/usr/share/python-cobra/data/invalid2.xml is in python-cobra-data 0.5.9-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | <sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" sboTerm="SBO:0000624" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false">
<model fbc:strict="true" id="invalid2">
<listOfUnitDefinitions>
<unitDefinition id="mmol_per_gDW_per_hr">
<listOfUnits>
<unit exponent="1" kind="mole" multiplier="1" scale="-3"/>
<unit exponent="-1" kind="gram" multiplier="1" scale="0"/>
<unit exponent="-1" kind="second" multiplier="3600" scale="0"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<fbc:listOfObjectives fbc:activeObjective="obj">
<fbc:objective fbc:id="obj" fbc:type="maximize">
<fbc:listOfFluxObjectives>
<fbc:fluxObjective fbc:reaction="R_ATPM" fbc:coefficient="1"/>
</fbc:listOfFluxObjectives>
</fbc:objective>
</fbc:listOfObjectives>
<listOfParameters>
<parameter constant="true" id="cobra_default_lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="8.39"/>
<parameter constant="true" id="cobra_default_ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="1000"/>
<parameter constant="true" id="cobra_0_bound" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="0"/>
</listOfParameters>
<listOfCompartments/>
<listOfSpecies>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_h2o_c" metaid="M_h2o_c" name="H2O" compartment="c" fbc:chemicalFormula="H2O">
<sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#M_h2o_c">
<bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Bag>
<rdf:li rdf:resource="http://random.org/bigg.metabolite/h2o"/>
</rdf:Bag>
</bqbiol:is>
<bqbiol:isEncodedBy xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/biocyc_WATER"/>
</rdf:Bag>
</bqbiol:isEncodedBy>
</rdf:Description>
</rdf:RDF>
</sbml:annotation>
</species>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_atp_c" name="ATP" compartment="c" fbc:chemicalFormula="C10H12N5O13P3"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_h_c" name="H+" compartment="c" fbc:chemicalFormula="H"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_adp_c" name="ADP" compartment="c" fbc:chemicalFormula="C10H12N5O10P2"/>
<species boundaryCondition="false" constant="false" hasOnlySubstanceUnits="false" id="M_pi_c" name="Phosphate" compartment="c" fbc:chemicalFormula="HO4P"/>
<species boundaryCondition="true" id="Please_never_use_this"/>
</listOfSpecies>
<listOfReactions>
<reaction fast="false" id="R_ATPM" reversible="false" name="ATP maintenance requirement" metaid="R_ATPM" fbc:upperFluxBound="cobra_default_lb" fbc:lowerFluxBound="cobra_default_ub">
<listOfReactants>
<speciesReference constant="true" species="M_atp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_h2o_c" stoichiometry="1"/>
<speciesReference constant="true" species="Please_never_use_this" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="M_adp_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_h_c" stoichiometry="1"/>
<speciesReference constant="true" species="M_pi_c" stoichiometry="1"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_b4025"/>
</fbc:geneProductAssociation>
</reaction>
</listOfReactions>
</model>
</sbml>
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