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updated reaction
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‎tests/sources/ATPlocs.cps‎

Lines changed: 24 additions & 52 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!-- generated with COPASI 4.45 (Build 298) (http://www.copasi.org) at 2025-09-12T00:12:03Z -->
2+
<!-- generated with COPASI 4.45 (Build 298) (http://www.copasi.org) at 2025-10-09T15:11:04Z -->
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<?oxygen RNGSchema="http://www.copasi.org/static/schema/CopasiML.rng" type="xml"?>
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<COPASI xmlns="http://www.copasi.org/static/schema" versionMajor="4" versionMinor="45" versionDevel="298" copasiSourcesModified="0">
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<ListOfFunctions>
@@ -93,63 +93,49 @@ The inclusion of braces in the names seems to cause a bug in sbmodelr
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</Comment>
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<ListOfCompartments>
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<Compartment key="Compartment_0" name="cytoplasm" simulationType="fixed" dimensionality="3" addNoise="false">
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<MiriamAnnotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Compartment_0">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
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</Compartment>
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<Compartment key="Compartment_1" name="mitochondria" simulationType="fixed" dimensionality="3" addNoise="false">
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<MiriamAnnotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Compartment_1">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
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</Compartment>
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</ListOfCompartments>
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<ListOfMetabolites>
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<Metabolite key="Metabolite_0" name="ATP" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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<MiriamAnnotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Metabolite_0">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
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</Metabolite>
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<Metabolite key="Metabolite_1" name="ATP" simulationType="reactions" compartment="Compartment_1" addNoise="false">
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<MiriamAnnotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Metabolite_1">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
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</Metabolite>
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<Metabolite key="Metabolite_2" name="a" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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<MiriamAnnotation>
139-
<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Metabolite_2">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
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</Metabolite>
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<Metabolite key="Metabolite_3" name="b" simulationType="reactions" compartment="Compartment_0" addNoise="false">
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<MiriamAnnotation>
127+
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Metabolite_3">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
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</Metabolite>
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<Metabolite key="Metabolite_4" name="c" simulationType="reactions" compartment="Compartment_0" addNoise="false">
134+
<MiriamAnnotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Metabolite_3">
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<rdf:Description rdf:about="#Metabolite_4">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
@@ -158,9 +144,7 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<ListOfModelValues>
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<ModelValue key="ModelValue_0" name="ratio" simulationType="assignment" addNoise="false">
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<MiriamAnnotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#ModelValue_0">
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</rdf:Description>
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</rdf:RDF>
@@ -172,14 +156,6 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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</ListOfModelValues>
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<ListOfReactions>
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<Reaction key="Reaction_0" name="transport" reversible="true" fast="false" addNoise="false">
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<MiriamAnnotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Reaction_0">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
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<ListOfSubstrates>
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<Substrate metabolite="Metabolite_0" stoichiometry="1"/>
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</ListOfSubstrates>
@@ -208,19 +184,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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</KineticLaw>
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</Reaction>
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<Reaction key="Reaction_1" name="r1" reversible="false" fast="false" addNoise="false">
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<MiriamAnnotation>
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<rdf:RDF
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#Reaction_1">
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</rdf:Description>
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</rdf:RDF>
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</MiriamAnnotation>
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<ListOfSubstrates>
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<Substrate metabolite="Metabolite_2" stoichiometry="1"/>
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<Substrate metabolite="Metabolite_3" stoichiometry="1"/>
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</ListOfSubstrates>
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<ListOfProducts>
223-
<Product metabolite="Metabolite_3" stoichiometry="1"/>
192+
<Product metabolite="Metabolite_4" stoichiometry="1"/>
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</ListOfProducts>
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<ListOfConstants>
226195
<Constant key="Parameter_2" name="k1" value="0.1"/>
@@ -232,6 +201,7 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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</CallParameter>
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<CallParameter functionParameter="FunctionParameter_81">
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<SourceParameter reference="Metabolite_2"/>
204+
<SourceParameter reference="Metabolite_3"/>
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</CallParameter>
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</ListOfCallParameters>
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</KineticLaw>
@@ -255,10 +225,11 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[mitochondria]" value="0.5" type="Compartment" simulationType="fixed"/>
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</ModelParameterGroup>
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<ModelParameterGroup cn="String=Initial Species Values" type="Group">
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<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[cytoplasm],Vector=Metabolites[ATP]" value="6.0221407599999791e+23" type="Species" simulationType="reactions"/>
259-
<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[mitochondria],Vector=Metabolites[ATP]" value="3.0110703799999899e+23" type="Species" simulationType="reactions"/>
260-
<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[cytoplasm],Vector=Metabolites[a]" value="6.0221407599999972e+23" type="Species" simulationType="reactions"/>
261-
<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[cytoplasm],Vector=Metabolites[b]" value="6.0221407599999979e+23" type="Species" simulationType="reactions"/>
228+
<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[cytoplasm],Vector=Metabolites[ATP]" value="6.022140759999973e+23" type="Species" simulationType="reactions"/>
229+
<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[mitochondria],Vector=Metabolites[ATP]" value="3.0110703799999868e+23" type="Species" simulationType="reactions"/>
230+
<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[cytoplasm],Vector=Metabolites[a]" value="6.0221407599999911e+23" type="Species" simulationType="reactions"/>
231+
<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[cytoplasm],Vector=Metabolites[b]" value="6.0221407599999918e+23" type="Species" simulationType="reactions"/>
232+
<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Compartments[cytoplasm],Vector=Metabolites[c]" value="6.0221407599999972e+23" type="Species" simulationType="reactions"/>
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</ModelParameterGroup>
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<ModelParameterGroup cn="String=Initial Global Quantities" type="Group">
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<ModelParameter cn="CN=Root,Model=Model to test bug in sbmodelr,Vector=Values[ratio]" value="0.99999999999999989" type="ModelValue" simulationType="assignment"/>
@@ -279,13 +250,14 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<StateTemplateVariable objectReference="Metabolite_0"/>
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<StateTemplateVariable objectReference="Metabolite_2"/>
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<StateTemplateVariable objectReference="Metabolite_3"/>
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<StateTemplateVariable objectReference="Metabolite_4"/>
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<StateTemplateVariable objectReference="Metabolite_1"/>
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<StateTemplateVariable objectReference="ModelValue_0"/>
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<StateTemplateVariable objectReference="Compartment_0"/>
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<StateTemplateVariable objectReference="Compartment_1"/>
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</StateTemplate>
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<InitialState type="initialState">
288-
0 6.0221407599999791e+23 6.0221407599999972e+23 6.0221407599999979e+23 3.0110703799999899e+23 0.99999999999999989 1 0.5
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0 6.022140759999973e+23 6.0221407599999911e+23 6.0221407599999918e+23 6.0221407599999972e+23 3.0110703799999868e+23 0.99999999999999989 1 0.5
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</InitialState>
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</Model>
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<ListOfTasks>

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