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createCelloSDProductionReactions create smallMolecule species

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Added support to create species for input small sensor molecules
This commit is contained in:
Pedro Fontanarrosa 2018-12-14 15:03:24 -07:00
parent ebf7418573
commit fe6de14d66
2 changed files with 23 additions and 2 deletions
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4
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBOL2SBML.java
View file

@ -358,7 +358,7 @@ public class SBOL2SBML {
ModuleDefinition resultMD = MDFlattener(sbolDoc, moduleDef);
//Remove Complex formation and sensor promoters from ModuleDefinition, so that no species is created for these
removeSensorPromotersAndComplexes(resultMD, sensorMolecules);
removeSensorInteractios(resultMD, sensorMolecules);
HashMap<FunctionalComponent, HashMap<String, String>> celloParameters = new HashMap<FunctionalComponent, HashMap<String, String>>();
boolean CelloModel = false;
@ -948,7 +948,7 @@ public class SBOL2SBML {
return CelloParameters2;
}
private static void removeSensorPromotersAndComplexes(ModuleDefinition moduleDef, HashMap<String, String> sensorMolecules) throws SBOLValidationException{
private static void removeSensorInteractios(ModuleDefinition moduleDef, HashMap<String, String> sensorMolecules) throws SBOLValidationException{
for (Interaction interact : moduleDef.getInteractions()) {
for (Participation part :interact.getParticipations()){

21
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -2058,8 +2058,29 @@ public class BioModel extends CoreObservable{
for (String modifi : promoterInteractions.get(promoter).keySet()) {
if (modifi.equals("sensor")) {
ModifierSpeciesReference input = r.createModifier();
if (sbml.getModel().getSpecies(promoterInteractions.get(promoter).get(modifi)) == null) {
Species smallMolecule = targetModel.getSBMLDocument().getModel().createSpecies();
smallMolecule.setId(promoterInteractions.get(promoter).get(modifi));
smallMolecule.setSBOTerm(GlobalConstants.SBO_SIMPLE_CHEMICAL);
smallMolecule.setConstant(false);
//smallMolecule.setBoundaryCondition(true);
createDirPort(smallMolecule.getId(), GlobalConstants.INPUT);
/*mRNA.setInitialAmount(0.0);
mRNA.setBoundaryCondition(false);
mRNA.setConstant(false);
mRNA.setHasOnlySubstanceUnits(true);
mRNA.setSBOTerm(GlobalConstants.SBO_MRNA);*/
input.setSpecies(smallMolecule);
input.setSBOTerm(GlobalConstants.SBO_ACTIVATION);
} else {
//input.setSpecies(targetModel.getSBMLDocument().getModel().getSpecies(promoterInteractions.get(promoter).get(modifi)));
input.setSpecies(sbml.getModel().getSpecies(promoterInteractions.get(promoter).get(modifi)));
input.setSBOTerm(GlobalConstants.SBO_ACTIVATION);
}
}
}
}