void CModelExpansion::createDiffusionReaction(const std::string & name, const std::string & metabkey1, const std::string & metabkey2, const std::string & parameterkey) { //try creating the object until we find a name that is not yet used CReaction* newObj; std::ostringstream name_; name_ << name; do { newObj = mpModel->createReaction(name_.str()); name_ << "_"; } while (!newObj); newObj->setReversible(true); newObj->addSubstrate(metabkey1, 1); newObj->addProduct(metabkey2, 1); newObj->setFunction("Mass action (reversible)"); newObj->addParameterMapping("substrate", metabkey1); newObj->addParameterMapping("product", metabkey2); newObj->setParameterMapping(0, parameterkey); newObj->setParameterMapping(2, parameterkey); }
// virtual bool CModelParameter::updateModel() { bool success = true; if (mpObject != NULL) { switch (mType) { case Model: { CModel * pModel = static_cast< CModel * >(mpObject); if (!pModel->isAutonomous()) { pModel->setInitialValue(mValue); } else { pModel->setInitialValue(0.0); } } break; case Compartment: case Species: case ModelValue: { CModelEntity * pEntity = static_cast< CModelEntity * >(mpObject); if (pEntity->getStatus() != CModelEntity::ASSIGNMENT) { pEntity->setInitialValue(mValue); if (mIsInitialExpressionValid) { pEntity->setInitialExpression(getInitialExpression()); } } } break; case ReactionParameter: { CCopasiParameter * pParameter = static_cast< CCopasiParameter * >(mpObject); CReaction * pReaction = static_cast< CReaction * >(mpObject->getObjectAncestor("Reaction")); if (mIsInitialExpressionValid && getInitialExpression() != "") { CModel * pModel = mpParent->getModel(); assert(pModel != NULL); std::vector< CCopasiContainer * > ListOfContainer; ListOfContainer.push_back(pModel); CCopasiObjectName CN = static_cast< CEvaluationNodeObject * >(mpInitialExpression->getRoot())->getObjectCN(); CCopasiObject * pObject = pModel->getObjectDataModel()->ObjectFromName(ListOfContainer, CN); assert(pObject != NULL); // We assign the object value pParameter->setValue(* (C_FLOAT64 *) pObject->getValuePointer()); // We map the parameter to the global quantity pReaction->setParameterMapping(pParameter->getObjectName(), pObject->getObjectParent()->getKey()); } else { pParameter->setValue(mValue); // We need to remove the existing mapping to a global quantity1. pReaction->setParameterMapping(pParameter->getObjectName(), pParameter->getKey()); } } break; default: success = false; break; } } return success; }
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()); }
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(); }
int main() { // initialize the backend library // since we are not interested in the arguments // that are passed to main, we pass 0 and NULL to // init CCopasiRootContainer::init(0, NULL); assert(CCopasiRootContainer::getRoot() != NULL); // create a new datamodel CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel(); assert(CCopasiRootContainer::getDatamodelList()->size() == 1); // get the model from the datamodel CModel* pModel = pDataModel->getModel(); assert(pModel != NULL); // set the units for the model // we want seconds as the time unit // microliter as the volume units // and nanomole as the substance units pModel->setTimeUnit(CModel::s); pModel->setVolumeUnit(CModel::microl); pModel->setQuantityUnit(CModel::nMol); // we have to keep a set of all the initial values that are changed during // the model building process // They are needed after the model has been built to make sure all initial // values are set to the correct initial value std::set<const CCopasiObject*> changedObjects; // create a compartment with the name cell and an initial volume of 5.0 // microliter CCompartment* pCompartment = pModel->createCompartment("cell", 5.0); const CCopasiObject* pObject = pCompartment->getValueReference(); assert(pObject != NULL); changedObjects.insert(pObject); assert(pCompartment != NULL); assert(pModel->getCompartments().size() == 1); // create a new metabolite with the name S and an inital // concentration of 10 nanomol // the metabolite belongs to the compartment we created and is is to be // fixed CMetab* pS = pModel->createMetabolite("S", pCompartment->getObjectName(), 10.0, CMetab::FIXED); pObject = pS->getInitialConcentrationReference(); assert(pObject != NULL); changedObjects.insert(pObject); assert(pCompartment != NULL); assert(pS != NULL); assert(pModel->getMetabolites().size() == 1); // create a second metabolite called P with an initial // concentration of 0. This metabolite is to be changed by reactions CMetab* pP = pModel->createMetabolite("P", pCompartment->getObjectName(), 0.0, CMetab::REACTIONS); assert(pP != NULL); pObject = pP->getInitialConcentrationReference(); assert(pObject != NULL); changedObjects.insert(pObject); assert(pModel->getMetabolites().size() == 2); // now we create a reaction CReaction* pReaction = pModel->createReaction("reaction"); assert(pReaction != NULL); assert(pModel->getReactions().size() == 1); // reaction converts S to P // we can set these on the chemical equation of the reaction CChemEq* pChemEq = &pReaction->getChemEq(); // S is a substrate with stoichiometry 1 pChemEq->addMetabolite(pS->getKey(), 1.0, CChemEq::SUBSTRATE); // P is a product with stoichiometry 1 pChemEq->addMetabolite(pP->getKey(), 1.0, CChemEq::PRODUCT); assert(pChemEq->getSubstrates().size() == 1); assert(pChemEq->getProducts().size() == 1); // this reaction is to be irreversible pReaction->setReversible(false); assert(pReaction->isReversible() == false); CModelValue* pMV = pModel->createModelValue("K", 42.0); // set the status to FIXED pMV->setStatus(CModelValue::FIXED); assert(pMV != NULL); pObject = pMV->getInitialValueReference(); assert(pObject != NULL); changedObjects.insert(pObject); assert(pModel->getModelValues().size() == 1); // now we ned to set a kinetic law on the reaction // for this we create a user defined function CFunctionDB* pFunDB = CCopasiRootContainer::getFunctionList(); assert(pFunDB != NULL); CKinFunction* pFunction = new CKinFunction("My Rate Law"); pFunDB->add(pFunction, true); CFunction* pRateLaw = dynamic_cast<CFunction*>(pFunDB->findFunction("My Rate Law")); assert(pRateLaw != NULL); // now we create the formula for the function and set it on the function std::string formula = "(1-0.4/(EXPONENTIALE^(temp-37)))*0.00001448471257*1.4^(temp-37)*substrate"; bool result = pFunction->setInfix(formula); assert(result == true); // make the function irreversible pFunction->setReversible(TriFalse); // the formula string should have been parsed now // and COPASI should have determined that the formula string contained 2 parameters (temp and substrate) CFunctionParameters& variables = pFunction->getVariables(); // per default the usage of those parameters will be set to VARIABLE size_t index = pFunction->getVariableIndex("temp"); assert(index != C_INVALID_INDEX); CFunctionParameter* pParam = variables[index]; assert(pParam->getUsage() == CFunctionParameter::VARIABLE); // This is correct for temp, but substrate should get the usage SUBSTRATE in order // for us to use the function with the reaction created above // So we need to set the usage for "substrate" manually index = pFunction->getVariableIndex("substrate"); assert(index != C_INVALID_INDEX); pParam = variables[index]; pParam->setUsage(CFunctionParameter::SUBSTRATE); // set the rate law for the reaction pReaction->setFunction(pFunction); assert(pReaction->getFunction() != NULL); // COPASI also needs to know what object it has to assocuiate with the individual function parameters // In our case we need to tell COPASI that substrate is to be replaced by the substrate of the reaction // and temp is to be replaced by the global parameter K pReaction->setParameterMapping("substrate", pS->getKey()); pReaction->setParameterMapping("temp", pMV->getKey()); // finally compile the model // compile needs to be done before updating all initial values for // the model with the refresh sequence pModel->compileIfNecessary(NULL); // now that we are done building the model, we have to make sure all // initial values are updated according to their dependencies std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects); std::vector<Refresh*>::iterator it2 = refreshes.begin(), endit2 = refreshes.end(); while (it2 != endit2) { // call each refresh (**it2)(); ++it2; } // save the model to a COPASI file // we save to a file named example1.cps, we don't want a progress report // and we want to overwrite any existing file with the same name // Default tasks are automatically generated and will always appear in cps // file unless they are explicitley deleted before saving. pDataModel->saveModel("example7.cps", NULL, true); // export the model to an SBML file // we save to a file named example1.xml, we want to overwrite any // existing file with the same name and we want SBML L2V3 pDataModel->exportSBML("example7.xml", true, 2, 3); // destroy the root container once we are done CCopasiRootContainer::destroy(); }
void CFixLocalReactionParameters::changeModel() { CCopasiParameter * pParameter = NULL; CModelValue * pModelValue = NULL; CReaction * pReaction = NULL; std::stringstream NameStream; std::stringstream Message; std::string OldCN; std::string NewCNBase; std::string NewCN; std::string Infix; std::string::size_type Start; // Loop through all changes. std::multimap< CCopasiParameter *, const CExpression * >::const_iterator itChanges = mChanges.begin(); std::multimap< CCopasiParameter *, const CExpression * >::const_iterator endChanges = mChanges.end(); for (; itChanges != endChanges; ++itChanges) { if (pParameter != itChanges->first) { // We have a new parameter pParameter = itChanges->first; OldCN = "<" + pParameter->getCN() + ",Reference="; // Create a global quantity of type FIXED. std::string Name = pParameter->getObjectName(); pReaction = static_cast< CReaction * >(pParameter->getObjectAncestor("Reaction")); Name += "{" + pReaction->getObjectName() + "}"; pModelValue = mpModel->createModelValue(Name, pParameter->getValue< C_FLOAT64 >()); // In case the created name is not unique we append _n with increasing n // until we succeed; C_INT32 index = 0; while (pModelValue == NULL) { NameStream.str(""); NameStream << Name << "_" << index++; pModelValue = mpModel->createModelValue(NameStream.str(), pParameter->getValue< C_FLOAT64 >()); } NewCNBase = "<" + pModelValue->getCN() + ",Reference="; // If the parameter is actually used in the reaction // it is changed to the global quantity. if (pReaction->isLocalParameter(pParameter->getObjectName())) pReaction->setParameterMapping(pParameter->getObjectName(), pModelValue->getKey()); Message << " " << pParameter->getObjectName() << " in " << pReaction->getObjectName() << " is replaced by " << pModelValue->getObjectName() << std::endl; } // We need to distinguish between initial and other expressions. if (itChanges->second->getObjectName().compare(0, 7, "Initial") == 0) NewCN = NewCNBase + "Initial"; else NewCN = NewCNBase; // Replace the OldCN of the parameter with the NewCN of global quantity in all expressions. Infix = itChanges->second->getInfix(); // There may be more than one occurrence. Start = 0; while ((Start = Infix.find(OldCN), Start) != std::string::npos) Infix.replace(Start, OldCN.length(), NewCN); const_cast< CExpression * >(itChanges->second)->setInfix(Infix); } CCopasiMessage(CCopasiMessage::WARNING, MCXML + 14, Message.str().c_str()); }
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; }