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changeset 0:44e54b56328d draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 24 Nov 2021 09:48:18 +0000
parents
children 21a900eee812
files rpthermo.xml test-data/rp_013_0001.xml test-data/rp_013_0001_with_thermo.xml
diffstat 3 files changed, 983 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpthermo.xml	Wed Nov 24 09:48:18 2021 +0000
@@ -0,0 +1,103 @@
+<tool id="rpThermo" name="Thermodynamics" version="5.9.2">
+    <description>Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML</description>
+    <requirements>
+        <requirement type="package" version="5.9.2">rptools</requirement>
+    </requirements>
+    <stdio>
+        <regex match="WARNING:" level="warning" />
+        <regex match="ERROR:" level="fatal" />
+        <regex match="ERROR:root:ChemAxon" level="warning" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rptools.rpthermo
+        '$input'
+        '$pathway_with_thermo' 
+        --ph '$adv.ph'
+        --ionic_strength '$adv.ionic_strength'
+        --pMg '$adv.pMg'
+        --temp_k '$adv.temp_k' 
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="xml" label="Input File" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="ph" type="float" value="7.5" label="Compartment PH of the pathway" />
+            <param name="ionic_strength" type="float" value="200.0" label="Compartment ionic strength of the pathway" />
+            <param name="pMg" type="float" value="10.0" label="Compartment pMg of the pathway" />
+            <param name="temp_k" type="float" value="298.15" label="Compartment temperature in Kelvin" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="pathway_with_thermo" format="xml" label="${tool.name} - ${input.name}" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="input" value="rp_013_0001.xml" />
+            <param name="model" value="e_coli_iML1515.sbml" />
+            <output name="pathway_with_thermo" file="rp_013_0001_with_thermo.xml" ftype="xml" compare="diff" sort="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Thermodynamics
+===============
+Calculate the formation energy of chemical species either using an internal database or estimate it by decomposing them using the `component contribution <https://gitlab.com/elad.noor/component-contribution>`_ method. Thereafter this tool predicts the Gibbs free energy of reactions and of the whole heterologous pathway by combining the formation energy of each individual compound.
+
+.. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpThermo/standalone/galaxy/img/rpThermo.png 
+	:width: 80 %
+	:align: center
+
+
+|
+
+
+Above is an illustration of the Gibbs free energy calculation using the component contribution package. The color-coded arrows from red (best) to blue (worst) show the best and worst-performing reactions.
+
+Required:
+
+* **input**\ : (string) Path to the input file
+* **output**\ : (string) Path to the output file 
+
+Advanced Options:
+
+* **--ph**\ :(float) Compartment PH of the pathway
+* **--ionic_strength**\ :(float) Compartment ionic strength of the pathway
+* **--pMg**\ :(float) Compartment pMg of the pathway
+* **--temp_k**\ :(float) Compartment temperature in Kelvin
+
+Project Links
+---------------------
+
+* `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpthermo>`_
+
+Version
+----------
+
+v5.9.2
+
+Authors
+-------
+
+* **Melchior du Lac** 
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+* Joan Hérisson
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@article{noor2013consistent,
+  title={Consistent estimation of Gibbs energy using component contributions},
+  author={Noor, Elad and Haraldsd{\'o}ttir, Hulda S and Milo, Ron and Fleming, Ronan MT},
+  journal={PLoS Comput Biol},
+  volume={9},
+  number={7},
+  pages={e1003098},
+  year={2013},
+  publisher={Public Library of Science}
+}
+        </citation>
+    </citations>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rp_013_0001.xml	Wed Nov 24 09:48:18 2021 +0000
@@ -0,0 +1,397 @@
+<?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">
+    <listOfCompartments>
+      <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
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+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
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+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC__10000" fbc:upperFluxBound="BRS_FBC_10000">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.13.11.1"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1O[H].O=O&gt;&gt;[H+].[H+].[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]"/>
+                <brsynth:rp2_transfo_id value="TRS_0_0_0"/>
+                <brsynth:rule_id value="RR-02-a0cc0be463ff412f-16-F"/>
+                <brsynth:tmpl_rxn_id value="MNXR96458"/>
+                <brsynth:rule_score value="0.5982208769718989"/>
+                <brsynth:idx_in_path value="3"/>
+                <brsynth:selenzy/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM6" stoichiometry="1" constant="true"/>
+          <speciesReference species="CMPD_0000000004" stoichiometry="3" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM5" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC__10000" fbc:upperFluxBound="BRS_FBC_10000">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/1.14.13.7"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1[H].[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;[H]Oc1c([H])c([H])c([H])c([H])c1O[H].[H]O[H].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_1_3"/>
+                <brsynth:rule_id value="RR-02-217503934671e143-16-F"/>
+                <brsynth:tmpl_rxn_id value="MNXR106703"/>
+                <brsynth:rule_score value="0.5683242688496836"/>
+                <brsynth:idx_in_path value="2"/>
+                <brsynth:selenzy/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
+          <speciesReference species="CMPD_0000000003" stoichiometry="2" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="MNXM1" stoichiometry="1" constant="true"/>
+          <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+      </reaction>
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC__10000" fbc:upperFluxBound="BRS_FBC_10000">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.61"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H+].[H]OC(=O)c1c([H])c([H])c(O[H])c([H])c1[H]&gt;&gt;[H]Oc1c([H])c([H])c([H])c([H])c1[H].O=C=O"/>
+                <brsynth:rp2_transfo_id value="TRS_0_2_60"/>
+                <brsynth:rule_id value="RR-02-d3b162f199b260fc-16-F"/>
+                <brsynth:tmpl_rxn_id value="MNXR106877"/>
+                <brsynth:rule_score value="0.7023718970192103"/>
+                <brsynth:idx_in_path value="1"/>
+                <brsynth:selenzy/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+        <listOfReactants>
+          <speciesReference species="MNXM188" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM6" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM1" stoichiometry="3" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="CMPD_0000000004" stoichiometry="1" constant="true"/>
+          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM15" 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: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="TARGET_0000000001"/>
+          <groups:member groups:idRef="MNXM4"/>
+          <groups:member groups:idRef="MNXM164"/>
+          <groups:member groups:idRef="CMPD_0000000004"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
+          <groups:member groups:idRef="MNXM6"/>
+        </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="MNXM5"/>
+          <groups:member groups:idRef="MNXM13"/>
+          <groups:member groups:idRef="MNXM2"/>
+          <groups:member groups:idRef="MNXM1"/>
+        </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>
+        </annotation>
+        <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM2"/>
+          <groups:member groups:idRef="MNXM13"/>
+          <groups:member groups:idRef="MNXM4"/>
+          <groups:member groups:idRef="MNXM1"/>
+          <groups:member groups:idRef="MNXM164"/>
+          <groups:member groups:idRef="MNXM5"/>
+          <groups:member groups:idRef="MNXM6"/>
+        </groups:listOfMembers>
+      </groups:group>
+    </groups:listOfGroups>
+  </model>
+</sbml>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rp_013_0001_with_thermo.xml	Wed Nov 24 09:48:18 2021 +0000
@@ -0,0 +1,483 @@
+<?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">
+    <listOfCompartments>
+      <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
+                  <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
+                  <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species metaid="_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb" id="MNXM6" name="MNXM6" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_565b5e3c38feed64054fc6727068060c34dcf6d8715c8474bdc4c11b810845fb">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[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]"/>
+                <brsynth:inchi value="InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)"/>
+                <brsynth:inchikey value="ACFIXJIJDZMPPO-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_5048d67a4507da50d2b6f7a950c531ac5a424ec6d7f1e84da7d56cbbfa7f782e" id="CMPD_0000000004" name="CMPD_0000000004" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_5048d67a4507da50d2b6f7a950c531ac5a424ec6d7f1e84da7d56cbbfa7f782e">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_5048d67a4507da50d2b6f7a950c531ac5a424ec6d7f1e84da7d56cbbfa7f782e">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1[H]"/>
+                <brsynth:inchi value="InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H"/>
+                <brsynth:inchikey value="ISWSIDIOOBJBQZ-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da" id="MNXM4" name="MNXM4" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#c18fc797adf5be2d9c14427deceaaecd152233bfd9b8c8ef9627274f3b2ee5da">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=O"/>
+                <brsynth:inchi value="InChI=1S/O2/c1-2"/>
+                <brsynth:inchikey value="MYMOFIZGZYHOMD-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]Oc1c([H])c([H])c([H])c([H])c1O[H]"/>
+                <brsynth:inchi value="InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H"/>
+                <brsynth:inchikey value="YCIMNLLNPGFGHC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H+]"/>
+                <brsynth:inchi value="InChI=1S/p+1"/>
+                <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
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+                <brsynth:inchi value="InChI=1S/H2O/h1H2"/>
+                <brsynth:inchikey value="XLYOFNOQVPJJNP-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
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+      </species>
+      <species metaid="_4a3e4e32a6db24e5ddaa18997f93519c4ef1c0172e96160cd56ad49ecf025995" id="MNXM5" name="MNXM5" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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+            </rdf:BRSynth>
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+    </listOfSpecies>
+    <listOfParameters>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC__10000_0" value="-10000" constant="true"/>
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+                  <brsynth:units value="kilojoule / mole"/>
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+        </annotation>
+        <listOfReactants>
+          <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>
+          <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
+          <speciesReference species="CMPD_0000000004" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM15" stoichiometry="1" constant="true"/>
+          <speciesReference species="MNXM5" stoichiometry="1" constant="true"/>
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+        <annotation>
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+                <brsynth:tmpl_rxn_ids/>
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+                <brsynth:idx_in_path value="2"/>
+                <brsynth:thermo_dG0_prime>
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+                  <brsynth:units value="kilojoule / mole"/>
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+                  <brsynth:units value="kilojoule / mole"/>
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+                  <brsynth:units value="kilojoule / mole"/>
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+                  <brsynth:units value="kilojoule / mole"/>
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+        </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>
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+        <annotation>
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+                <brsynth:rp2_transfo_id value="TRS_0_0_0"/>
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+                <brsynth:rule_score value="0.5982208769718989"/>
+                <brsynth:idx_in_path value="3"/>
+                <brsynth:thermo_dG0_prime>
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+                  <brsynth:units value="kilojoule / mole"/>
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+                <brsynth:thermo_dGm_prime>
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+                  <brsynth:units value="kilojoule / mole"/>
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+                <brsynth:thermo_dG_prime>
+                  <brsynth:value value="-999.1492217936127"/>
+                  <brsynth:error value="10.250976801552927"/>
+                  <brsynth:units value="kilojoule / mole"/>
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+                <brsynth:thermo_dG>
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+                  <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/">
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+                  <brsynth:units value="kilojoule / mole"/>
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+                <brsynth:thermo_dG_prime>
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+                  <brsynth:units value="kilojoule / mole"/>
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+                  <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/">
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+        </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>
+        </annotation>
+        <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>