReference( "S1" );
P0 = getVariableReference( "P0" );
E0 = getVariableReference( "E0" );
E1 = getVariableReference( "E1" );
E2 = getVariableReference( "E2" );
Real mgbpgphf = 3.2 * 0.001 *
( Kmgbpg + pow( 10, -1 * E0.getValue() ) * Khbpg * Kmghbpg ) /
( 1 + ( pow( 10, -1 * E0.getValue() ) * Khbpg ) +
( pow( 10, -2 * E0.getValue() ) * Khbpg * Kh2bpg ) +
( E1.getMolarConc() * Kkbpg ) +
( E1.getMolarConc() * pow( 10, -1 * E0.getValue() ) * Khbpg * Kkhbpg ) );
theKmgbpga = kmgbpga * mgbpgphf;
}
virtual void initialize()
{
Process::initialize();
C0 = getVariableReference( "C0" );
}
