14 #include "utilities.hpp"
20 #include "sbml/SBMLDocument.h"
21 #include "sbml/Model.h"
22 #include "sbml/Rule.h"
23 #include "sbml/Species.h"
24 #include "sbml/Parameter.h"
25 #include "sbml/math/ASTNode.h"
47 std::set<std::string> ids;
49 if (pSBMLModel != NULL)
52 const SBase* pSBase = NULL;
55 if (pSBMLModel->isSetId())
57 id = pSBMLModel->getId();
59 if (ids.find(
id) == ids.end())
70 pSBase = pSBMLModel->getListOfFunctionDefinitions();
74 if (pSBase->isSetId())
78 if (ids.find(
id) == ids.end())
88 unsigned int i, iMax = pSBMLModel->getListOfFunctionDefinitions()->size();
90 for (i = 0; i < iMax; ++i)
92 pSBase = pSBMLModel->getListOfFunctionDefinitions()->get(i);
94 if (pSBase->isSetId())
98 if (ids.find(
id) == ids.end())
111 pSBase = pSBMLModel->getListOfCompartmentTypes();
115 if (pSBase->isSetId())
117 id = pSBase->getId();
119 if (ids.find(
id) == ids.end())
130 unsigned int i, iMax = pSBMLModel->getListOfCompartmentTypes()->size();
132 for (i = 0; i < iMax; ++i)
134 pSBase = pSBMLModel->getCompartmentType(i);
135 assert(pSBase != NULL);
137 if (pSBase->isSetId())
139 id = pSBase->getId();
141 if (ids.find(
id) == ids.end())
154 pSBase = pSBMLModel->getListOfSpeciesTypes();
158 if (pSBase->isSetId())
160 id = pSBase->getId();
162 if (ids.find(
id) == ids.end())
173 unsigned int i, iMax = pSBMLModel->getListOfSpeciesTypes()->size();
175 for (i = 0; i < iMax; ++i)
177 pSBase = pSBMLModel->getSpeciesType(i);
178 assert(pSBase != NULL);
180 if (pSBase->isSetId())
182 id = pSBase->getId();
184 if (ids.find(
id) == ids.end())
197 pSBase = pSBMLModel->getListOfCompartments();
201 if (pSBase->isSetId())
203 id = pSBase->getId();
205 if (ids.find(
id) == ids.end())
216 unsigned int i, iMax = pSBMLModel->getListOfCompartments()->size();
218 for (i = 0; i < iMax; ++i)
220 pSBase = pSBMLModel->getCompartment(i);
221 assert(pSBase != NULL);
223 if (pSBase->isSetId())
225 id = pSBase->getId();
227 if (ids.find(
id) == ids.end())
240 pSBase = pSBMLModel->getListOfSpecies();
244 if (pSBase->isSetId())
246 id = pSBase->getId();
248 if (ids.find(
id) == ids.end())
259 unsigned int i, iMax = pSBMLModel->getListOfSpecies()->size();
261 for (i = 0; i < iMax; ++i)
263 pSBase = pSBMLModel->getSpecies(i);
264 assert(pSBase != NULL);
266 if (pSBase->isSetId())
268 id = pSBase->getId();
270 if (ids.find(
id) == ids.end())
283 pSBase = pSBMLModel->getListOfParameters();
287 if (pSBase->isSetId())
289 id = pSBase->getId();
291 if (ids.find(
id) == ids.end())
302 unsigned int i, iMax = pSBMLModel->getListOfParameters()->size();
304 for (i = 0; i < iMax; ++i)
306 pSBase = pSBMLModel->getParameter(i);
307 assert(pSBase != NULL);
309 if (pSBase->isSetId())
311 id = pSBase->getId();
313 if (ids.find(
id) == ids.end())
326 pSBase = pSBMLModel->getListOfInitialAssignments();
330 if (pSBase->isSetId())
332 id = pSBase->getId();
334 if (ids.find(
id) == ids.end())
346 pSBase = pSBMLModel->getListOfRules();
350 if (pSBase->isSetId())
352 id = pSBase->getId();
354 if (ids.find(
id) == ids.end())
366 pSBase = pSBMLModel->getListOfConstraints();
370 if (pSBase->isSetId())
372 id = pSBase->getId();
374 if (ids.find(
id) == ids.end())
386 pSBase = pSBMLModel->getListOfReactions();
390 if (pSBase->isSetId())
392 id = pSBase->getId();
394 if (ids.find(
id) == ids.end())
405 unsigned int i, iMax = pSBMLModel->getListOfReactions()->size();
407 for (i = 0; i < iMax; ++i)
409 const Reaction* pReaction = pSBMLModel->getReaction(i);
410 assert(pReaction != NULL);
412 if (pReaction->isSetId())
414 id = pReaction->getId();
416 if (ids.find(
id) == ids.end())
429 if (pReaction->getListOfReactants() != NULL)
431 pSBase = pReaction->getListOfReactants();
432 unsigned int j, jMax = pReaction->getListOfReactants()->size();
434 for (j = 0; j < jMax; ++j)
436 pSBase = pReaction->getReactant(j);
437 assert(pSBase != NULL);
440 if (pSBase->isSetId())
442 id = pSBase->getId();
444 if (ids.find(
id) == ids.end())
456 if (pReaction->getListOfProducts() != NULL)
458 pSBase = pReaction->getListOfProducts();
459 unsigned int j, jMax = pReaction->getListOfProducts()->size();
461 for (j = 0; j < jMax; ++j)
463 pSBase = pReaction->getProduct(j);
464 assert(pSBase != NULL);
467 if (pSBase->isSetId())
469 id = pSBase->getId();
471 if (ids.find(
id) == ids.end())
483 if (pReaction->getListOfModifiers() != NULL)
485 pSBase = pReaction->getListOfModifiers();
486 unsigned int j, jMax = pReaction->getListOfModifiers()->size();
488 for (j = 0; j < jMax; ++j)
490 pSBase = pReaction->getModifier(j);
491 assert(pSBase != NULL);
494 if (pSBase->isSetId())
496 id = pSBase->getId();
498 if (ids.find(
id) == ids.end())
513 pSBase = pSBMLModel->getListOfEvents();
517 if (pSBase->isSetId())
519 id = pSBase->getId();
521 if (ids.find(
id) == ids.end())
549 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
551 const Model* pSBMLModel = pDocument->getModel();
552 CPPUNIT_ASSERT(pSBMLModel != NULL);
553 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
554 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
555 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
556 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
557 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
558 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
561 CPPUNIT_ASSERT(pModel != NULL);
562 CCompartment* pCompartment = pModel->createCompartment(
"compartment_2");
563 CPPUNIT_ASSERT(pCompartment != NULL);
564 pModel->compileIfNecessary(NULL);
565 std::set<const CCopasiObject*> changedObjects;
567 CPPUNIT_ASSERT(pObject != NULL);
568 changedObjects.insert(pObject);
569 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
570 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
572 while (refreshIt != refreshEndit)
579 pSBMLModel = pDocument->getModel();
580 CPPUNIT_ASSERT(pSBMLModel != NULL);
581 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
582 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 2);
583 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
584 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
585 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
586 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
594 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
596 const Model* pSBMLModel = pDocument->getModel();
597 CPPUNIT_ASSERT(pSBMLModel != NULL);
598 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
599 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
600 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
601 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
602 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
603 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
606 CPPUNIT_ASSERT(pModel != NULL);
608 CPPUNIT_ASSERT(pMetabolite != NULL);
609 pModel->compileIfNecessary(NULL);
610 std::set<const CCopasiObject*> changedObjects;
612 CPPUNIT_ASSERT(pObject != NULL);
613 changedObjects.insert(pObject);
614 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
615 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
617 while (refreshIt != refreshEndit)
624 pSBMLModel = pDocument->getModel();
625 CPPUNIT_ASSERT(pSBMLModel != NULL);
626 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
627 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
628 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 2);
629 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
630 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
631 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
639 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
641 const Model* pSBMLModel = pDocument->getModel();
642 CPPUNIT_ASSERT(pSBMLModel != NULL);
643 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
644 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
645 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
646 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
647 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
648 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
651 CPPUNIT_ASSERT(pModel != NULL);
652 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
653 CPPUNIT_ASSERT(pModelValue != NULL);
654 pModel->compileIfNecessary(NULL);
655 std::set<const CCopasiObject*> changedObjects;
657 CPPUNIT_ASSERT(pObject != NULL);
658 changedObjects.insert(pObject);
659 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
660 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
662 while (refreshIt != refreshEndit)
669 pSBMLModel = pDocument->getModel();
670 CPPUNIT_ASSERT(pSBMLModel != NULL);
671 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
672 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
673 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
674 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
675 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
676 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
684 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
686 const Model* pSBMLModel = pDocument->getModel();
687 CPPUNIT_ASSERT(pSBMLModel != NULL);
688 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
689 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
690 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
691 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
692 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
693 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
696 CPPUNIT_ASSERT(pModel != NULL);
697 CReaction* pReaction = pModel->createReaction(
"influx");
698 CPPUNIT_ASSERT(pReaction != NULL);
699 pReaction->
addProduct(pModel->getMetabolites()[0]->getKey());
700 pReaction->
setFunction(
"Constant flux (irreversible)");
702 pModel->compileIfNecessary(NULL);
703 std::set<const CCopasiObject*> changedObjects;
705 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
706 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
708 while (refreshIt != refreshEndit)
715 pSBMLModel = pDocument->getModel();
716 CPPUNIT_ASSERT(pSBMLModel != NULL);
717 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
718 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
719 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
720 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 2);
721 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
722 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
730 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
732 const Model* pSBMLModel = pDocument->getModel();
733 CPPUNIT_ASSERT(pSBMLModel != NULL);
734 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
735 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
736 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
737 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
738 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
739 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
742 CPPUNIT_ASSERT(pModel != NULL);
744 CPPUNIT_ASSERT(pMetabolite != NULL);
745 pModel->compileIfNecessary(NULL);
746 std::set<const CCopasiObject*> changedObjects;
748 CPPUNIT_ASSERT(pObject != NULL);
749 changedObjects.insert(pObject);
750 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
751 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
753 while (refreshIt != refreshEndit)
760 pSBMLModel = pDocument->getModel();
761 CPPUNIT_ASSERT(pSBMLModel != NULL);
762 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
763 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
764 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 2);
765 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
766 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
767 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
775 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
777 const Model* pSBMLModel = pDocument->getModel();
778 CPPUNIT_ASSERT(pSBMLModel != NULL);
779 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
780 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
781 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
782 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
783 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
784 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
787 CPPUNIT_ASSERT(pModel != NULL);
788 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
789 CPPUNIT_ASSERT(pModelValue != NULL);
790 pModel->compileIfNecessary(NULL);
791 std::set<const CCopasiObject*> changedObjects;
793 CPPUNIT_ASSERT(pObject != NULL);
794 changedObjects.insert(pObject);
795 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
796 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
798 while (refreshIt != refreshEndit)
805 pSBMLModel = pDocument->getModel();
806 CPPUNIT_ASSERT(pSBMLModel != NULL);
807 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
808 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
809 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
810 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
811 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
812 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
820 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
822 const Model* pSBMLModel = pDocument->getModel();
823 CPPUNIT_ASSERT(pSBMLModel != NULL);
824 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
825 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
826 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
827 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
828 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
829 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
832 CPPUNIT_ASSERT(pModel != NULL);
833 CReaction* pReaction = pModel->createReaction(
"influx");
834 CPPUNIT_ASSERT(pReaction != NULL);
835 pReaction->
addProduct(pModel->getMetabolites()[0]->getKey());
836 pReaction->
setFunction(
"Constant flux (irreversible)");
838 pModel->compileIfNecessary(NULL);
839 std::set<const CCopasiObject*> changedObjects;
841 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
842 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
844 while (refreshIt != refreshEndit)
851 pSBMLModel = pDocument->getModel();
852 CPPUNIT_ASSERT(pSBMLModel != NULL);
853 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
854 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
855 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
856 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 2);
857 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
858 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
866 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
868 const Model* pSBMLModel = pDocument->getModel();
869 CPPUNIT_ASSERT(pSBMLModel != NULL);
870 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
871 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
872 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
873 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
874 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
875 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
878 CPPUNIT_ASSERT(pModel != NULL);
879 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
880 CPPUNIT_ASSERT(pModelValue != NULL);
881 pModel->compileIfNecessary(NULL);
882 std::set<const CCopasiObject*> changedObjects;
884 CPPUNIT_ASSERT(pObject != NULL);
885 changedObjects.insert(pObject);
886 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
887 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
889 while (refreshIt != refreshEndit)
896 pSBMLModel = pDocument->getModel();
897 CPPUNIT_ASSERT(pSBMLModel != NULL);
898 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
899 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
900 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
901 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
902 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
903 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
911 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
913 const Model* pSBMLModel = pDocument->getModel();
914 CPPUNIT_ASSERT(pSBMLModel != NULL);
915 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
916 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
917 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
918 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
919 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
920 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
923 CPPUNIT_ASSERT(pModel != NULL);
924 CReaction* pReaction = pModel->createReaction(
"influx");
925 CPPUNIT_ASSERT(pReaction != NULL);
926 pReaction->
addProduct(pModel->getMetabolites()[0]->getKey());
927 pReaction->
setFunction(
"Constant flux (irreversible)");
929 pModel->compileIfNecessary(NULL);
930 std::set<const CCopasiObject*> changedObjects;
932 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
933 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
935 while (refreshIt != refreshEndit)
942 pSBMLModel = pDocument->getModel();
943 CPPUNIT_ASSERT(pSBMLModel != NULL);
944 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
945 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
946 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
947 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 2);
948 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
949 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
957 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
959 const Model* pSBMLModel = pDocument->getModel();
960 CPPUNIT_ASSERT(pSBMLModel != NULL);
961 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
962 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
963 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
964 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
965 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
966 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
969 CPPUNIT_ASSERT(pModel != NULL);
970 CReaction* pReaction = pModel->createReaction(
"influx");
971 CPPUNIT_ASSERT(pReaction != NULL);
972 pReaction->
addProduct(pModel->getMetabolites()[0]->getKey());
973 pReaction->
setFunction(
"Constant flux (irreversible)");
975 pModel->compileIfNecessary(NULL);
976 std::set<const CCopasiObject*> changedObjects;
978 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
979 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
981 while (refreshIt != refreshEndit)
988 pSBMLModel = pDocument->getModel();
989 CPPUNIT_ASSERT(pSBMLModel != NULL);
990 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
991 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
992 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
993 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 2);
994 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
995 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1004 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1006 CPPUNIT_ASSERT(pDocument == NULL);
1009 CPPUNIT_ASSERT(pModel != NULL);
1011 CPPUNIT_ASSERT(pMetabolite != NULL);
1013 std::set<const CCopasiObject*> changedObjects;
1015 CPPUNIT_ASSERT(pObject != NULL);
1016 changedObjects.insert(pObject);
1018 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1020 while (refreshIt != refreshEndit)
1027 const Model* pSBMLModel = pDocument->getModel();
1028 CPPUNIT_ASSERT(pSBMLModel != NULL);
1029 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
1030 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1031 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 2);
1032 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1033 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1034 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1043 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1045 CPPUNIT_ASSERT(pDocument == NULL);
1048 CPPUNIT_ASSERT(pModel != NULL);
1050 CPPUNIT_ASSERT(pModelValue != NULL);
1052 std::set<const CCopasiObject*> changedObjects;
1054 CPPUNIT_ASSERT(pObject != NULL);
1055 changedObjects.insert(pObject);
1057 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1059 while (refreshIt != refreshEndit)
1066 const Model* pSBMLModel = pDocument->getModel();
1067 CPPUNIT_ASSERT(pSBMLModel != NULL);
1068 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
1069 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1070 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1071 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1072 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1073 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
1082 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1084 CPPUNIT_ASSERT(pDocument == NULL);
1087 CPPUNIT_ASSERT(pModel != NULL);
1089 CPPUNIT_ASSERT(pReaction != NULL);
1091 pReaction->
setFunction(
"Constant flux (irreversible)");
1094 std::set<const CCopasiObject*> changedObjects;
1097 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1099 while (refreshIt != refreshEndit)
1106 const Model* pSBMLModel = pDocument->getModel();
1107 CPPUNIT_ASSERT(pSBMLModel != NULL);
1108 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1109 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1110 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1111 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 2);
1112 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1113 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1122 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1124 CPPUNIT_ASSERT(pDocument == NULL);
1127 CPPUNIT_ASSERT(pModel != NULL);
1129 CPPUNIT_ASSERT(pModelValue != NULL);
1131 std::set<const CCopasiObject*> changedObjects;
1133 CPPUNIT_ASSERT(pObject != NULL);
1134 changedObjects.insert(pObject);
1136 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1138 while (refreshIt != refreshEndit)
1145 const Model* pSBMLModel = pDocument->getModel();
1146 CPPUNIT_ASSERT(pSBMLModel != NULL);
1147 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
1148 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1149 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1150 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1151 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1152 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
1161 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1163 CPPUNIT_ASSERT(pDocument == NULL);
1166 CPPUNIT_ASSERT(pModel != NULL);
1168 CPPUNIT_ASSERT(pReaction != NULL);
1170 pReaction->
setFunction(
"Constant flux (irreversible)");
1173 std::set<const CCopasiObject*> changedObjects;
1176 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1178 while (refreshIt != refreshEndit)
1185 const Model* pSBMLModel = pDocument->getModel();
1186 CPPUNIT_ASSERT(pSBMLModel != NULL);
1187 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1188 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1189 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1190 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 2);
1191 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1192 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1201 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1203 CPPUNIT_ASSERT(pDocument == NULL);
1206 CPPUNIT_ASSERT(pModel != NULL);
1208 CPPUNIT_ASSERT(pReaction != NULL);
1210 pReaction->
setFunction(
"Constant flux (irreversible)");
1213 std::set<const CCopasiObject*> changedObjects;
1216 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1218 while (refreshIt != refreshEndit)
1225 const Model* pSBMLModel = pDocument->getModel();
1226 CPPUNIT_ASSERT(pSBMLModel != NULL);
1227 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1228 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1229 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1230 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 2);
1231 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1232 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1240 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1242 const Model* pSBMLModel = pDocument->getModel();
1243 CPPUNIT_ASSERT(pSBMLModel != NULL);
1244 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
1245 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1246 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1247 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1248 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1249 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1252 CPPUNIT_ASSERT(pModel != NULL);
1255 CPPUNIT_ASSERT(pFunctionDefinition != NULL);
1256 CPPUNIT_ASSERT(pFunctionDefinition->
setInfix(
"3 * 5") ==
true);
1257 pFunctionDefinition->
compile();
1260 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
1261 CPPUNIT_ASSERT(pModelValue != NULL);
1265 pModel->compileIfNecessary(NULL);
1266 std::set<const CCopasiObject*> changedObjects;
1268 CPPUNIT_ASSERT(pObject != NULL);
1269 changedObjects.insert(pObject);
1270 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
1271 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1273 while (refreshIt != refreshEndit)
1280 pSBMLModel = pDocument->getModel();
1281 CPPUNIT_ASSERT(pSBMLModel != NULL);
1282 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1283 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1284 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1285 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1286 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 1);
1287 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
1295 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1297 const Model* pSBMLModel = pDocument->getModel();
1298 CPPUNIT_ASSERT(pSBMLModel != NULL);
1299 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
1300 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1301 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1302 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1303 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1304 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1307 CPPUNIT_ASSERT(pModel != NULL);
1310 CPPUNIT_ASSERT(pFunctionDefinition != NULL);
1311 CPPUNIT_ASSERT(pFunctionDefinition->
setInfix(
"3 * 5") ==
true);
1312 pFunctionDefinition->
compile();
1315 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
1316 CPPUNIT_ASSERT(pModelValue != NULL);
1320 pModel->compileIfNecessary(NULL);
1321 std::set<const CCopasiObject*> changedObjects;
1323 CPPUNIT_ASSERT(pObject != NULL);
1324 changedObjects.insert(pObject);
1325 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
1326 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1328 while (refreshIt != refreshEndit)
1335 pSBMLModel = pDocument->getModel();
1336 CPPUNIT_ASSERT(pSBMLModel != NULL);
1337 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1338 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1339 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1340 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1341 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 1);
1342 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
1350 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1352 const Model* pSBMLModel = pDocument->getModel();
1353 CPPUNIT_ASSERT(pSBMLModel != NULL);
1354 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
1355 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1356 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1357 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1358 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1359 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1362 CPPUNIT_ASSERT(pModel != NULL);
1365 CPPUNIT_ASSERT(pFunctionDefinition != NULL);
1366 CPPUNIT_ASSERT(pFunctionDefinition->
setInfix(
"3 * 5") ==
true);
1367 pFunctionDefinition->
compile();
1370 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
1371 CPPUNIT_ASSERT(pModelValue != NULL);
1375 pModel->compileIfNecessary(NULL);
1376 std::set<const CCopasiObject*> changedObjects;
1378 CPPUNIT_ASSERT(pObject != NULL);
1379 changedObjects.insert(pObject);
1380 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
1381 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1383 while (refreshIt != refreshEndit)
1390 pSBMLModel = pDocument->getModel();
1391 CPPUNIT_ASSERT(pSBMLModel != NULL);
1392 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1393 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1394 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1395 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1396 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 1);
1397 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
1405 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1407 const Model* pSBMLModel = pDocument->getModel();
1408 CPPUNIT_ASSERT(pSBMLModel != NULL);
1409 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 1);
1410 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1411 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1412 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1413 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 0);
1414 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 1);
1417 CPPUNIT_ASSERT(pModel != NULL);
1420 CPPUNIT_ASSERT(pFunctionDefinition != NULL);
1421 CPPUNIT_ASSERT(pFunctionDefinition->
setInfix(
"3 * 5") ==
true);
1422 pFunctionDefinition->
compile();
1425 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
1426 CPPUNIT_ASSERT(pModelValue != NULL);
1430 pModel->compileIfNecessary(NULL);
1431 std::set<const CCopasiObject*> changedObjects;
1433 CPPUNIT_ASSERT(pObject != NULL);
1434 changedObjects.insert(pObject);
1435 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
1436 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1438 while (refreshIt != refreshEndit)
1445 pSBMLModel = pDocument->getModel();
1446 CPPUNIT_ASSERT(pSBMLModel != NULL);
1447 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1448 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1449 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1450 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1451 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 1);
1452 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
1464 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1467 CPPUNIT_ASSERT(pModel != NULL);
1470 CPPUNIT_ASSERT(pFunctionDefinition != NULL);
1471 CPPUNIT_ASSERT(pFunctionDefinition->
setInfix(
"3 * 5") ==
true);
1472 pFunctionDefinition->
compile();
1475 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
1476 CPPUNIT_ASSERT(pModelValue != NULL);
1480 pModel->compileIfNecessary(NULL);
1481 std::set<const CCopasiObject*> changedObjects;
1483 CPPUNIT_ASSERT(pObject != NULL);
1484 changedObjects.insert(pObject);
1485 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
1486 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1488 while (refreshIt != refreshEndit)
1495 const Model* pSBMLModel = pDocument->getModel();
1496 CPPUNIT_ASSERT(pSBMLModel != NULL);
1497 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1498 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1499 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1500 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1501 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 1);
1502 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
1515 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1518 CPPUNIT_ASSERT(pModel != NULL);
1521 CPPUNIT_ASSERT(pFunctionDefinition != NULL);
1522 CPPUNIT_ASSERT(pFunctionDefinition->
setInfix(
"3 * 5") ==
true);
1523 pFunctionDefinition->
compile();
1526 CModelValue* pModelValue = pModel->createModelValue(
"parameter_2");
1527 CPPUNIT_ASSERT(pModelValue != NULL);
1531 pModel->compileIfNecessary(NULL);
1532 std::set<const CCopasiObject*> changedObjects;
1534 CPPUNIT_ASSERT(pObject != NULL);
1535 changedObjects.insert(pObject);
1536 std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
1537 std::vector<Refresh*>::iterator refreshIt = refreshes.begin(), refreshEndit = refreshes.end();
1539 while (refreshIt != refreshEndit)
1546 const Model* pSBMLModel = pDocument->getModel();
1547 CPPUNIT_ASSERT(pSBMLModel != NULL);
1548 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 2);
1549 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1550 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 1);
1551 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1552 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 1);
1553 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 2);
1562 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1563 std::string modelString;
1571 CPPUNIT_ASSERT(
false);
1574 CPPUNIT_ASSERT(modelString.empty() ==
false);
1582 CPPUNIT_ASSERT(
false);
1585 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
1587 const Model* pSBMLModel = pDocument->getModel();
1588 CPPUNIT_ASSERT(pSBMLModel != NULL);
1589 CPPUNIT_ASSERT(pSBMLModel->getNumFunctionDefinitions() == 0);
1590 CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 1);
1591 CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 3);
1592 CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 1);
1593 CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 1);
1594 CPPUNIT_ASSERT(pSBMLModel->getNumInitialAssignments() == 2);
1595 CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 5);
1601 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
1602 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
1603 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
1604 " <listOfFunctionDefinitions>\n"
1605 " <functionDefinition metaid=\"_000004\" id=\"compartment_2\" name=\"function_1\">\n"
1606 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1621 " </functionDefinition>\n"
1622 " </listOfFunctionDefinitions> \n"
1623 " <listOfUnitDefinitions>\n"
1624 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
1626 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
1628 " </unitDefinition>\n"
1629 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
1631 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
1633 " </unitDefinition>\n"
1634 " </listOfUnitDefinitions> \n"
1635 " <listOfCompartments>\n"
1636 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
1638 " </listOfCompartments>\n"
1639 " <listOfSpecies>\n"
1640 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
1641 " </listOfSpecies> \n"
1642 " <listOfParameters>\n"
1643 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
1644 " </listOfParameters>\n"
1645 " <listOfReactions>\n"
1646 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
1647 " <listOfReactants>\n"
1648 " <speciesReference species=\"species_1\"/>\n"
1649 " </listOfReactants>\n"
1651 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1654 " <ci> compartment_1 </ci>\n"
1656 " <ci> compartment_2 </ci>\n"
1657 " <ci> parameter_1 </ci>\n"
1658 " <ci> species_1 </ci>\n"
1664 " </listOfReactions>\n"
1670 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
1671 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
1672 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
1673 " <listOfFunctionDefinitions>\n"
1674 " <functionDefinition metaid=\"_000004\" id=\"species_2\" name=\"function_1\">\n"
1675 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1690 " </functionDefinition>\n"
1691 " </listOfFunctionDefinitions> \n"
1692 " <listOfUnitDefinitions>\n"
1693 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
1695 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
1697 " </unitDefinition>\n"
1698 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
1700 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
1702 " </unitDefinition>\n"
1703 " </listOfUnitDefinitions> \n"
1704 " <listOfCompartments>\n"
1705 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
1707 " </listOfCompartments>\n"
1708 " <listOfSpecies>\n"
1709 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
1710 " </listOfSpecies> \n"
1711 " <listOfParameters>\n"
1712 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
1713 " </listOfParameters>\n"
1714 " <listOfReactions>\n"
1715 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
1716 " <listOfReactants>\n"
1717 " <speciesReference species=\"species_1\"/>\n"
1718 " </listOfReactants>\n"
1720 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1723 " <ci> compartment_1 </ci>\n"
1725 " <ci> species_2 </ci>\n"
1726 " <ci> parameter_1 </ci>\n"
1727 " <ci> species_1 </ci>\n"
1733 " </listOfReactions>\n"
1739 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
1740 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
1741 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
1742 " <listOfFunctionDefinitions>\n"
1743 " <functionDefinition metaid=\"_000004\" id=\"parameter_2\" name=\"function_1\">\n"
1744 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1759 " </functionDefinition>\n"
1760 " </listOfFunctionDefinitions> \n"
1761 " <listOfUnitDefinitions>\n"
1762 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
1764 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
1766 " </unitDefinition>\n"
1767 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
1769 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
1771 " </unitDefinition>\n"
1772 " </listOfUnitDefinitions> \n"
1773 " <listOfCompartments>\n"
1774 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
1776 " </listOfCompartments>\n"
1777 " <listOfSpecies>\n"
1778 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
1779 " </listOfSpecies> \n"
1780 " <listOfParameters>\n"
1781 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
1782 " </listOfParameters>\n"
1783 " <listOfReactions>\n"
1784 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
1785 " <listOfReactants>\n"
1786 " <speciesReference species=\"species_1\"/>\n"
1787 " </listOfReactants>\n"
1789 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1792 " <ci> compartment_1 </ci>\n"
1794 " <ci> parameter_2 </ci>\n"
1795 " <ci> parameter_1 </ci>\n"
1796 " <ci> species_1 </ci>\n"
1802 " </listOfReactions>\n"
1808 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
1809 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
1810 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
1811 " <listOfFunctionDefinitions>\n"
1812 " <functionDefinition metaid=\"_000004\" id=\"reaction_2\" name=\"function_1\">\n"
1813 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1828 " </functionDefinition>\n"
1829 " </listOfFunctionDefinitions> \n"
1830 " <listOfUnitDefinitions>\n"
1831 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
1833 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
1835 " </unitDefinition>\n"
1836 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
1838 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
1840 " </unitDefinition>\n"
1841 " </listOfUnitDefinitions> \n"
1842 " <listOfCompartments>\n"
1843 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
1845 " </listOfCompartments>\n"
1846 " <listOfSpecies>\n"
1847 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
1848 " </listOfSpecies> \n"
1849 " <listOfParameters>\n"
1850 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
1851 " </listOfParameters>\n"
1852 " <listOfReactions>\n"
1853 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
1854 " <listOfReactants>\n"
1855 " <speciesReference species=\"species_1\"/>\n"
1856 " </listOfReactants>\n"
1858 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1861 " <ci> compartment_1 </ci>\n"
1863 " <ci> reaction_2 </ci>\n"
1864 " <ci> parameter_1 </ci>\n"
1865 " <ci> species_1 </ci>\n"
1871 " </listOfReactions>\n"
1877 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
1878 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
1879 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
1880 " <listOfFunctionDefinitions>\n"
1881 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
1882 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1897 " </functionDefinition>\n"
1898 " </listOfFunctionDefinitions> \n"
1899 " <listOfUnitDefinitions>\n"
1900 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
1902 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
1904 " </unitDefinition>\n"
1905 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
1907 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
1909 " </unitDefinition>\n"
1910 " </listOfUnitDefinitions> \n"
1911 " <listOfCompartments>\n"
1912 " <compartment metaid=\"_000005\" id=\"species_2\" name=\"compartment_1\" size=\"1e-16\">\n"
1914 " </listOfCompartments>\n"
1915 " <listOfSpecies>\n"
1916 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"species_2\" initialAmount=\"1.0\"/>\n"
1917 " </listOfSpecies> \n"
1918 " <listOfParameters>\n"
1919 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
1920 " </listOfParameters>\n"
1921 " <listOfReactions>\n"
1922 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
1923 " <listOfReactants>\n"
1924 " <speciesReference species=\"species_1\"/>\n"
1925 " </listOfReactants>\n"
1927 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1930 " <ci> species_2 </ci>\n"
1932 " <ci> function_1 </ci>\n"
1933 " <ci> parameter_1 </ci>\n"
1934 " <ci> species_1 </ci>\n"
1940 " </listOfReactions>\n"
1946 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
1947 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
1948 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
1949 " <listOfFunctionDefinitions>\n"
1950 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
1951 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1966 " </functionDefinition>\n"
1967 " </listOfFunctionDefinitions> \n"
1968 " <listOfUnitDefinitions>\n"
1969 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
1971 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
1973 " </unitDefinition>\n"
1974 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
1976 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
1978 " </unitDefinition>\n"
1979 " </listOfUnitDefinitions> \n"
1980 " <listOfCompartments>\n"
1981 " <compartment metaid=\"_000005\" id=\"parameter_2\" name=\"compartment_1\" size=\"1e-16\">\n"
1983 " </listOfCompartments>\n"
1984 " <listOfSpecies>\n"
1985 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"parameter_2\" initialAmount=\"1.0\"/>\n"
1986 " </listOfSpecies> \n"
1987 " <listOfParameters>\n"
1988 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
1989 " </listOfParameters>\n"
1990 " <listOfReactions>\n"
1991 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
1992 " <listOfReactants>\n"
1993 " <speciesReference species=\"species_1\"/>\n"
1994 " </listOfReactants>\n"
1996 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
1999 " <ci> parameter_2 </ci>\n"
2001 " <ci> function_1 </ci>\n"
2002 " <ci> parameter_1 </ci>\n"
2003 " <ci> species_1 </ci>\n"
2009 " </listOfReactions>\n"
2015 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2016 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
2017 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
2018 " <listOfFunctionDefinitions>\n"
2019 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
2020 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2035 " </functionDefinition>\n"
2036 " </listOfFunctionDefinitions> \n"
2037 " <listOfUnitDefinitions>\n"
2038 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
2040 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
2042 " </unitDefinition>\n"
2043 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
2045 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
2047 " </unitDefinition>\n"
2048 " </listOfUnitDefinitions> \n"
2049 " <listOfCompartments>\n"
2050 " <compartment metaid=\"_000005\" id=\"reaction_2\" name=\"compartment_1\" size=\"1e-16\">\n"
2052 " </listOfCompartments>\n"
2053 " <listOfSpecies>\n"
2054 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"reaction_2\" initialAmount=\"1.0\"/>\n"
2055 " </listOfSpecies> \n"
2056 " <listOfParameters>\n"
2057 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
2058 " </listOfParameters>\n"
2059 " <listOfReactions>\n"
2060 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
2061 " <listOfReactants>\n"
2062 " <speciesReference species=\"species_1\"/>\n"
2063 " </listOfReactants>\n"
2065 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2068 " <ci> reaction_2 </ci>\n"
2070 " <ci> function_1 </ci>\n"
2071 " <ci> parameter_1 </ci>\n"
2072 " <ci> species_1 </ci>\n"
2078 " </listOfReactions>\n"
2084 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2085 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
2086 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
2087 " <listOfFunctionDefinitions>\n"
2088 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
2089 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2104 " </functionDefinition>\n"
2105 " </listOfFunctionDefinitions> \n"
2106 " <listOfUnitDefinitions>\n"
2107 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
2109 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
2111 " </unitDefinition>\n"
2112 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
2114 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
2116 " </unitDefinition>\n"
2117 " </listOfUnitDefinitions> \n"
2118 " <listOfCompartments>\n"
2119 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
2121 " </listOfCompartments>\n"
2122 " <listOfSpecies>\n"
2123 " <species metaid=\"_000006\" id=\"parameter_2\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
2124 " </listOfSpecies> \n"
2125 " <listOfParameters>\n"
2126 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
2127 " </listOfParameters>\n"
2128 " <listOfReactions>\n"
2129 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
2130 " <listOfReactants>\n"
2131 " <speciesReference species=\"parameter_2\"/>\n"
2132 " </listOfReactants>\n"
2134 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2137 " <ci> compartment_1 </ci>\n"
2139 " <ci> function_1 </ci>\n"
2140 " <ci> parameter_1 </ci>\n"
2141 " <ci> parameter_2 </ci>\n"
2147 " </listOfReactions>\n"
2153 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2154 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
2155 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
2156 " <listOfFunctionDefinitions>\n"
2157 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
2158 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2173 " </functionDefinition>\n"
2174 " </listOfFunctionDefinitions> \n"
2175 " <listOfUnitDefinitions>\n"
2176 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
2178 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
2180 " </unitDefinition>\n"
2181 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
2183 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
2185 " </unitDefinition>\n"
2186 " </listOfUnitDefinitions> \n"
2187 " <listOfCompartments>\n"
2188 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
2190 " </listOfCompartments>\n"
2191 " <listOfSpecies>\n"
2192 " <species metaid=\"_000006\" id=\"reaction_2\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
2193 " </listOfSpecies> \n"
2194 " <listOfParameters>\n"
2195 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
2196 " </listOfParameters>\n"
2197 " <listOfReactions>\n"
2198 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
2199 " <listOfReactants>\n"
2200 " <speciesReference species=\"reaction_2\"/>\n"
2201 " </listOfReactants>\n"
2203 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2206 " <ci> compartment_1 </ci>\n"
2208 " <ci> function_1 </ci>\n"
2209 " <ci> parameter_1 </ci>\n"
2210 " <ci> reaction_2 </ci>\n"
2216 " </listOfReactions>\n"
2222 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2223 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
2224 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
2225 " <listOfFunctionDefinitions>\n"
2226 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
2227 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2242 " </functionDefinition>\n"
2243 " </listOfFunctionDefinitions> \n"
2244 " <listOfUnitDefinitions>\n"
2245 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
2247 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
2249 " </unitDefinition>\n"
2250 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
2252 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
2254 " </unitDefinition>\n"
2255 " </listOfUnitDefinitions> \n"
2256 " <listOfCompartments>\n"
2257 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
2259 " </listOfCompartments>\n"
2260 " <listOfSpecies>\n"
2261 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
2262 " </listOfSpecies> \n"
2263 " <listOfParameters>\n"
2264 " <parameter metaid=\"_000007\" id=\"reaction_2\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
2265 " </listOfParameters>\n"
2266 " <listOfReactions>\n"
2267 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
2268 " <listOfReactants>\n"
2269 " <speciesReference species=\"species_1\"/>\n"
2270 " </listOfReactants>\n"
2272 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2275 " <ci> compartment_1 </ci>\n"
2277 " <ci> function_1 </ci>\n"
2278 " <ci> reaction_2 </ci>\n"
2279 " <ci> species_1 </ci>\n"
2285 " </listOfReactions>\n"
2291 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2292 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-04-29 13:08:40 UTC -->\n"
2293 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
2294 " <ListOfFunctions>\n"
2295 " <Function key=\"Function_40\" name=\"Function for reaction_1\" type=\"UserDefined\" reversible=\"true\">\n"
2297 " parameter_1*species_1\n"
2299 " <ListOfParameterDescriptions>\n"
2300 " <ParameterDescription key=\"FunctionParameter_250\" name=\"parameter_1\" order=\"0\" role=\"constant\"/>\n"
2301 " <ParameterDescription key=\"FunctionParameter_254\" name=\"species_1\" order=\"1\" role=\"substrate\"/>\n"
2302 " </ListOfParameterDescriptions>\n"
2304 " </ListOfFunctions>\n"
2305 " <Model key=\"Model_1\" name=\"model_1\" timeUnit=\"s\" volumeUnit=\"l\" quantityUnit=\"mol\" type=\"deterministic\">\n"
2307 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
2311 " <ListOfCompartments>\n"
2312 " <Compartment key=\"Compartment_0\" name=\"compartment_1\" simulationType=\"fixed\">\n"
2314 " </ListOfCompartments>\n"
2315 " <ListOfMetabolites>\n"
2316 " <Metabolite key=\"Metabolite_0\" name=\"species_1\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
2318 " </ListOfMetabolites>\n"
2319 " <ListOfModelValues>\n"
2320 " <ModelValue key=\"ModelValue_0\" name=\"parameter_1\" simulationType=\"fixed\">\n"
2322 " </ListOfModelValues>\n"
2323 " <ListOfReactions>\n"
2324 " <Reaction key=\"Reaction_0\" name=\"reaction_1\" reversible=\"true\">\n"
2325 " <ListOfSubstrates>\n"
2326 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
2327 " </ListOfSubstrates>\n"
2328 " <ListOfConstants>\n"
2329 " <Constant key=\"Parameter_81\" name=\"parameter_1\" value=\"1\"/>\n"
2330 " </ListOfConstants>\n"
2331 " <KineticLaw function=\"Function_40\">\n"
2332 " <ListOfCallParameters>\n"
2333 " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
2334 " <SourceParameter reference=\"ModelValue_0\"/>\n"
2335 " </CallParameter>\n"
2336 " <CallParameter functionParameter=\"FunctionParameter_254\">\n"
2337 " <SourceParameter reference=\"Metabolite_0\"/>\n"
2338 " </CallParameter>\n"
2339 " </ListOfCallParameters>\n"
2342 " </ListOfReactions>\n"
2343 " <StateTemplate>\n"
2344 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
2345 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
2346 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
2347 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
2348 " </StateTemplate>\n"
2349 " <InitialState type=\"initialState\">\n"
2350 " 0 6.0221415e+23 3 1e-16\n"
2351 " </InitialState>\n"
2353 " <SBMLReference file=\"test000059.xml\">\n"
2354 " <SBMLMap SBMLid=\"species_2\" COPASIkey=\"Compartment_0\"/>\n"
2355 " <SBMLMap SBMLid=\"parameter_1\" COPASIkey=\"ModelValue_0\"/>\n"
2356 " <SBMLMap SBMLid=\"reaction_1\" COPASIkey=\"Reaction_0\"/>\n"
2357 " <SBMLMap SBMLid=\"species_1\" COPASIkey=\"Metabolite_0\"/>\n"
2358 " </SBMLReference>\n"
2363 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2364 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-04-29 13:08:40 UTC -->\n"
2365 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
2366 " <ListOfFunctions>\n"
2367 " <Function key=\"Function_40\" name=\"Function for reaction_1\" type=\"UserDefined\" reversible=\"true\">\n"
2369 " parameter_1*species_1\n"
2371 " <ListOfParameterDescriptions>\n"
2372 " <ParameterDescription key=\"FunctionParameter_250\" name=\"parameter_1\" order=\"0\" role=\"constant\"/>\n"
2373 " <ParameterDescription key=\"FunctionParameter_254\" name=\"species_1\" order=\"1\" role=\"substrate\"/>\n"
2374 " </ListOfParameterDescriptions>\n"
2376 " </ListOfFunctions>\n"
2377 " <Model key=\"Model_1\" name=\"model_1\" timeUnit=\"s\" volumeUnit=\"l\" quantityUnit=\"mol\" type=\"deterministic\">\n"
2379 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
2383 " <ListOfCompartments>\n"
2384 " <Compartment key=\"Compartment_0\" name=\"compartment_1\" simulationType=\"fixed\">\n"
2386 " </ListOfCompartments>\n"
2387 " <ListOfMetabolites>\n"
2388 " <Metabolite key=\"Metabolite_0\" name=\"species_1\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
2390 " </ListOfMetabolites>\n"
2391 " <ListOfModelValues>\n"
2392 " <ModelValue key=\"ModelValue_0\" name=\"parameter_1\" simulationType=\"fixed\">\n"
2394 " </ListOfModelValues>\n"
2395 " <ListOfReactions>\n"
2396 " <Reaction key=\"Reaction_0\" name=\"reaction_1\" reversible=\"true\">\n"
2397 " <ListOfSubstrates>\n"
2398 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
2399 " </ListOfSubstrates>\n"
2400 " <ListOfConstants>\n"
2401 " <Constant key=\"Parameter_81\" name=\"parameter_1\" value=\"1\"/>\n"
2402 " </ListOfConstants>\n"
2403 " <KineticLaw function=\"Function_40\">\n"
2404 " <ListOfCallParameters>\n"
2405 " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
2406 " <SourceParameter reference=\"ModelValue_0\"/>\n"
2407 " </CallParameter>\n"
2408 " <CallParameter functionParameter=\"FunctionParameter_254\">\n"
2409 " <SourceParameter reference=\"Metabolite_0\"/>\n"
2410 " </CallParameter>\n"
2411 " </ListOfCallParameters>\n"
2414 " </ListOfReactions>\n"
2415 " <StateTemplate>\n"
2416 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
2417 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
2418 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
2419 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
2420 " </StateTemplate>\n"
2421 " <InitialState type=\"initialState\">\n"
2422 " 0 6.0221415e+23 3 1e-16\n"
2423 " </InitialState>\n"
2425 " <SBMLReference file=\"test000059.xml\">\n"
2426 " <SBMLMap SBMLid=\"parameter_2\" COPASIkey=\"Compartment_0\"/>\n"
2427 " <SBMLMap SBMLid=\"parameter_1\" COPASIkey=\"ModelValue_0\"/>\n"
2428 " <SBMLMap SBMLid=\"reaction_1\" COPASIkey=\"Reaction_0\"/>\n"
2429 " <SBMLMap SBMLid=\"species_1\" COPASIkey=\"Metabolite_0\"/>\n"
2430 " </SBMLReference>\n"
2435 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2436 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-04-29 13:08:40 UTC -->\n"
2437 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
2438 " <ListOfFunctions>\n"
2439 " <Function key=\"Function_40\" name=\"Function for reaction_1\" type=\"UserDefined\" reversible=\"true\">\n"
2441 " parameter_1*species_1\n"
2443 " <ListOfParameterDescriptions>\n"
2444 " <ParameterDescription key=\"FunctionParameter_250\" name=\"parameter_1\" order=\"0\" role=\"constant\"/>\n"
2445 " <ParameterDescription key=\"FunctionParameter_254\" name=\"species_1\" order=\"1\" role=\"substrate\"/>\n"
2446 " </ListOfParameterDescriptions>\n"
2448 " </ListOfFunctions>\n"
2449 " <Model key=\"Model_1\" name=\"model_1\" timeUnit=\"s\" volumeUnit=\"l\" quantityUnit=\"mol\" type=\"deterministic\">\n"
2451 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
2455 " <ListOfCompartments>\n"
2456 " <Compartment key=\"Compartment_0\" name=\"compartment_1\" simulationType=\"fixed\">\n"
2458 " </ListOfCompartments>\n"
2459 " <ListOfMetabolites>\n"
2460 " <Metabolite key=\"Metabolite_0\" name=\"species_1\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
2462 " </ListOfMetabolites>\n"
2463 " <ListOfModelValues>\n"
2464 " <ModelValue key=\"ModelValue_0\" name=\"parameter_1\" simulationType=\"fixed\">\n"
2466 " </ListOfModelValues>\n"
2467 " <ListOfReactions>\n"
2468 " <Reaction key=\"Reaction_0\" name=\"reaction_1\" reversible=\"true\">\n"
2469 " <ListOfSubstrates>\n"
2470 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
2471 " </ListOfSubstrates>\n"
2472 " <ListOfConstants>\n"
2473 " <Constant key=\"Parameter_81\" name=\"parameter_1\" value=\"1\"/>\n"
2474 " </ListOfConstants>\n"
2475 " <KineticLaw function=\"Function_40\">\n"
2476 " <ListOfCallParameters>\n"
2477 " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
2478 " <SourceParameter reference=\"ModelValue_0\"/>\n"
2479 " </CallParameter>\n"
2480 " <CallParameter functionParameter=\"FunctionParameter_254\">\n"
2481 " <SourceParameter reference=\"Metabolite_0\"/>\n"
2482 " </CallParameter>\n"
2483 " </ListOfCallParameters>\n"
2486 " </ListOfReactions>\n"
2487 " <StateTemplate>\n"
2488 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
2489 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
2490 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
2491 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
2492 " </StateTemplate>\n"
2493 " <InitialState type=\"initialState\">\n"
2494 " 0 6.0221415e+23 3 1e-16\n"
2495 " </InitialState>\n"
2497 " <SBMLReference file=\"test000059.xml\">\n"
2498 " <SBMLMap SBMLid=\"reaction_2\" COPASIkey=\"Compartment_0\"/>\n"
2499 " <SBMLMap SBMLid=\"parameter_1\" COPASIkey=\"ModelValue_0\"/>\n"
2500 " <SBMLMap SBMLid=\"reaction_1\" COPASIkey=\"Reaction_0\"/>\n"
2501 " <SBMLMap SBMLid=\"species_1\" COPASIkey=\"Metabolite_0\"/>\n"
2502 " </SBMLReference>\n"
2507 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2508 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-04-29 13:08:40 UTC -->\n"
2509 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
2510 " <ListOfFunctions>\n"
2511 " <Function key=\"Function_40\" name=\"Function for reaction_1\" type=\"UserDefined\" reversible=\"true\">\n"
2513 " parameter_1*species_1\n"
2515 " <ListOfParameterDescriptions>\n"
2516 " <ParameterDescription key=\"FunctionParameter_250\" name=\"parameter_1\" order=\"0\" role=\"constant\"/>\n"
2517 " <ParameterDescription key=\"FunctionParameter_254\" name=\"species_1\" order=\"1\" role=\"substrate\"/>\n"
2518 " </ListOfParameterDescriptions>\n"
2520 " </ListOfFunctions>\n"
2521 " <Model key=\"Model_1\" name=\"model_1\" timeUnit=\"s\" volumeUnit=\"l\" quantityUnit=\"mol\" type=\"deterministic\">\n"
2523 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
2527 " <ListOfCompartments>\n"
2528 " <Compartment key=\"Compartment_0\" name=\"compartment_1\" simulationType=\"fixed\">\n"
2530 " </ListOfCompartments>\n"
2531 " <ListOfMetabolites>\n"
2532 " <Metabolite key=\"Metabolite_0\" name=\"species_1\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
2534 " </ListOfMetabolites>\n"
2535 " <ListOfModelValues>\n"
2536 " <ModelValue key=\"ModelValue_0\" name=\"parameter_1\" simulationType=\"fixed\">\n"
2538 " </ListOfModelValues>\n"
2539 " <ListOfReactions>\n"
2540 " <Reaction key=\"Reaction_0\" name=\"reaction_1\" reversible=\"true\">\n"
2541 " <ListOfSubstrates>\n"
2542 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
2543 " </ListOfSubstrates>\n"
2544 " <ListOfConstants>\n"
2545 " <Constant key=\"Parameter_81\" name=\"parameter_1\" value=\"1\"/>\n"
2546 " </ListOfConstants>\n"
2547 " <KineticLaw function=\"Function_40\">\n"
2548 " <ListOfCallParameters>\n"
2549 " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
2550 " <SourceParameter reference=\"ModelValue_0\"/>\n"
2551 " </CallParameter>\n"
2552 " <CallParameter functionParameter=\"FunctionParameter_254\">\n"
2553 " <SourceParameter reference=\"Metabolite_0\"/>\n"
2554 " </CallParameter>\n"
2555 " </ListOfCallParameters>\n"
2558 " </ListOfReactions>\n"
2559 " <StateTemplate>\n"
2560 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
2561 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
2562 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
2563 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
2564 " </StateTemplate>\n"
2565 " <InitialState type=\"initialState\">\n"
2566 " 0 6.0221415e+23 3 1e-16\n"
2567 " </InitialState>\n"
2569 " <SBMLReference file=\"test000059.xml\">\n"
2570 " <SBMLMap SBMLid=\"compartment_1\" COPASIkey=\"Compartment_0\"/>\n"
2571 " <SBMLMap SBMLid=\"parameter_1\" COPASIkey=\"ModelValue_0\"/>\n"
2572 " <SBMLMap SBMLid=\"reaction_1\" COPASIkey=\"Reaction_0\"/>\n"
2573 " <SBMLMap SBMLid=\"parameter_2\" COPASIkey=\"Metabolite_0\"/>\n"
2574 " </SBMLReference>\n"
2579 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2580 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-04-29 13:08:40 UTC -->\n"
2581 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
2582 " <ListOfFunctions>\n"
2583 " <Function key=\"Function_40\" name=\"Function for reaction_1\" type=\"UserDefined\" reversible=\"true\">\n"
2585 " parameter_1*species_1\n"
2587 " <ListOfParameterDescriptions>\n"
2588 " <ParameterDescription key=\"FunctionParameter_250\" name=\"parameter_1\" order=\"0\" role=\"constant\"/>\n"
2589 " <ParameterDescription key=\"FunctionParameter_254\" name=\"species_1\" order=\"1\" role=\"substrate\"/>\n"
2590 " </ListOfParameterDescriptions>\n"
2592 " </ListOfFunctions>\n"
2593 " <Model key=\"Model_1\" name=\"model_1\" timeUnit=\"s\" volumeUnit=\"l\" quantityUnit=\"mol\" type=\"deterministic\">\n"
2595 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
2599 " <ListOfCompartments>\n"
2600 " <Compartment key=\"Compartment_0\" name=\"compartment_1\" simulationType=\"fixed\">\n"
2602 " </ListOfCompartments>\n"
2603 " <ListOfMetabolites>\n"
2604 " <Metabolite key=\"Metabolite_0\" name=\"species_1\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
2606 " </ListOfMetabolites>\n"
2607 " <ListOfModelValues>\n"
2608 " <ModelValue key=\"ModelValue_0\" name=\"parameter_1\" simulationType=\"fixed\">\n"
2610 " </ListOfModelValues>\n"
2611 " <ListOfReactions>\n"
2612 " <Reaction key=\"Reaction_0\" name=\"reaction_1\" reversible=\"true\">\n"
2613 " <ListOfSubstrates>\n"
2614 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
2615 " </ListOfSubstrates>\n"
2616 " <ListOfConstants>\n"
2617 " <Constant key=\"Parameter_81\" name=\"parameter_1\" value=\"1\"/>\n"
2618 " </ListOfConstants>\n"
2619 " <KineticLaw function=\"Function_40\">\n"
2620 " <ListOfCallParameters>\n"
2621 " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
2622 " <SourceParameter reference=\"ModelValue_0\"/>\n"
2623 " </CallParameter>\n"
2624 " <CallParameter functionParameter=\"FunctionParameter_254\">\n"
2625 " <SourceParameter reference=\"Metabolite_0\"/>\n"
2626 " </CallParameter>\n"
2627 " </ListOfCallParameters>\n"
2630 " </ListOfReactions>\n"
2631 " <StateTemplate>\n"
2632 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
2633 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
2634 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
2635 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
2636 " </StateTemplate>\n"
2637 " <InitialState type=\"initialState\">\n"
2638 " 0 6.0221415e+23 3 1e-16\n"
2639 " </InitialState>\n"
2641 " <SBMLReference file=\"test000059.xml\">\n"
2642 " <SBMLMap SBMLid=\"compartment_1\" COPASIkey=\"Compartment_0\"/>\n"
2643 " <SBMLMap SBMLid=\"parameter_1\" COPASIkey=\"ModelValue_0\"/>\n"
2644 " <SBMLMap SBMLid=\"reaction_1\" COPASIkey=\"Reaction_0\"/>\n"
2645 " <SBMLMap SBMLid=\"reaction_2\" COPASIkey=\"Metabolite_0\"/>\n"
2646 " </SBMLReference>\n"
2651 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2652 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-04-29 13:08:40 UTC -->\n"
2653 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
2654 " <ListOfFunctions>\n"
2655 " <Function key=\"Function_40\" name=\"Function for reaction_1\" type=\"UserDefined\" reversible=\"true\">\n"
2657 " parameter_1*species_1\n"
2659 " <ListOfParameterDescriptions>\n"
2660 " <ParameterDescription key=\"FunctionParameter_250\" name=\"parameter_1\" order=\"0\" role=\"constant\"/>\n"
2661 " <ParameterDescription key=\"FunctionParameter_254\" name=\"species_1\" order=\"1\" role=\"substrate\"/>\n"
2662 " </ListOfParameterDescriptions>\n"
2664 " </ListOfFunctions>\n"
2665 " <Model key=\"Model_1\" name=\"model_1\" timeUnit=\"s\" volumeUnit=\"l\" quantityUnit=\"mol\" type=\"deterministic\">\n"
2667 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
2671 " <ListOfCompartments>\n"
2672 " <Compartment key=\"Compartment_0\" name=\"compartment_1\" simulationType=\"fixed\">\n"
2674 " </ListOfCompartments>\n"
2675 " <ListOfMetabolites>\n"
2676 " <Metabolite key=\"Metabolite_0\" name=\"species_1\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
2678 " </ListOfMetabolites>\n"
2679 " <ListOfModelValues>\n"
2680 " <ModelValue key=\"ModelValue_0\" name=\"parameter_1\" simulationType=\"fixed\">\n"
2682 " </ListOfModelValues>\n"
2683 " <ListOfReactions>\n"
2684 " <Reaction key=\"Reaction_0\" name=\"reaction_1\" reversible=\"true\">\n"
2685 " <ListOfSubstrates>\n"
2686 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
2687 " </ListOfSubstrates>\n"
2688 " <ListOfConstants>\n"
2689 " <Constant key=\"Parameter_81\" name=\"parameter_1\" value=\"1\"/>\n"
2690 " </ListOfConstants>\n"
2691 " <KineticLaw function=\"Function_40\">\n"
2692 " <ListOfCallParameters>\n"
2693 " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
2694 " <SourceParameter reference=\"ModelValue_0\"/>\n"
2695 " </CallParameter>\n"
2696 " <CallParameter functionParameter=\"FunctionParameter_254\">\n"
2697 " <SourceParameter reference=\"Metabolite_0\"/>\n"
2698 " </CallParameter>\n"
2699 " </ListOfCallParameters>\n"
2702 " </ListOfReactions>\n"
2703 " <StateTemplate>\n"
2704 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
2705 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
2706 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
2707 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
2708 " </StateTemplate>\n"
2709 " <InitialState type=\"initialState\">\n"
2710 " 0 6.0221415e+23 3 1e-16\n"
2711 " </InitialState>\n"
2713 " <SBMLReference file=\"test000059.xml\">\n"
2714 " <SBMLMap SBMLid=\"compartment_1\" COPASIkey=\"Compartment_0\"/>\n"
2715 " <SBMLMap SBMLid=\"reaction_2\" COPASIkey=\"ModelValue_0\"/>\n"
2716 " <SBMLMap SBMLid=\"reaction_1\" COPASIkey=\"Reaction_0\"/>\n"
2717 " <SBMLMap SBMLid=\"species_1\" COPASIkey=\"Metabolite_0\"/>\n"
2718 " </SBMLReference>\n"
2723 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2724 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
2725 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
2726 " <listOfFunctionDefinitions>\n"
2727 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
2728 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2743 " </functionDefinition>\n"
2744 " </listOfFunctionDefinitions> \n"
2745 " <listOfUnitDefinitions>\n"
2746 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
2748 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
2750 " </unitDefinition>\n"
2751 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
2753 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
2755 " </unitDefinition>\n"
2756 " </listOfUnitDefinitions> \n"
2757 " <listOfCompartments>\n"
2758 " <compartment metaid=\"_000005\" id=\"function_2\" name=\"compartment_1\" size=\"1e-16\">\n"
2760 " </listOfCompartments>\n"
2761 " <listOfSpecies>\n"
2762 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"function_2\" initialAmount=\"1.0\"/>\n"
2763 " </listOfSpecies> \n"
2764 " <listOfParameters>\n"
2765 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
2766 " </listOfParameters>\n"
2767 " <listOfReactions>\n"
2768 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
2769 " <listOfReactants>\n"
2770 " <speciesReference species=\"species_1\"/>\n"
2771 " </listOfReactants>\n"
2773 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2776 " <ci> function_2 </ci>\n"
2778 " <ci> function_1 </ci>\n"
2779 " <ci> parameter_1 </ci>\n"
2780 " <ci> species_1 </ci>\n"
2786 " </listOfReactions>\n"
2792 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2793 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
2794 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
2795 " <listOfFunctionDefinitions>\n"
2796 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
2797 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2812 " </functionDefinition>\n"
2813 " </listOfFunctionDefinitions> \n"
2814 " <listOfUnitDefinitions>\n"
2815 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
2817 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
2819 " </unitDefinition>\n"
2820 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
2822 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
2824 " </unitDefinition>\n"
2825 " </listOfUnitDefinitions> \n"
2826 " <listOfCompartments>\n"
2827 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
2829 " </listOfCompartments>\n"
2830 " <listOfSpecies>\n"
2831 " <species metaid=\"_000006\" id=\"function_2\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
2832 " </listOfSpecies> \n"
2833 " <listOfParameters>\n"
2834 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
2835 " </listOfParameters>\n"
2836 " <listOfReactions>\n"
2837 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
2838 " <listOfReactants>\n"
2839 " <speciesReference species=\"function_2\"/>\n"
2840 " </listOfReactants>\n"
2842 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2845 " <ci> compartment_1 </ci>\n"
2847 " <ci> function_1 </ci>\n"
2848 " <ci> parameter_1 </ci>\n"
2849 " <ci> function_2 </ci>\n"
2855 " </listOfReactions>\n"
2861 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2862 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
2863 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
2864 " <listOfFunctionDefinitions>\n"
2865 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
2866 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2881 " </functionDefinition>\n"
2882 " </listOfFunctionDefinitions> \n"
2883 " <listOfUnitDefinitions>\n"
2884 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
2886 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
2888 " </unitDefinition>\n"
2889 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
2891 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
2893 " </unitDefinition>\n"
2894 " </listOfUnitDefinitions> \n"
2895 " <listOfCompartments>\n"
2896 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
2898 " </listOfCompartments>\n"
2899 " <listOfSpecies>\n"
2900 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
2901 " </listOfSpecies> \n"
2902 " <listOfParameters>\n"
2903 " <parameter metaid=\"_000007\" id=\"function_2\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
2904 " </listOfParameters>\n"
2905 " <listOfReactions>\n"
2906 " <reaction metaid=\"_000008\" id=\"reaction_1\" name=\"reaction_1\">\n"
2907 " <listOfReactants>\n"
2908 " <speciesReference species=\"species_1\"/>\n"
2909 " </listOfReactants>\n"
2911 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2914 " <ci> compartment_1 </ci>\n"
2916 " <ci> function_1 </ci>\n"
2917 " <ci> function_2 </ci>\n"
2918 " <ci> species_1 </ci>\n"
2924 " </listOfReactions>\n"
2930 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
2931 "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" metaid=\"_000000\" level=\"2\" version=\"1\">\n"
2932 " <model metaid=\"_000001\" id=\"model_1\" name=\"model_1\">\n"
2933 " <listOfFunctionDefinitions>\n"
2934 " <functionDefinition metaid=\"_000004\" id=\"function_1\" name=\"function_1\">\n"
2935 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2950 " </functionDefinition>\n"
2951 " </listOfFunctionDefinitions> \n"
2952 " <listOfUnitDefinitions>\n"
2953 " <unitDefinition metaid=\"_000002\" id=\"time\" name=\"time\">\n"
2955 " <unit kind=\"second\" scale=\"0\" multiplier=\"1\"/>\n"
2957 " </unitDefinition>\n"
2958 " <unitDefinition metaid=\"_000003\" id=\"unit_2\" name=\"unit_2\">\n"
2960 " <unit kind=\"second\" exponent=\"-1\" scale=\"0\" multiplier=\"1\"/>\n"
2962 " </unitDefinition>\n"
2963 " </listOfUnitDefinitions> \n"
2964 " <listOfCompartments>\n"
2965 " <compartment metaid=\"_000005\" id=\"compartment_1\" name=\"compartment_1\" size=\"1e-16\">\n"
2967 " </listOfCompartments>\n"
2968 " <listOfSpecies>\n"
2969 " <species metaid=\"_000006\" id=\"species_1\" name=\"species_1\" compartment=\"compartment_1\" initialAmount=\"1.0\"/>\n"
2970 " </listOfSpecies> \n"
2971 " <listOfParameters>\n"
2972 " <parameter metaid=\"_000007\" id=\"parameter_1\" name=\"parameter_1\" value=\"3.0\" constant=\"false\" units=\"unit_2\"/>\n"
2973 " </listOfParameters>\n"
2974 " <listOfReactions>\n"
2975 " <reaction metaid=\"_000008\" id=\"function_2\" name=\"reaction_1\">\n"
2976 " <listOfReactants>\n"
2977 " <speciesReference species=\"species_1\"/>\n"
2978 " </listOfReactants>\n"
2980 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
2983 " <ci> compartment_1 </ci>\n"
2985 " <ci> function_1 </ci>\n"
2986 " <ci> parameter_1 </ci>\n"
2987 " <ci> species_1 </ci>\n"
2993 " </listOfReactions>\n"
2999 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
3000 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-04-29 13:08:40 UTC -->\n"
3001 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
3002 " <ListOfFunctions>\n"
3003 " <Function key=\"Function_40\" name=\"Function for reaction_1\" type=\"UserDefined\" reversible=\"true\">\n"
3005 " parameter_1*species_1\n"
3007 " <ListOfParameterDescriptions>\n"
3008 " <ParameterDescription key=\"FunctionParameter_250\" name=\"parameter_1\" order=\"0\" role=\"constant\"/>\n"
3009 " <ParameterDescription key=\"FunctionParameter_254\" name=\"species_1\" order=\"1\" role=\"substrate\"/>\n"
3010 " </ListOfParameterDescriptions>\n"
3012 " </ListOfFunctions>\n"
3013 " <Model key=\"Model_1\" name=\"model_1\" timeUnit=\"s\" volumeUnit=\"l\" quantityUnit=\"mol\" type=\"deterministic\">\n"
3015 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
3019 " <ListOfCompartments>\n"
3020 " <Compartment key=\"Compartment_0\" name=\"compartment_1\" simulationType=\"fixed\">\n"
3022 " </ListOfCompartments>\n"
3023 " <ListOfMetabolites>\n"
3024 " <Metabolite key=\"Metabolite_0\" name=\"species_1\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
3026 " </ListOfMetabolites>\n"
3027 " <ListOfModelValues>\n"
3028 " <ModelValue key=\"ModelValue_0\" name=\"parameter_1\" simulationType=\"fixed\">\n"
3030 " </ListOfModelValues>\n"
3031 " <ListOfReactions>\n"
3032 " <Reaction key=\"Reaction_0\" name=\"reaction_1\" reversible=\"true\">\n"
3033 " <ListOfSubstrates>\n"
3034 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
3035 " </ListOfSubstrates>\n"
3036 " <ListOfConstants>\n"
3037 " <Constant key=\"Parameter_81\" name=\"parameter_1\" value=\"1\"/>\n"
3038 " </ListOfConstants>\n"
3039 " <KineticLaw function=\"Function_40\">\n"
3040 " <ListOfCallParameters>\n"
3041 " <CallParameter functionParameter=\"FunctionParameter_250\">\n"
3042 " <SourceParameter reference=\"ModelValue_0\"/>\n"
3043 " </CallParameter>\n"
3044 " <CallParameter functionParameter=\"FunctionParameter_254\">\n"
3045 " <SourceParameter reference=\"Metabolite_0\"/>\n"
3046 " </CallParameter>\n"
3047 " </ListOfCallParameters>\n"
3050 " </ListOfReactions>\n"
3051 " <StateTemplate>\n"
3052 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
3053 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
3054 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
3055 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
3056 " </StateTemplate>\n"
3057 " <InitialState type=\"initialState\">\n"
3058 " 0 6.0221415e+23 3 1e-16\n"
3059 " </InitialState>\n"
3061 " <SBMLReference file=\"test000059.xml\">\n"
3062 " <SBMLMap SBMLid=\"compartment_1\" COPASIkey=\"Compartment_0\"/>\n"
3063 " <SBMLMap SBMLid=\"function_1\" COPASIkey=\"Function_40\"/>\n"
3064 " <SBMLMap SBMLid=\"reaction_2\" COPASIkey=\"ModelValue_0\"/>\n"
3065 " <SBMLMap SBMLid=\"reaction_1\" COPASIkey=\"Reaction_0\"/>\n"
3066 " <SBMLMap SBMLid=\"species_1\" COPASIkey=\"Metabolite_0\"/>\n"
3067 " </SBMLReference>\n"
3072 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
3073 "<!-- generated with COPASI 4.4.29 (Debug) (http://www.copasi.org) at 2009-01-12 15:53:36 UTC -->\n"
3074 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"29\">\n"
3075 " <ListOfFunctions>\n"
3076 " <Function key=\"Function_14\" name=\"Mass action (reversible)\" type=\"MassAction\" reversible=\"true\">\n"
3078 " k1*PRODUCT<substrate_i>-k2*PRODUCT<product_j>\n"
3080 " <ListOfParameterDescriptions>\n"
3081 " <ParameterDescription key=\"FunctionParameter_62\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
3082 " <ParameterDescription key=\"FunctionParameter_39\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
3083 " <ParameterDescription key=\"FunctionParameter_67\" name=\"k2\" order=\"2\" role=\"constant\"/>\n"
3084 " <ParameterDescription key=\"FunctionParameter_71\" name=\"product\" order=\"3\" role=\"product\"/>\n"
3085 " </ListOfParameterDescriptions>\n"
3087 " </ListOfFunctions>\n"
3088 " <Model key=\"Model_1\" name=\"New Model\" timeUnit=\"s\" volumeUnit=\"ml\" quantityUnit=\"mmol\" type=\"deterministic\">\n"
3090 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
3094 " <ListOfCompartments>\n"
3095 " <Compartment key=\"Compartment_0\" name=\"compartment\" simulationType=\"fixed\">\n"
3097 " </ListOfCompartments>\n"
3098 " <ListOfMetabolites>\n"
3099 " <Metabolite key=\"Metabolite_0\" name=\"A\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
3101 " <Metabolite key=\"Metabolite_1\" name=\"B\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
3103 " <Metabolite key=\"Metabolite_2\" name=\"C\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
3105 " </ListOfMetabolites>\n"
3106 " <ListOfModelValues>\n"
3107 " <ModelValue key=\"ModelValue_0\" name=\"quantity\" simulationType=\"fixed\">\n"
3108 " <InitialExpression>\n"
3109 " <CN=Root,Model=New Model,Vector=Reactions[reaction],ParameterGroup=Parameters,Parameter=k1,Reference=Value>\n"
3110 " </InitialExpression>\n"
3112 " <ModelValue key=\"ModelValue_1\" name=\"quantity_1\" simulationType=\"fixed\">\n"
3113 " <InitialExpression>\n"
3114 " 2*<CN=Root,Model=New Model,Vector=Values[quantity],Reference=InitialValue>\n"
3115 " </InitialExpression>\n"
3117 " <ModelValue key=\"ModelValue_2\" name=\"quantity_2\" simulationType=\"assignment\">\n"
3119 " 2*<CN=Root,Model=New Model,Vector=Reactions[reaction],ParameterGroup=Parameters,Parameter=k2,Reference=Value>\n"
3122 " </ListOfModelValues>\n"
3123 " <ListOfReactions>\n"
3124 " <Reaction key=\"Reaction_0\" name=\"reaction\" reversible=\"true\">\n"
3125 " <ListOfSubstrates>\n"
3126 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
3127 " <Substrate metabolite=\"Metabolite_1\" stoichiometry=\"2\"/>\n"
3128 " </ListOfSubstrates>\n"
3129 " <ListOfProducts>\n"
3130 " <Product metabolite=\"Metabolite_2\" stoichiometry=\"1\"/>\n"
3131 " </ListOfProducts>\n"
3132 " <ListOfConstants>\n"
3133 " <Constant key=\"Parameter_971\" name=\"k1\" value=\"0.1\"/>\n"
3134 " <Constant key=\"Parameter_970\" name=\"k2\" value=\"10\"/>\n"
3135 " </ListOfConstants>\n"
3136 " <KineticLaw function=\"Function_14\">\n"
3137 " <ListOfCallParameters>\n"
3138 " <CallParameter functionParameter=\"FunctionParameter_62\">\n"
3139 " <SourceParameter reference=\"Parameter_971\"/>\n"
3140 " </CallParameter>\n"
3141 " <CallParameter functionParameter=\"FunctionParameter_39\">\n"
3142 " <SourceParameter reference=\"Metabolite_0\"/>\n"
3143 " <SourceParameter reference=\"Metabolite_1\"/>\n"
3144 " <SourceParameter reference=\"Metabolite_1\"/>\n"
3145 " </CallParameter>\n"
3146 " <CallParameter functionParameter=\"FunctionParameter_67\">\n"
3147 " <SourceParameter reference=\"Parameter_970\"/>\n"
3148 " </CallParameter>\n"
3149 " <CallParameter functionParameter=\"FunctionParameter_71\">\n"
3150 " <SourceParameter reference=\"Metabolite_2\"/>\n"
3151 " </CallParameter>\n"
3152 " </ListOfCallParameters>\n"
3155 " </ListOfReactions>\n"
3156 " <StateTemplate>\n"
3157 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
3158 " <StateTemplateVariable objectReference=\"Metabolite_1\"/>\n"
3159 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
3160 " <StateTemplateVariable objectReference=\"Metabolite_2\"/>\n"
3161 " <StateTemplateVariable objectReference=\"ModelValue_2\"/>\n"
3162 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
3163 " <StateTemplateVariable objectReference=\"ModelValue_1\"/>\n"
3164 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
3165 " </StateTemplate>\n"
3166 " <InitialState type=\"initialState\">\n"
3167 " 0 6.022141500000001e+19 6.022141500000001e+19 6.022141500000001e+19 20 0.1 0.2 1\n"
3168 " </InitialState>\n"
SBMLDocument * getCurrentSBMLDocument()
static const char * MODEL_STRING16
CFunction * addAndAdaptName(CFunction *pFunction)
static const char * MODEL_STRING17
Header file of class CModelEntity and CModelValue.
static const char * MODEL_STRING22
static const char * MODEL_STRING4
static const char * MODEL_STRING21
const CCopasiVector< CMetab > & getMetabolites() const
const std::string & getObjectName() const
static CCopasiDataModel * pCOPASIDATAMODEL
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
static const char * MODEL_STRING3
static bool checkIfIdsUnique(const Model *pSBMLModel)
CCopasiObject * getInitialValueReference() const
void setParameterValue(const std::string ¶meterName, const C_FLOAT64 &value, const bool &updateStatus=true)
static const char * MODEL_STRING14
CCopasiObject * getValueReference() const
bool addProduct(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
CModelValue * createModelValue(const std::string &name, const C_FLOAT64 &value=0.0)
virtual bool setInfix(const std::string &infix)
bool load_cps_model_from_stream(std::istream &is, CCopasiDataModel &dataModel)
virtual const std::string & getKey() const
static const char * MODEL_STRING7
static const char * MODEL_STRING15
void test_unique_id_21_2()
bool setFunction(const std::string &functionName)
virtual void setStatus(const CModelEntity::Status &status)
CReaction * createReaction(const std::string &name)
static const char * MODEL_STRING19
static const char * MODEL_STRING11
CCopasiParameter * getParameter(const std::string &name)
static const char * MODEL_STRING1
static CFunctionDB * getFunctionList()
static CCopasiDataModel * addDatamodel()
static const char * MODEL_STRING20
static const char * MODEL_STRING6
bool compileIfNecessary(CProcessReport *pProcessReport)
const CCopasiParameterGroup & getParameters() const
static const char * MODEL_STRING18
bool importSBMLFromString(const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true)
static const char * MODEL_STRING9
The class for handling a chemical kinetic function.
static const char * MODEL_STRING8
static const char * MODEL_STRING12
static void init(int argc, char *argv[], const bool &withGui=false)
static const char * MODEL_STRING13
std::vector< Refresh * > buildInitialRefreshSequence(std::set< const CCopasiObject * > &changedObjects)
bool setExpression(const std::string &expression)
static const char * MODEL_STRING10
static const char * MODEL_STRING2
static const char * MODEL_STRING5
CMetab * createMetabolite(const std::string &name, const std::string &compartment, const C_FLOAT64 &iconc=1.0, const CModelEntity::Status &status=CModelEntity::REACTIONS)