void checkReactions(Model* model, set<string>& components, set<string>& tests, const map<string, vector<double> >& results, int type)
{
if (model->getNumReactions() > 0) {
components.insert("Reaction");
for (unsigned int r=0; r<model->getNumReactions(); r++) {
Reaction* rxn = model->getReaction(r);
if (rxn->isSetFast() && rxn->getFast()) {
tests.insert("FastReaction");
}
if (rxn->isSetReversible() && rxn->getReversible()) {
if (type!=1) {
tests.insert("ReversibleReaction [?]");
}
}
ListOfSpeciesReferences* reactants = rxn->getListOfReactants();
checkSpeciesRefs(model, reactants, components, tests, results);
ListOfSpeciesReferences* products = rxn->getListOfProducts();
checkSpeciesRefs(model, products, components, tests, results);
if (rxn->isSetKineticLaw()) {
KineticLaw* kl = rxn->getKineticLaw();
if (kl->getNumParameters() > 0) {
tests.insert("LocalParameters");
}
if (kl->isSetMath() == false) {
tests.insert("NoMathML");
}
}
}
}
}
void
Model::assignRequiredValues()
{
// when converting to L3 some attributes which have default values in L1/L2
// but are required in L3 are not present or set
unsigned int i, n;
if (getNumUnitDefinitions() > 0)
{
for (i = 0; i < getNumUnitDefinitions(); i++)
{
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
Unit *u = getUnitDefinition(i)->getUnit(n);
if (!u->isSetExponent())
u->setExponent(1.0);
if (!u->isSetScale())
u->setScale(0);
if (!u->isSetMultiplier())
u->setMultiplier(1.0);
}
}
}
if (getNumCompartments() > 0)
{
for (i = 0; i < getNumCompartments(); i++)
{
Compartment *c = getCompartment(i);
c->setConstant(c->getConstant());
}
}
if (getNumSpecies() > 0)
{
for (i = 0; i < getNumSpecies(); i++)
{
Species * s = getSpecies(i);
s->setBoundaryCondition(s->getBoundaryCondition());
s->setHasOnlySubstanceUnits(s->getHasOnlySubstanceUnits());
s->setConstant(s->getConstant());
}
}
if (getNumParameters() > 0)
{
for (i = 0; i < getNumParameters(); i++)
{
Parameter * p = getParameter(i);
p->setConstant(p->getConstant());
}
}
if (getNumReactions() > 0)
{
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->setFast(r->getFast());
r->setReversible(r->getReversible());
if (r->getNumReactants() > 0)
{
for (n = 0; n < r->getNumReactants(); n++)
{
SpeciesReference *sr = r->getReactant(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
if (r->getNumProducts() > 0)
{
for (n = 0; n < r->getNumProducts(); n++)
{
SpeciesReference *sr = r->getProduct(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
}
}
if (getNumEvents() > 0)
{
for (i = 0; i < getNumEvents(); i++)
{
Event * e = getEvent(i);
e->setUseValuesFromTriggerTime(e->getUseValuesFromTriggerTime());
if (e->isSetTrigger())
{
Trigger *t = e->getTrigger();
t->setPersistent(true);
t->setInitialValue(true);
}
}
}
}
//create REACTION
void SbmlReader::createReaction( map< string,Id > &molMap )
{
map< string,double > rctMap;
map< string,double >::iterator rctMap_iter;
map< string,double >pdtMap;
map< string,double >::iterator pdtMap_iter;
map< string,Eref >::iterator elemt_iter;
map< string,EnzymeInfo >enzInfoMap;
double rctorder,pdtorder;
static const Cinfo* moleculeCinfo = initMoleculeCinfo();
static const Finfo* reacFinfo =moleculeCinfo->findFinfo( "reac" );
static const Cinfo* reactionCinfo = initReactionCinfo();
static const Finfo* subFinfo = reactionCinfo->findFinfo( "sub" );
static const Finfo* prdFinfo = reactionCinfo->findFinfo( "prd" );
static const Finfo* kfFinfo = reactionCinfo->findFinfo( "kf" );
static const Finfo* kbFinfo = reactionCinfo->findFinfo( "kb" );
Reaction* reac;
for ( unsigned int r = 0; r < model_->getNumReactions(); r++ )
{
reac = model_->getReaction( r );
const string id=reac->getId();
//cout<<"reaction is "<<id<<endl;
std::string name;
if ( reac->isSetName() ){
name = reac->getName();
}
string grpname = getAnnotation( reac,enzInfoMap );
if ( (grpname != "") && (enzInfoMap[grpname].stage == 3) )
setupEnzymaticReaction( enzInfoMap[grpname],grpname );
else if ( grpname == "" )
{
if ( reac->getNumModifiers()> 0 )
setupMMEnzymeReaction( reac,id );
else{
bool rev=reac->getReversible();
bool fast=reac->getFast();
if ( fast ){
cout<<"warning: for now fast attribute is not handled"<<endl;
errorFlag_ = true;
}
int numRcts = reac->getNumReactants();
int numPdts = reac->getNumProducts();
if ( numRcts == 0 && numPdts != 0 ){
const SpeciesReference* pdt = reac->getProduct( 0 );
std::string spName = pdt->getSpecies();
Id parent = molMap.find( spName )->second; //gives compartment of spName
string parentCompt = parent()->name();
//cout<<"parent of reactant :"<<parentCompt<<endl;
ostringstream spId;
spId <<id<<"_Src";
molecule_ = Neutral::create( "Molecule",spId.str(),parent,Id::scratchId() );//create Molecule
molMap[spId.str()] = parent;
elmtMap_[spId.str()] = Eref( molecule_ );
::set< double >( molecule_,"conc", 1 );
::set< int >( molecule_,"mode",4 );
reaction_ = Neutral::create( "Reaction",id,parent,Id::scratchId() ); //create Reaction
Eref( reaction_ ).add( subFinfo->msg(),elmtMap_[spId.str()],reacFinfo->msg(),ConnTainer::Default );
}
else{
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
Id m = molMap.find(sp)->second; //gives compartment of sp
reaction_ = Neutral::create( "Reaction",id,m,Id::scratchId() ); //create Reaction
double rctcount=0.0;
rctMap.clear();
for ( unsigned int rt=0;rt<reac->getNumReactants();rt++ )
{
const SpeciesReference* rct=reac->getReactant(rt);
sp=rct->getSpecies();
rctMap_iter = rctMap.find(sp);
if ( rctMap_iter != rctMap.end() ){
rctcount = rctMap_iter->second;
}
else {
rctcount = 0.0;
}
rctcount += rct->getStoichiometry();
rctMap[sp] = rctcount;
for ( int i=0;(int)i<rct->getStoichiometry();i++ )
{
Eref(reaction_).add( subFinfo->msg(),elmtMap_[sp],reacFinfo->msg(),ConnTainer::Default );
}
}
}
double pdtcount = 0.0;
pdtMap.clear();
for ( unsigned int pt=0;pt<reac->getNumProducts();pt++ )
{
const SpeciesReference* pdt=reac->getProduct(pt);
std::string sp=pdt->getSpecies();
pdtMap_iter = pdtMap.find(sp);
if ( pdtMap_iter != pdtMap.end() ){
pdtcount = pdtMap_iter->second;
}
else {
pdtcount = 0.0;
}
pdtcount += pdt->getStoichiometry();
pdtMap[sp] = pdtcount;
for ( int i=0;i<pdt->getStoichiometry();i++ )
{
Eref(reaction_).add( prdFinfo->msg(),elmtMap_[sp],reacFinfo->msg(),ConnTainer::Default );
}
}
//order of reactants
rctorder = 0.0;
string rsp = "",psp = "";
for ( rctMap_iter=rctMap.begin();rctMap_iter!=rctMap.end();rctMap_iter++ )
{
rctorder += rctMap_iter->second;
rsp=rctMap_iter->first; //species of the reactant
}
//cout<<"rct order = "<<rctorder<<endl;
//order of products
pdtorder = 0.0;
for ( pdtMap_iter=pdtMap.begin();pdtMap_iter!=pdtMap.end();pdtMap_iter++ )
{
pdtorder += pdtMap_iter->second;
psp=pdtMap_iter->first; //species of the product
}
//cout<<"pdt order = "<<pdtorder<<endl;
if ( reac->isSetKineticLaw() )
{ KineticLaw * klaw=reac->getKineticLaw();
//vector< double > rate = getKLaw( klaw,rev );
vector< double > rate;
rate.clear();
getKLaw( klaw,rev,rate );
if ( errorFlag_ )
return;
else if ( !errorFlag_ ){
::set< double >( reaction_, kfFinfo, rate[0] );
::set< double >( reaction_, kbFinfo, rate[1] );
}
}
}//else modifier
}//else
}//reaction
}//create reaction
void SbmlReader::createReaction(const map< string, Id > &molSidcmptMIdMap ) {
Reaction* reac;
map< string,double > rctMap;
map< string,double >::iterator rctMap_iter;
map< string,double >prdMap;
map< string,double >::iterator prdMap_iter;
map< string,EnzymeInfo >enzInfoMap;
for ( unsigned int r = 0; r < model_->getNumReactions(); r++ ) {
Id reaction_;
reac = model_->getReaction( r );
noOfsub_ = 0;
noOfprd_ = 0;
std:: string id; //=reac->getId();
if ( reac->isSetId() )
id = reac->getId();
std::string name;
if ( reac->isSetName() ) {
name = reac->getName();
name = nameString(name);
}
if (name.empty()) {
if (id.empty())
assert("Reaction id and name is empty");
else
name = id;
}
string grpname = getAnnotation( reac,enzInfoMap );
if ( (grpname != "") && (enzInfoMap[grpname].stage == 3) ) {
setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap,name);
}
//if (grpname != "")
// {
//cout << "\n enz matic reaction " << enzInfoMap[grpname].stage;
//setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap);
//}
else if ( grpname == "" ) {
if (reac->getNumModifiers() > 0)
setupMMEnzymeReaction( reac,id,name ,molSidcmptMIdMap);
else {
bool rev=reac->getReversible();
bool fast=reac->getFast();
if ( fast ) {
cout<<"warning: for now fast attribute is not handled"<<endl;
errorFlag_ = true;
}
int numRcts = reac->getNumReactants();
int numPdts = reac->getNumProducts();
if ( numRcts == 0 && numPdts != 0 ) {
cout << "Reaction with zero Substrate is not possible but exist in this model";
const SpeciesReference* pdt = reac->getProduct( 0 );
std::string spName = pdt->getSpecies();
Id parent = molSidcmptMIdMap.find( spName )->second; //gives compartment of spName
cout << " \n \t ################################# Sub = 0 and prd != 0 need to the reac ############### ";
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
reaction_ = shell->doCreate("Reac", meshEntry, name, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
//Get Substrate
addSubPrd(reac,reaction_,"prd");
} //if numRcts == 0
else {
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
reaction_ = shell->doCreate("Reac", comptRef, name, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
//Get Substrate
addSubPrd(reac,reaction_,"sub");
//Get Product
addSubPrd(reac,reaction_,"prd");
}
if ( reac->isSetKineticLaw() ) {
KineticLaw * klaw=reac->getKineticLaw();
//vector< double > rate = getKLaw( klaw,rev );
vector< double > rate;
rate.clear();
getKLaw( klaw,rev,rate );
if ( errorFlag_ )
return;
else if ( !errorFlag_ ) {
//cout << " Reaction name " << name << " kf " << rate[0] << " kb " << rate[1]<<endl;
Field < double > :: set( reaction_, "Kf", rate[0] );
Field < double > :: set( reaction_, "Kb", rate[1] );
/*if (numRcts > 1)
rate[0] = rate[0]*pow(1e3,1.0);
cout << "Reaction " << id << " " << name << " " << rate[0] << " " << rate[1]<<endl;
Field < double > :: set( reaction_, "Kf", rate[0] );
Field < double > :: set( reaction_, "Kb", rate[1] );
*/
}
} //issetKineticLaw
} //else
} // else grpname == ""
}//for unsigned
} //reaction