Mercurial > repos > tduigou > rptools_rpviz
diff test-data/rp_002_0011.xml @ 0:bf6f117ef632 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
| author | tduigou |
|---|---|
| date | Wed, 16 Nov 2022 11:11:25 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rp_002_0011.xml Wed Nov 16 11:11:25 2022 +0000 @@ -0,0 +1,588 @@ +<?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="b8c1523a13bf5120b604ab91344086ae4f6519e7153eba9eeacb319187964033" id="RP_model_002_0011" name="002_0011" 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 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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:fba_biomass_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="None"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="-2261.3806478863044"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + </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_0_0" value="0" constant="true"/> + </listOfParameters> + <listOfReactions> + <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.82"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4"> + <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].[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]>>[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].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O"/> + <brsynth:rp2_transfo_id value="TRS_0_2_740"/> + <brsynth:rule_ids> + <brsynth:RR-02-0c33a3bfd9bf5ad5-14-F/> + <brsynth:RR-02-6692e4af37fbca2d-14-F/> + </brsynth:rule_ids> + <brsynth:tmpl_rxn_ids> + <brsynth:MNXR132231/> + <brsynth:MNXR112683/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="0.5706379442030705"/> + <brsynth:idx_in_path value="1"/> + <brsynth:selenzy/> + <brsynth:fba_biomass> + <brsynth:value value="0.0"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="0.6301198587096097"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-1544.3333670420595"/> + <brsynth:error value="4.6679220722885155"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-1561.4482045767807"/> + <brsynth:error value="4.6679220722885155"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-1544.3333670420595"/> + <brsynth:error value="4.6679220722885155"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-1881.1378556154446"/> + <brsynth:error value="4.6679220722885155"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="MNXM100" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM83" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM11" stoichiometry="2" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.96"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.99"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.32"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff"> + <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])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]>>[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].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O"/> + <brsynth:rp2_transfo_id value="TRS_0_1_9"/> + <brsynth:rule_ids> + <brsynth:RR-02-bedda4e2f5001e0c-14-F/> + </brsynth:rule_ids> + <brsynth:tmpl_rxn_ids> + <brsynth:MNXR111250/> + <brsynth:MNXR111499/> + <brsynth:MNXR113543/> + <brsynth:MNXR118024/> + <brsynth:MNXR139549/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="0.5518755963407151"/> + <brsynth:idx_in_path value="2"/> + <brsynth:selenzy/> + <brsynth:fba_biomass> + <brsynth:value value="0.0"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="0.6301198587096097"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-119.13360567395966"/> + <brsynth:error value="11.000567449695138"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-153.36328074340173"/> + <brsynth:error value="11.000567449695138"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-119.13360567395966"/> + <brsynth:error value="11.000567449695138"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-1501.0650763644926"/> + <brsynth:error value="11.000567449695138"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM11" stoichiometry="2" constant="true"/> + </listOfProducts> + </reaction> + <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/ec-code/1.3.99.31"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d"> + <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]>>[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]"/> + <brsynth:rp2_transfo_id value="TRS_0_0_1"/> + <brsynth:rule_ids> + <brsynth:RR-02-ae41ec5771136ea5-14-F/> + </brsynth:rule_ids> + <brsynth:tmpl_rxn_ids> + <brsynth:MNXR117536/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="0.7358363677022237"/> + <brsynth:idx_in_path value="3"/> + <brsynth:selenzy/> + <brsynth:fba_biomass> + <brsynth:value value="0.0"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="0.6301198587096097"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="225.28622017594057"/> + <brsynth:error value="5.600796500160482"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="225.28622017594057"/> + <brsynth:error value="5.600796500160482"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="225.28622017594057"/> + <brsynth:error value="5.600796500160482"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="408.1812115547325"/> + <brsynth:error value="5.600796500160482"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM8975" stoichiometry="4" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="MNXM36" stoichiometry="4" constant="true"/> + <speciesReference species="TARGET_0000000001" 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:fba_biomass> + <brsynth:value value="0.8769972144269764"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="0.6301198587096097"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-1438.1807525400782"/> + <brsynth:error value="18.15737885804391"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-1489.5252651442413"/> + <brsynth:error value="18.15737885804391"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-1438.1807525400782"/> + <brsynth:error value="18.15737885804391"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-2974.021720425204"/> + <brsynth:error value="18.15737885804391"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + <brsynth:global_score value="0.9851486444473266"/> + </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 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groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="MNXM83"/> + <groups:member groups:idRef="MNXM100"/> + </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="MNXM8975"/> + <groups:member groups:idRef="MNXM36"/> + <groups:member groups:idRef="MNXM11"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> + <annotation> 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<groups:listOfMembers> + <groups:member groups:idRef="MNXM8975"/> + <groups:member groups:idRef="MNXM36"/> + </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:listOfMembers> + <groups:member groups:idRef="MNXM8975"/> + <groups:member groups:idRef="MNXM36"/> + <groups:member groups:idRef="TARGET_0000000001"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>