Mercurial > repos > tduigou > rpcompletion

diff test-data/rp_002_0001.xml @ 4:e8d56cb2be03 draft

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planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author tduigou
date Wed, 21 Sep 2022 09:41:34 +0000
parents b8242cf18cc0
children
line wrap: on
line diff
--- a/test-data/rp_002_0001.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_002_0001.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,60 +23,6 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" 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="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
-                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
-                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" 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="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" 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="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" 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/">
@@ -95,42 +41,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" 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="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
-                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="(2E)-geranyl diphosphate" 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="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
-                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" 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/">
@@ -167,13 +77,103 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" 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="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
+                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="(2E)-geranyl diphosphate" 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="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
+                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" 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="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" 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="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" 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="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
+                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" 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">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" 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">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" 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">
@@ -326,11 +326,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM100"/>
           <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -342,9 +342,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM11"/>
           <groups:member groups:idRef="MNXM8975"/>
-          <groups:member groups:idRef="MNXM24"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -357,8 +357,8 @@
         </annotation>
         <groups:listOfMembers>
           <groups:member groups:idRef="MNXM100"/>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>