krlhBlupine/iBioSim
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

createCelloSDProductionReactions create smallMolecule species

Browse source 
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
Download patch file Download diff file Expand all files Collapse all files

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

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

@ -2058,12 +2058,33 @@ public class BioModel extends CoreObservable{
for (String modifi : promoterInteractions.get(promoter).keySet()) { for (String modifi : promoterInteractions.get(promoter).keySet()) {
if (modifi.equals("sensor")) { if (modifi.equals("sensor")) {
ModifierSpeciesReference input = r.createModifier(); 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.setSpecies(sbml.getModel().getSpecies(promoterInteractions.get(promoter).get(modifi)));
input.setSBOTerm(GlobalConstants.SBO_ACTIVATION); input.setSBOTerm(GlobalConstants.SBO_ACTIVATION);
} }
} }
} }
} }
}
mRNA.setCompartment(r.getCompartment()); mRNA.setCompartment(r.getCompartment());
mRNA.setInitialAmount(0.0); mRNA.setInitialAmount(0.0);