| Previous changeset 3:fcc8f3e2d4da (2022-05-04) Next changeset 5:37bed74bbd44 (2022-11-18) |
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Commit message:
planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty |
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modified:
rpcompletion.xml test-data/rp_001_0001.xml test-data/rp_001_0006.xml test-data/rp_001_0011.xml test-data/rp_002_0001.xml test-data/rp_002_0011.xml test-data/rp_002_0021.xml test-data/rp_003_0001.xml test-data/rp_003_0131.xml test-data/rp_003_0261.xml |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 rpcompletion.xml --- a/rpcompletion.xml Wed May 04 10:05:47 2022 +0000 +++ b/rpcompletion.xml Wed Sep 21 09:41:34 2022 +0000 |
| b |
| @@ -1,7 +1,7 @@ -<tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="19.09"> +<tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="21.09"> <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description> <macros> - <token name="@TOOL_VERSION@">5.12.3</token> + <token name="@TOOL_VERSION@">5.13.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> @@ -27,9 +27,9 @@ <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" /> <param name="sink" type="data" format="csv" label="Sink from SBML" /> <section name="adv" title="Advanced Options" expanded="false"> - <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" /> - <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" /> - <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" /> + <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." /> + <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." /> + <param argument="lower_flux_bound" type="integer" value="0" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." /> </section> </inputs> <outputs> @@ -61,24 +61,28 @@ rpCompletion ============ -Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data. +Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data. Input ----- Required: -* **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file -* **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink -* **rp2paths_compounds**: (string) Path to the rp2paths compounds file -* **rp2paths_pathways**: (string) Path to the rp2paths pathways file -* **outdir**: (string) Path to the output directory containing sbml completed pathways +* **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file +* **Sink from SBML**: rpextractsink file containing infos on molecules in the sink +* **RP2paths compounds**: rp2paths compounds file +* **RP2paths pathways**: rp2paths pathways file Advanced options: -* **-upper_flux_bound**: (integer, default=9999) Upper flux bound value -* **-lower_flux_bound**: (integer, default=0) Lower flux bound value -* **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path +* **Upper flux bound**: (integer, default=9999) Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created. +* **Lower flux bound**: (integer, default=0) Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created. +* **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway. + +Output +------ + +* **pathways**: SBML completed pathways Project Links --------------------- @@ -87,7 +91,7 @@ Version ---------- -5.12.1 +5.13.1 Authors ------- |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_001_0001.xml --- a/test-data/rp_001_0001.xml Wed May 04 10:05:47 2022 +0000 +++ b/test-data/rp_001_0001.xml Wed Sep 21 09:41:34 2022 +0000 |
| [ |
| b'@@ -23,78 +23,6 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n- <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n- <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc" id="MNXM132" name="dimethylallyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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])[H]"/>\n- <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)"/>\n- <brsynth:inchikey value="CBIDRCWHNCKSTO-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bc'..b'oTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -323,11 +323,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM132"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -339,9 +339,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM24"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -353,9 +353,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_001_0006.xml --- a/test-data/rp_001_0006.xml Wed May 04 10:05:47 2022 +0000 +++ b/test-data/rp_001_0006.xml Wed Sep 21 09:41:34 2022 +0000 |
| [ |
| b'@@ -23,19 +23,55 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n+ <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n+ <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C40H56/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/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>\n+ <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n- <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n- <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biol'..b'true"/>\n </listOfParameters>\n <listOfReactions>\n- <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -323,11 +323,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM132"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -339,8 +339,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM8975"/>\n </groups:listOfMembers>\n </groups:group>\n@@ -353,9 +353,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_001_0011.xml --- a/test-data/rp_001_0011.xml Wed May 04 10:05:47 2022 +0000 +++ b/test-data/rp_001_0011.xml Wed Sep 21 09:41:34 2022 +0000 |
| [ |
| b'@@ -23,19 +23,55 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n+ <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n+ <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C40H56/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/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>\n+ <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n- <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n- <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biol'..b'sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -323,11 +323,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM132"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -339,9 +339,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM24"/>\n <groups:member groups:idRef="MNXM35"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -353,9 +353,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_002_0001.xml --- 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 |
| b |
| b'@@ -23,60 +23,6 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n- <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n- <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n@@ -95,42 +41,6 @@\n </rdf:RDF>\n </annotation>\n </species>\n- <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" const'..b'ction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -326,11 +326,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM100"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -342,9 +342,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM24"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -357,8 +357,8 @@\n </annotation>\n <groups:listOfMembers>\n <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_002_0011.xml --- a/test-data/rp_002_0011.xml Wed May 04 10:05:47 2022 +0000 +++ b/test-data/rp_002_0011.xml Wed Sep 21 09:41:34 2022 +0000 |
| [ |
| b'@@ -23,6 +23,78 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n+ <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C40H56/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/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>\n+ <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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])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]"/>\n+ '..b'oTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>\n </listOfParameters>\n <listOfReactions>\n- <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -326,11 +326,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM100"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -342,8 +342,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM8975"/>\n </groups:listOfMembers>\n </groups:group>\n@@ -357,8 +357,8 @@\n </annotation>\n <groups:listOfMembers>\n <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_002_0021.xml --- a/test-data/rp_002_0021.xml Wed May 04 10:05:47 2022 +0000 +++ b/test-data/rp_002_0021.xml Wed Sep 21 09:41:34 2022 +0000 |
| [ |
| b'@@ -23,6 +23,60 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n+ <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C40H56/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/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>\n+ <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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])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]"/>\n+ '..b'eaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -326,11 +326,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM100"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -342,9 +342,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM24"/>\n <groups:member groups:idRef="MNXM35"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -357,8 +357,8 @@\n </annotation>\n <groups:listOfMembers>\n <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_003_0001.xml --- a/test-data/rp_003_0001.xml Wed May 04 10:05:47 2022 +0000 +++ b/test-data/rp_003_0001.xml Wed Sep 21 09:41:34 2022 +0000 |
| b |
| b'@@ -23,60 +23,6 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n- <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n- <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n@@ -95,24 +41,6 @@\n </rdf:RDF>\n </annotation>\n </species>\n- <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" const'..b'e1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -364,11 +364,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM34"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -380,9 +380,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM24"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -394,9 +394,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM11"/>\n+ <groups:member groups:idRef="MNXM34"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="MNXM34"/>\n+ <groups:member groups:idRef="MNXM11"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_003_0131.xml --- a/test-data/rp_003_0131.xml Wed May 04 10:05:47 2022 +0000 +++ b/test-data/rp_003_0131.xml Wed Sep 21 09:41:34 2022 +0000 |
| [ |
| b'@@ -23,6 +23,78 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n+ <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C40H56/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/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>\n+ <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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])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]"/>\n+ '..b'r" constant="true"/>\n </listOfParameters>\n <listOfReactions>\n- <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -364,11 +364,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM34"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -380,8 +380,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM8975"/>\n </groups:listOfMembers>\n </groups:group>\n@@ -394,9 +394,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM11"/>\n+ <groups:member groups:idRef="MNXM34"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="MNXM34"/>\n+ <groups:member groups:idRef="MNXM11"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_003_0261.xml --- a/test-data/rp_003_0261.xml Wed May 04 10:05:47 2022 +0000 +++ b/test-data/rp_003_0261.xml Wed Sep 21 09:41:34 2022 +0000 |
| [ |
| b'@@ -23,6 +23,60 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n+ <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=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])[H])C([H])([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C40H56/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/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>\n+ <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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])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]"/>\n+ '..b'3ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">\n@@ -208,7 +208,7 @@\n <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">\n@@ -248,7 +248,7 @@\n <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>\n </listOfProducts>\n </reaction>\n- <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">\n+ <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">\n@@ -364,11 +364,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM83"/>\n <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM34"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -380,9 +380,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM24"/>\n <groups:member groups:idRef="MNXM35"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -394,9 +394,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM11"/>\n+ <groups:member groups:idRef="MNXM34"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="MNXM34"/>\n+ <groups:member groups:idRef="MNXM11"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |