Fixed import and export for Transition Condition FREE

virtualcell · Oct 10, 2024 · 72c9b93 · 72c9b93
1 parent d8a86a6
commit 72c9b93
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Showing 2 changed files with 9 additions and 24 deletions.
diff --git a/vcell-core/src/main/java/cbit/vcell/mapping/ReactionRuleSpec.java b/vcell-core/src/main/java/cbit/vcell/mapping/ReactionRuleSpec.java
@@ -737,16 +737,11 @@ private void writeTransitionData(StringBuilder sb, Subtype subtype, Map<String,
 	List<ReactantPattern> rpList = reactionRule.getReactantPatterns();		// we already know that this list is not empty
 	List<MolecularTypePattern> mtpReactantList = rpList.get(0).getSpeciesPattern().getMolecularTypePatterns();
 
-	TransitionCondition transitionCondition = TransitionCondition.FREE;		// molecules with just one site belong to free
+	TransitionCondition transitionCondition = TransitionCondition.NONE;		// no restriction
 	if(mtpReactantList.size() == 1) {	// transition reaction condition "None" or "Free"
-		for(MolecularComponentPattern mcpOtherReactant : mtpTransitionReactant.getComponentPatternList()) {
-			if(mcpOtherReactant != mcpTransitionReactant) {
-				if(BondType.None == mcpOtherReactant.getBondType()) {
-					// transition "None" has the bond types of all sites set to "None" (except the transitioning site which is "Possible")
-					transitionCondition = TransitionCondition.NONE;
-					break;
-				}
-			}
+		if(BondType.None == mcpTransitionReactant.getBondType()) {
+			// transition "FREE" has the bond types of all sites set to "Possible" (except the transitioning site which is Unbound)
+			transitionCondition = TransitionCondition.FREE;
 		}
 	} else if(mtpReactantList.size() == 2) {	// transition reaction condition "Bound"
 		transitionCondition = TransitionCondition.BOUND;

diff --git a/vcell-core/src/main/java/org/vcell/model/ssld/SsldUtils.java b/vcell-core/src/main/java/org/vcell/model/ssld/SsldUtils.java
@@ -991,14 +991,9 @@ private void adjustTransitionReactionSites(TransitionReaction ssldReaction, Mapp
         ComponentStatePattern cspTransitionReactant = new ComponentStatePattern(csdInitial);
         mcpTransitionReactant.setComponentStatePattern(cspTransitionReactant);
         // bond is already set to Any
-        if(ssldReaction.getCondition().equals(TransitionReaction.NO_CONDITION)) {
-            for(MolecularComponentPattern mcp : mtpTransitionReactant.getComponentPatternList()) {
-                if(mcp == mcpTransitionReactant) {
-                    continue;
-                }
-                mcp.setBondType(MolecularComponentPattern.BondType.None);
-            }
-        } else if(ssldReaction.getCondition().equals(TransitionReaction.BOUND_CONDITION)) {
+        if(ssldReaction.getCondition().equals(TransitionReaction.FREE_CONDITION)) {
+            mcpTransitionReactant.setBondType(MolecularComponentPattern.BondType.None);
+       } else if(ssldReaction.getCondition().equals(TransitionReaction.BOUND_CONDITION)) {
             // we know for sure that this is the only explicit bond in each of the 2 molecular type patterns of the reactant
             int bondId = 1;     // correct would be:  sp.nextBondId();
             mcpConditionReactant.setBondId(bondId);    // this also sets the BondType to Specified
@@ -1016,13 +1011,8 @@ private void adjustTransitionReactionSites(TransitionReaction ssldReaction, Mapp
         ComponentStatePattern cspTransitionProduct = new ComponentStatePattern(csdFinal);
         mcpTransitionProduct.setComponentStatePattern(cspTransitionProduct);
         System.out.println("  " + ssldReaction.getCondition());
-        if(ssldReaction.getCondition().equals(TransitionReaction.NO_CONDITION)) {
-            for(MolecularComponentPattern mcp : mtpTransitionProduct.getComponentPatternList()) {
-                if(mcp == mcpTransitionProduct) {
-                    continue;
-                }
-                mcp.setBondType(MolecularComponentPattern.BondType.None);
-            }
+        if(ssldReaction.getCondition().equals(TransitionReaction.FREE_CONDITION)) {
+            mcpTransitionProduct.setBondType(MolecularComponentPattern.BondType.None);
         } else if(ssldReaction.getCondition().equals(TransitionReaction.BOUND_CONDITION)) {
             // we know for sure that this is the only explicit bond in each of the 2 molecular type patterns of the product
             int bondId = 1;     // correct would be:  sp.nextBondId();