updating validation, removing a compare block

src/NFreactions/reactions/reaction.cpp

@@ -317,7 +317,7 @@ bool BasicRxnClass::tryToAdd(Molecule *m, unsigned int reactantPos)
 		}
 	}
 
-	//Here we get the standard update...
+	// Here we get the standard update...
 	// if(m->getRxnListMappingId(rxnIndex)>=0)
 	// {
 	// 	if(!reactantTemplates[reactantPos]->compare(m)) {
@@ -343,37 +343,37 @@ bool BasicRxnClass::tryToAdd(Molecule *m, unsigned int reactantPos)
 	// not change its position if the molecule still matches with the template.
 	// This will prevent the simulation trajectory being dependent on whether
 	// reaction-molecules pairs with unchanged membership are checked or not.
-	if (connectivityFlag) {
-		if(m->getRxnListMappingId(rxnIndex)>=0)
-		{
-			// Insted of removing the mappingSet
-			// and then getting a different clean one from the reactant list,
-			// get the mapping set corresponding to the molecule
-			ms = rl->getWriteableMappingSet(m->getRxnListMappingId(rxnIndex));
-			// and clear it before use.
-			ms->clear();
-			// If the molecule matches again,
-			// the mappingSet gets updated during the compare routine.
-			// If the molecule does not match anymore, remove the mapping set
-			// and remove the rxn form the molecule's reaction membership.
-			if(!reactantTemplates[reactantPos]->compare(m,rl,ms)) {
-				rl->removeMappingSet(ms->getId());
-				m->setRxnListMappingId(rxnIndex,Molecule::NOT_IN_RXN);
-			}
-			// case when the molecule is not in the reaction
-		} else {
-			// Get a clean mappingSet from the reactantList
-			// typically from the end: see the code for pusNextAvailableMappingSet()
-			ms = rl->pushNextAvailableMappingSet();
-			if(!reactantTemplates[reactantPos]->compare(m,rl,ms)) {
-				//we must remove, if we did not match.  This will also remove
-				//everything that was cloned off of the mapping set
-				rl->removeMappingSet(ms->getId());
-			} else {
-				m->setRxnListMappingId(rxnIndex,ms->getId());
-			}
-		}
-	}
+	// if (connectivityFlag) {
+	// 	if(m->getRxnListMappingId(rxnIndex)>=0)
+	// 	{
+	// 		// Insted of removing the mappingSet
+	// 		// and then getting a different clean one from the reactant list,
+	// 		// get the mapping set corresponding to the molecule
+	// 		ms = rl->getWriteableMappingSet(m->getRxnListMappingId(rxnIndex));
+	// 		// and clear it before use.
+	// 		ms->clear();
+	// 		// If the molecule matches again,
+	// 		// the mappingSet gets updated during the compare routine.
+	// 		// If the molecule does not match anymore, remove the mapping set
+	// 		// and remove the rxn form the molecule's reaction membership.
+	// 		if(!reactantTemplates[reactantPos]->compare(m,rl,ms)) {
+	// 			rl->removeMappingSet(ms->getId());
+	// 			m->setRxnListMappingId(rxnIndex,Molecule::NOT_IN_RXN);
+	// 		}
+	// 		// case when the molecule is not in the reaction
+	// 	} else {
+	// 		// Get a clean mappingSet from the reactantList
+	// 		// typically from the end: see the code for pusNextAvailableMappingSet()
+	// 		ms = rl->pushNextAvailableMappingSet();
+	// 		if(!reactantTemplates[reactantPos]->compare(m,rl,ms)) {
+	// 			//we must remove, if we did not match.  This will also remove
+	// 			//everything that was cloned off of the mapping set
+	// 			rl->removeMappingSet(ms->getId());
+	// 		} else {
+	// 			m->setRxnListMappingId(rxnIndex,ms->getId());
+	// 		}
+	// 	}
+	// }
 
 	//Here we get the standard update...
 	while(m->getRxnListMappingId(rxnIndex)>=0) {

validate/basicModels/r20.txt

@@ -1,2 +1,2 @@
 connectivity testing, simple binding, unbinding, and phosphorylation system
--sim 100 -oSteps 100 -connect -rxnlog v20_rxns.tsv -trackconnected -printconnected -printmoltypes -printrxncounts
+-sim 100 -oSteps 100 -connect -rxnlog basicModels/v20_rxns.tsv -trackconnected -printconnected -printmoltypes -printrxncounts

validate/basicModels/r21.txt

@@ -1,2 +1,2 @@
 connectivity testing, mRNA monomer model
--sim 100 -oSteps 100 -connect -rxnlog v20_rxns.tsv -utl 3 -gml 1000000 -trackconnected -printconnected -printmoltypes -printrxncounts
+-sim 10 -oSteps 100 -connect -rxnlog basicModels/v21_rxns.tsv -utl 3 -gml 1000000 -trackconnected -printconnected -printmoltypes -printrxncounts