void MakeModel(char *Title, char *comments, CCopasiVector < CGene > &gene, C_INT32 n, C_INT32 k, CModel &model, C_INT32 specific)
{
C_INT32 i, j, r, s, pos, neg;
char strname[512], strname2[512], streq[512];
string compname = "cell", rname, rchemeq, kiname;
CReaction *react;
std::vector <std::string> subnames;
subnames.resize(1);
// two reactions per gene
r = 2 * n;
// set the title and comments
model.setTitle(Title);
model.setComments(comments);
// add one compartment to the model
model.addCompartment(compname, 1.0);
// create one metabolite for each gene
for (i = 0; i < n; i++)
model.addMetabolite(gene[i]->getName(), compname, 1.0, 1);
model.initializeMetabolites();
// create two reactions for each gene
for (i = 0; i < n; i++)
{
// transcription
sprintf(strname, "%s synthesis", gene[i]->getName().data());
sprintf(streq, "-> %s", gene[i]->getName().data());
rname = strname;
rchemeq = streq;
react = new CReaction(rname);
if (react == NULL)
{
fprintf(stderr, "Failed to create a CReaction object");
abort();
}
react->setChemEq(streq);
s = gene[i]->getModifierNumber();
for (j = 0; j < s; j++)
{
react->addModifier(gene[i]->getModifier(j)->getName());
}
if (specific)
sprintf(strname, "basal %ld inh %ld spec act (indp)", gene[i]->getNegativeModifiers(),
gene[i]->getPositiveModifiers());
else
sprintf(strname, "transcr %ld inh %ld act (indp)", gene[i]->getNegativeModifiers(),
gene[i]->getPositiveModifiers());
kiname = strname;
react->setFunction(kiname);
for (j = 0, pos = 1; j < s; j++)
{
if (gene[i]->getModifierType(j) == 1)
{
sprintf(strname, "A%ld", pos++);
react->setParameterMapping(strname, gene[i]->getModifier(j)->getName());
}
}
for (j = 0, neg = 1; j < s; j++)
{
if (gene[i]->getModifierType(j) == 0)
{
sprintf(strname, "I%ld", neg++);
react->setParameterMapping(strname, gene[i]->getModifier(j)->getName());
}
}
// first the basal rate
sprintf(strname, "V");
react->setParameterValue(strname, gene[i]->getRate());
// we have two more constants per modifier
for (j = 0, pos = neg = 1; j < s; j++)
{
if (gene[i]->getModifierType(j) == 0)
{
sprintf(strname, "Ki%ld", neg);
sprintf(strname2, "ni%ld", neg++);
}
else
{
sprintf(strname, "Ka%ld", pos);
sprintf(strname2, "na%ld", pos++);
}
react->setParameterValue(strname, gene[i]->getK(j));
react->setParameterValue(strname2, gene[i]->getn(j));
}
model.addReaction(*react);
// mRNA degradation
sprintf(strname, "%s degradation", gene[i]->getName().data());
sprintf(streq, "%s ->", gene[i]->getName().data());
rname = strname;
rchemeq = streq;
react = new CReaction(rname);
if (react == NULL)
{
fprintf(stderr, "Failed to create a CReaction object");
abort();
}
react->setChemEq(streq);
kiname = "Mass action (irreversible)";
react->setFunction(kiname);
// first the kinetic constant
sprintf(strname, "k1");
react->setParameterValue(strname, gene[i]->getDegradationRate());
// now the substrate
sprintf(strname, "substrate_0");
subnames[0] = gene[i]->getName();
react->setParameterMapping(strname, subnames);
model.addReaction(*react);
}
// structural analysis (moieties, etc.)
model.compile();
}
void CModelExpansion::duplicateReaction(const CReaction* source, const std::string & index, const SetOfModelElements & sourceSet, ElementsMap & emap)
{
//if the source object has already been duplicated: do nothing
if (emap.exists(source))
return;
//try creating the object until we find a name that is not yet used
CReaction* newObj;
std::ostringstream infix;
do
{
std::ostringstream name;
name << source->getObjectName() << infix.str() << index;
newObj = mpModel->createReaction(name.str());
infix << "_";
}
while (!newObj);
//add duplicated object to the map
emap.add(source, newObj);
//now copy the chemical equation
size_t i;
for (i = 0; i < source->getChemEq().getSubstrates().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getSubstrates()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addSubstrate(pMetab->getKey(), sourceElement->getMultiplicity());
}
for (i = 0; i < source->getChemEq().getProducts().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getProducts()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addProduct(pMetab->getKey(), sourceElement->getMultiplicity());
}
for (i = 0; i < source->getChemEq().getModifiers().size(); ++i)
{
const CChemEqElement * sourceElement = source->getChemEq().getModifiers()[i];
const CMetab* pMetab = NULL;
if (sourceSet.contains(sourceElement->getMetabolite()))
{
if (!emap.exists(sourceElement->getMetabolite()))
duplicateMetab(sourceElement->getMetabolite(), index, sourceSet, emap);
pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));
}
else //add the original metab
{
pMetab = sourceElement->getMetabolite();
}
if (pMetab)
newObj->addModifier(pMetab->getKey());
}
newObj->setReversible(source->isReversible());
//set the kinetic function
newObj->setFunction(const_cast<CFunction*>(source->getFunction()));
//mapping and local parameters
for (i = 0; i < newObj->getFunctionParameters().size(); ++i)
{
switch (newObj->getFunctionParameters()[i]->getUsage())
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
{
bool isVector = (newObj->getFunctionParameters()[i]->getType() == CFunctionParameter::VFLOAT64);
if (isVector)
newObj->clearParameterMapping(i);
size_t k;
for (k = 0; k < source->getParameterMappings()[i].size(); ++k)
{
//we assume that by now the metab was copied if necessary.
//therefore we only need to check the map.
std::string targetKey;
if (emap.exists(source->getParameterMappings()[i][k]))
targetKey = emap.getDuplicateKey(source->getParameterMappings()[i][k]);
else
targetKey = source->getParameterMappings()[i][k];
if (isVector)
newObj->addParameterMapping(i, targetKey);
else
newObj->setParameterMapping(i, targetKey);
}
}
break;
case CFunctionParameter::TIME:
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
break;
case CFunctionParameter::VOLUME:
if (sourceSet.contains(source->getParameterMappings()[i][0]))
{
if (!emap.exists(source->getParameterMappings()[i][0]))
{
const CCompartment* pSource = dynamic_cast<const CCompartment*>(
(CCopasiRootContainer::getKeyFactory()->get(source->getParameterMappings()[i][0])));
duplicateCompartment(pSource, index, sourceSet, emap);
}
newObj->setParameterMapping(i, emap.getDuplicateKey(source->getParameterMappings()[i][0]));
}
else //add the original metab
{
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
}
break;
case CFunctionParameter::PARAMETER:
if (newObj->isLocalParameter(i))
{
//just copy the value
newObj->setParameterValue(newObj->getFunctionParameters()[i]->getObjectName(),
source->getParameterValue(newObj->getFunctionParameters()[i]->getObjectName()));
}
else
{
if (sourceSet.contains(source->getParameterMappings()[i][0]))
{
if (!emap.exists(source->getParameterMappings()[i][0]))
{
const CModelValue* pSource = dynamic_cast<const CModelValue*>(
(CCopasiRootContainer::getKeyFactory()->get(source->getParameterMappings()[i][0])));
duplicateGlobalQuantity(pSource, index, sourceSet, emap);
}
newObj->setParameterMapping(i, emap.getDuplicateKey(source->getParameterMappings()[i][0]));
}
else //add the original global quantity
{
newObj->setParameterMapping(i, source->getParameterMappings()[i][0]);
}
}
break;
default:
break;
}
}
newObj->setNotes(source->getNotes());
newObj->setMiriamAnnotation(source->getMiriamAnnotation(), newObj->getKey(), source->getKey());
}
bool CModelAdd::addReactions(std::string name)
{
bool info = false;
//create copies of the relevant reactions
size_t i, imax = mmModel->getReactions().size();
size_t ic, icmax = mmModel->getCompartments().size();
for (ic = 0; ic < icmax; ++ic)
{
const CCompartment* sourceComp = &mmModel->getCompartments()[ic];
if (!sourceComp) return info;
for (i = 0; i < imax; ++i)
{
CReaction * sourceReac = &mmModel->getReactions()[i];
if (reactionInvolvesCompartment(sourceReac, sourceComp))
{
std::string newName = sourceReac->getObjectName() + "_" + name;
CReaction* newReac = mpModel->createReaction(newName);
if (!newReac) return info;
//copy the chemical equation. If the involved metabs are among those that
//were copied with the compartment, replace them. Otherwise keep the original metab
newReac->setReversible(sourceReac->isReversible());
std::map<std::string, std::string>::const_iterator mapIt;
std::string targetKey;
size_t j, jmax = sourceReac->getChemEq().getSubstrates().size();
for (j = 0; j < jmax; ++j)
{
const CChemEqElement * sourceElement = &sourceReac->getChemEq().getSubstrates()[j];
//check if the metab is in the map. If yes, translate it, otherwise not.
mapIt = keyMap.find(sourceElement->getMetaboliteKey());
if (mapIt == keyMap.end())
{
targetKey = sourceElement->getMetaboliteKey();
}
else
targetKey = mapIt->second;
newReac->addSubstrate(targetKey, sourceElement->getMultiplicity());
}
jmax = sourceReac->getChemEq().getProducts().size();
for (j = 0; j < jmax; ++j)
{
const CChemEqElement * sourceElement = &sourceReac->getChemEq().getProducts()[j];
//check if the metab is in the map. If yes, translate it, otherwise not.
mapIt = keyMap.find(sourceElement->getMetaboliteKey());
if (mapIt == keyMap.end())
{
targetKey = sourceElement->getMetaboliteKey();
}
else
targetKey = mapIt->second;
newReac->addProduct(targetKey, sourceElement->getMultiplicity());
}
jmax = sourceReac->getChemEq().getModifiers().size();
for (j = 0; j < jmax; ++j)
{
const CChemEqElement * sourceElement = &sourceReac->getChemEq().getModifiers()[j];
//check if the metab is in the map. If yes, translate it, otherwise not.
mapIt = keyMap.find(sourceElement->getMetaboliteKey());
if (mapIt == keyMap.end())
{
targetKey = sourceElement->getMetaboliteKey();
}
else
targetKey = mapIt->second;
newReac->addModifier(targetKey);
}
//set the kinetic function
newReac->setFunction(const_cast<CFunction*>(sourceReac->getFunction()));
//mapping and local parameters
for (j = 0; j < newReac->getFunctionParameters().size(); ++j)
{
switch (newReac->getFunctionParameters()[j]->getUsage())
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
//translate the metab keys
{
bool isVector = (newReac->getFunctionParameters()[j]->getType() == CFunctionParameter::VFLOAT64);
//we assume that only SUBSTRATE, PRODUCT, MODIFIER can be vectors
if (isVector)
newReac->clearParameterMapping(j);
size_t k;
for (k = 0; k < sourceReac->getParameterMappings()[j].size(); ++k)
{
mapIt = keyMap.find(sourceReac->getParameterMappings()[j][k]);
if (mapIt == keyMap.end())
{
targetKey = sourceReac->getParameterMappings()[j][k];
}
else
targetKey = mapIt->second;
if (isVector)
newReac->addParameterMapping(j, targetKey);
else
newReac->setParameterMapping(j, targetKey);
}
}
break;
case CFunctionParameter::TIME:
//just copy the key
{
mapIt = keyMap.find(sourceReac->getParameterMappings()[j][0]);
if (mapIt == keyMap.end())
{
targetKey = sourceReac->getParameterMappings()[j][0];
}
else
targetKey = mapIt->second;
newReac->setParameterMapping(j, targetKey);
}
break;
case CFunctionParameter::VOLUME:
//translate the compartment key if necessary
if (sourceReac->getParameterMappings()[j][0] == sourceComp->getKey())
newReac->setParameterMapping(j, keyMap[sourceComp->getKey()]);
else
{
mapIt = keyMap.find(sourceReac->getParameterMappings()[j][0]);
if (mapIt == keyMap.end())
{
targetKey = sourceReac->getParameterMappings()[j][0];
}
else
targetKey = mapIt->second;
newReac->setParameterMapping(j, targetKey);
}
//TODO: this needs to be adapted when sets of compartments will be copied
break;
case CFunctionParameter::PARAMETER:
if (sourceReac->isLocalParameter(j))
newReac->setParameterValue(newReac->getFunctionParameters()[j]->getObjectName(),
sourceReac->getParameterValue(newReac->getFunctionParameters()[j]->getObjectName()));
else
{
mapIt = keyMap.find(sourceReac->getParameterMappings()[j][0]);
if (mapIt == keyMap.end())
{
targetKey = sourceReac->getParameterMappings()[j][0];
}
else
targetKey = mapIt->second;
newReac->setParameterMapping(j, targetKey);
}
break;
default:
return info;
break;
}
}
}
}
}
return true;
}
