WIP, testing model exchange between springsalad and vcell, roundtripp…

…ing between the 2
virtualcell · Sep 18, 2024 · 710dfab · 710dfab
1 parent 1517731
commit 710dfab
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Showing 2 changed files with 8 additions and 7 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
@@ -75,7 +75,7 @@ public static ReactionRuleMappingType fromDatabaseName(String databaseName){
 		}
 	}
 
-	public static final String ANY_STATE = "Any_State";		// SpringSaLaD stuff
+	public static final String ANY_STATE_STRING = "Any_State";		// SpringSaLaD stuff
 	private double fieldBondLength = 1;		// only used for Subtype.BINDING reactions
 
 	public enum Subtype {
@@ -346,7 +346,7 @@ public void analizeReaction(Map<String, Object> analysisResults) {
 			if(cspReactant == null) {
 				stateReactant = "ERROR";
 			} else if(cspReactant.isAny()) {
-				stateReactant = ANY_STATE;
+				stateReactant = ANY_STATE_STRING;
 			} else {
 				ComponentStateDefinition csdReactant = cspReactant.getComponentStateDefinition();
 				stateReactant = csdReactant.getName();
@@ -703,7 +703,7 @@ private void writeTransitionData(StringBuilder sb, Subtype subtype, Map<String,
 
 	MolecularTypePattern mtpConditionReactant = null;			// the bound condition molecule
 	MolecularComponentPattern mcpConditionReactant = null;		// the bound condition site (must be bond type "Exists")
-	String stateConditionReactant = ANY_STATE;
+	String stateConditionReactant = ANY_STATE_STRING;
 
 	// we may have 2 mtp if the reaction condition is "Bound"!
 	List<ReactantPattern> rpList = reactionRule.getReactantPatterns();		// we already know that this list is not empty

diff --git a/vcell-core/src/main/java/org/vcell/solver/langevin/LangevinLngvWriter.java b/vcell-core/src/main/java/org/vcell/solver/langevin/LangevinLngvWriter.java
@@ -430,8 +430,8 @@ private static void writeBindingReactions(StringBuilder sb) {
 					(new ArrayList<Map.Entry<ParticleMolecularTypePattern, ParticleMolecularComponentPattern>>(mapSet)).get(0);
 			Map.Entry<ParticleMolecularTypePattern, ParticleMolecularComponentPattern> elementTwo = 
 					(new ArrayList<Map.Entry<ParticleMolecularTypePattern, ParticleMolecularComponentPattern>>(mapSet)).get(1);
-			String nameOne = "Any_State";
-			String nameTwo = "Any_State";
+			String nameOne = ReactionRuleSpec.ANY_STATE_STRING;
+			String nameTwo = ReactionRuleSpec.ANY_STATE_STRING;
 			if(elementOne.getValue().getComponentStatePattern().getParticleComponentStateDefinition() != null) {
 				nameOne = elementOne.getValue().getComponentStatePattern().getParticleComponentStateDefinition().getName();
 			}
@@ -659,7 +659,8 @@ private static void writeTransitionReactions(StringBuilder sb) {
 					}
 					// identify the binding condition site and state 
 					for(ParticleMolecularComponentPattern pmcp : pmtpConditionReactant.getMolecularComponentPatternList()) {
-						if(pmcp.getComponentStatePattern().isAny()) {
+						// condition state may be "any". We need to look for an "existing" bond
+						if(!(pmcp.getBondType() == ParticleMolecularComponentPattern.ParticleBondType.Exists)) {
 							continue;
 						}
 						ParticleComponentStatePattern pcsp = pmcp.getComponentStatePattern();
@@ -708,7 +709,7 @@ private static void writeTransitionReactions(StringBuilder sb) {
 				if(TransitionCondition.BOUND == transitionCondition) {
 					sb.append(" '").append(pmtpConditionReactant.getMolecularType().getName()).append("' : '")
 					.append(pmcpConditionReactant.getMolecularComponent().getName()).append("' : '")
-					.append(pcsdConditionReactant);
+					.append(pmcpConditionReactant.getComponentStatePattern().isAny() ? ReactionRuleSpec.ANY_STATE_STRING : pcsdConditionReactant);
 				}
 				sb.append("\n");
 			}						// end if Subtype.TRANSITION