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import BNGL model without scaling #1567

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1 change: 1 addition & 0 deletions vcell-client/src/main/java/cbit/vcell/client/ClientRequestManager.java
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Expand Up @@ -3196,6 +3196,7 @@ private void openAfterChecking(VCDocumentInfo documentInfo, final TopLevelWindow
boolean bRuleBased = true;
SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("temp NFSim app",
SimulationContext.Application.RULE_BASED_STOCHASTIC);
ruleBasedSimContext.setUsingConcentration(bngUnitSystem.isConcentration(), false);
List<SimulationContext> appList = new ArrayList<SimulationContext>();
appList.add(ruleBasedSimContext);

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7 changes: 5 additions & 2 deletions vcell-core/src/main/java/cbit/vcell/mapping/SimulationContext.java
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Expand Up @@ -2984,8 +2984,11 @@ public void setUsingMassConservationModelReduction(boolean bMassConservationMode
}

public void setUsingConcentration(boolean bUseConcentration, boolean bTransformIfNeeded) throws PropertyVetoException, MappingException, MatrixException, ModelException, MathException, ExpressionException /*throws MappingException, PropertyVetoException*/{
if(applicationType == Application.NETWORK_STOCHASTIC || applicationType == Application.RULE_BASED_STOCHASTIC ||
applicationType == Application.SPRINGSALAD) {
if (applicationType == Application.NETWORK_STOCHASTIC ||
applicationType == Application.RULE_BASED_STOCHASTIC ||
applicationType == Application.SPRINGSALAD ||
(applicationType == Application.NETWORK_DETERMINISTIC && getGeometry().getDimension() == 0)
) {
boolean oldValue = bConcentration;
if(bUseConcentration != oldValue && bTransformIfNeeded){
MathMapping mathMapping = createNewMathMapping();
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17 changes: 8 additions & 9 deletions vcell-core/src/main/java/org/vcell/model/rbm/RbmUtils.java
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Expand Up @@ -199,18 +199,17 @@ public Object visit(ASTSeedSpecies node, Object data) {
SpeciesContext speciesContext = model.createSpeciesContext(structure, seedSpecies.getSpeciesPattern());
for(SimulationContext application : appList) {
SpeciesContextSpec scs = application.getReactionContext().getSpeciesContextSpec(speciesContext);
if (bngUnitSystem.isConcentration() && application.isUsingConcentration()){
if (bngUnitSystem.isConcentration() != application.isUsingConcentration()) {
throw new RuntimeException("BNGL model unit system is " + (bngUnitSystem.isConcentration() ? "concentration" : "count") +
" but application is using " + (application.isUsingConcentration() ? "concentration" : "count") +
". Please change the application unit system to match the model unit system.");
}
if (application.isUsingConcentration()){
scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).setExpression(exp);
}else if (!bngUnitSystem.isConcentration() && !application.isUsingConcentration()){
}else{
scs.getParameter(SpeciesContextSpec.ROLE_InitialCount).setExpression(exp);
}else if (!bngUnitSystem.isConcentration() && application.isUsingConcentration()){
Expression covertedConcentration = scs.convertParticlesToConcentration(exp);
scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).setExpression(covertedConcentration);
}else if (bngUnitSystem.isConcentration() && !application.isUsingConcentration()){
Expression covertedAmount = scs.convertConcentrationToParticles(exp);
scs.getParameter(SpeciesContextSpec.ROLE_InitialCount).setExpression(covertedAmount);
}
scs.setConstant(node.isClamped());
scs.setClamped(node.isClamped());
}
} catch (Exception ex) {
throw new RuntimeException(ex.getMessage(), ex);
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