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" ); }