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view test-data/rp_013_0001_with_thermo.xml @ 0:44e54b56328d draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 24 Nov 2021 09:48:18 +0000
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false">
  <model metaid="_2db93def850b5b412e9c6bfb2f3ae31a33b90fb03a3777278e0e69de0adbd9b8" id="RP_model_013_0001" name="013_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
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    <listOfParameters>
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    <listOfReactions>
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                  <brsynth:units value="kilojoule / mole"/>
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          <speciesReference species="MNXM1" stoichiometry="3" constant="true"/>
          <speciesReference species="MNXM188" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM6" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
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          <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
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          <speciesReference species="MNXM5" stoichiometry="1" constant="true"/>
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              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1O[H].[H]Oc1c([H])c([H])c([H])c([H])c1O[H].O=O&gt;&gt;[H+].[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]"/>
                <brsynth:rp2_transfo_id value="TRS_0_1_3"/>
                <brsynth:rule_ids/>
                <brsynth:tmpl_rxn_ids/>
                <brsynth:rule_score value="0.5683242688496836"/>
                <brsynth:idx_in_path value="2"/>
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="-294.3657675294261"/>
                  <brsynth:error value="9.81314488510582"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG0_prime>
                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="-260.136092459984"/>
                  <brsynth:error value="9.81314488510582"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dGm_prime>
                <brsynth:thermo_dG_prime>
                  <brsynth:value value="-294.3657675294261"/>
                  <brsynth:error value="9.81314488510582"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG_prime>
                <brsynth:thermo_dG>
                  <brsynth:value value="56.91941717742026"/>
                  <brsynth:error value="9.81314488510582"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="CMPD_0000000003" stoichiometry="2" constant="true"/>
          <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="MNXM1" stoichiometry="1" constant="true"/>
          <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
        </listOfProducts>
      </reaction>
      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC__10000_0" fbc:upperFluxBound="BRS_FBC_10000_0">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.13.11.1"/>
                </rdf:Bag>
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                <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1[H].[H]Oc1c([H])c([H])c([H])c([H])c1[H].[H]Oc1c([H])c([H])c([H])c([H])c1[H].O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]&gt;&gt;O=C=O.N=C(O)c1ccc[n+](C2OC(COP(=O)(O)OP(=O)(O)OCC3OC(n4cnc5c(N)ncnc54)C(OP(=O)(O)O)C3O)C(O)C2O)c1"/>
                <brsynth:rp2_transfo_id value="TRS_0_0_0"/>
                <brsynth:rule_ids/>
                <brsynth:tmpl_rxn_ids/>
                <brsynth:rule_score value="0.5982208769718989"/>
                <brsynth:idx_in_path value="3"/>
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="-999.1492217936127"/>
                  <brsynth:error value="10.250976801552927"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG0_prime>
                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="-947.8047091894496"/>
                  <brsynth:error value="10.250976801552927"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dGm_prime>
                <brsynth:thermo_dG_prime>
                  <brsynth:value value="-999.1492217936127"/>
                  <brsynth:error value="10.250976801552927"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG_prime>
                <brsynth:thermo_dG>
                  <brsynth:value value="-177.08517765567103"/>
                  <brsynth:error value="10.250976801552927"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="CMPD_0000000004" stoichiometry="3" constant="true"/>
          <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM6" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM5" stoichiometry="1" constant="true"/>
        </listOfProducts>
      </reaction>
    </listOfReactions>
    <groups:listOfGroups>
      <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
            <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="-2309.7560063522865"/>
                  <brsynth:error value="22.459032062576664"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG0_prime>
                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="-2309.7560063522865"/>
                  <brsynth:error value="22.459032062576664"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dGm_prime>
                <brsynth:thermo_dG_prime>
                  <brsynth:value value="-2309.7560063522865"/>
                  <brsynth:error value="22.459032062576664"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG_prime>
                <brsynth:thermo_dG>
                  <brsynth:value value="-2151.847639515009"/>
                  <brsynth:error value="22.459032062576664"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG>
                <brsynth:global_score value="-1"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="rxn_1"/>
          <groups:member groups:idRef="rxn_2"/>
          <groups:member groups:idRef="rxn_3"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
            <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="CMPD_0000000004"/>
          <groups:member groups:idRef="CMPD_0000000003"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
            <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="MNXM4"/>
          <groups:member groups:idRef="CMPD_0000000004"/>
          <groups:member groups:idRef="MNXM6"/>
          <groups:member groups:idRef="CMPD_0000000003"/>
          <groups:member groups:idRef="MNXM164"/>
          <groups:member groups:idRef="TARGET_0000000001"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
            <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="MNXM1"/>
          <groups:member groups:idRef="MNXM13"/>
          <groups:member groups:idRef="MNXM2"/>
          <groups:member groups:idRef="MNXM5"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
            <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
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        <groups:listOfMembers>
          <groups:member groups:idRef="MNXM4"/>
          <groups:member groups:idRef="MNXM6"/>
          <groups:member groups:idRef="MNXM2"/>
          <groups:member groups:idRef="MNXM1"/>
          <groups:member groups:idRef="MNXM13"/>
          <groups:member groups:idRef="MNXM164"/>
          <groups:member groups:idRef="MNXM5"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection">
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
            <rdf:BRSynth rdf:about="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </groups:group>
    </groups:listOfGroups>
  </model>
</sbml>