Mercurial > repos > tduigou > rpscore
changeset 0:f818d489ca7d draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Tue, 07 Dec 2021 15:53:15 +0000 |
| parents | |
| children | da8ae7fa5ed3 |
| files | test-data/pathway.xml test-data/scored_pathway.xml wrap.xml |
| diffstat | 3 files changed, 898 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathway.xml Tue Dec 07 15:53:15 2021 +0000 @@ -0,0 +1,444 @@ +<?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="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true"> + <listOfCompartments> + <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/> + <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/> + <rdf:li rdf:resource="http://identifiers.org/seed/c"/> + <rdf:li rdf:resource="http://identifiers.org/seed/c0"/> + <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/> + <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </compartment> + </listOfCompartments> + <listOfSpecies> + <species metaid="_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/"> + <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/> + <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/> + <brsynth:fba_biomass_shadow_price> + <brsynth:value value="-0.0"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="-1.0"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="208.92559504464236"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H+]"/> + <brsynth:inchi value="InChI=1S/p+1"/> + <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/> + <brsynth: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="NaN"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16" id="CMPD_0000000002" name="CMPD_0000000002" 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="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:inchi value="InChI=1S/C9H8O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-7H,(H,10,11)"/> + <brsynth:inchikey value="WBYWAXJHAXSJNI-UHFFFAOYSA-N"/> + <brsynth:fba_biomass_shadow_price> + <brsynth:value value="-0.0009404190769783985"/> + </brsynth:fba_biomass_shadow_price> + <brsynth:fba_fraction_shadow_price> + <brsynth:value value="-1.0057339449541285"/> + </brsynth:fba_fraction_shadow_price> + <brsynth:thermo_standard_dg_formation> + <brsynth:value value="-127.1962856224608"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" 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="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="N"/> + <brsynth:inchi value="InChI=1S/H3N/h1H3"/> + <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/> + <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="-81.91776181003092"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" 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="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="O=C=O"/> + <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/> + <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/> + <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="-386.0000000000019"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_standard_dg_formation> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" 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="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/> + <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/> + <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="-207.07052002003908"/> + <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/4.3.1.25"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.24"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]>>[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].N"/> + <brsynth:rp2_transfo_id value="TRS_0_1_1"/> + <brsynth:rule_id value="RR-02-3545d6ed74034d56-16-F"/> + <brsynth:tmpl_rxn_ids> + <brsynth:MNXR106649/> + <brsynth:MNXR131345/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="0.5869134225065102"/> + <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="1.3666677776240859"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-3.619165315209898"/> + <brsynth:error value="0.5540714922475698"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-20.73400284993093"/> + <brsynth:error value="0.5540714922475698"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-3.619165315209898"/> + <brsynth:error value="0.5540714922475698"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-2.0435274124526472"/> + <brsynth:error value="0.5540714922475698"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="MNXM97" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM15" stoichiometry="1" 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/4.1.1.102"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].[H+]>>O=C=O.[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:rp2_transfo_id value="TRS_0_0_0"/> + <brsynth:rule_id value="RR-02-caf68bc1dcd9ce0f-16-F"/> + <brsynth:tmpl_rxn_ids> + <brsynth:MNXR114372/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="1.0"/> + <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="1.3666677776240859"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-5.570411694686811"/> + <brsynth:error value="5.365139708628456"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-22.685249229407844"/> + <brsynth:error value="5.365139708628456"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-5.570411694686811"/> + <brsynth:error value="5.365139708628456"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-49.87811933289868"/> + <brsynth:error value="5.365139708628456"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM1" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="MNXM13" stoichiometry="1" 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="0.8769972144269752"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="1.3666677776240859"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-9.189577009896766"/> + <brsynth:error value="5.336452836371218"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-43.41925207933883"/> + <brsynth:error value="5.336452836371218"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-9.189577009896766"/> + <brsynth:error value="5.336452836371218"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-51.92164674535138"/> + <brsynth:error value="5.336452836371218"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="rxn_1"/> + <groups:member groups:idRef="rxn_2"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="CMPD_0000000002"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="MNXM97"/> + <groups:member groups:idRef="CMPD_0000000002"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM15"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM97"/> + <groups:member groups:idRef="MNXM15"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_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="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </groups:group> + <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scored_pathway.xml Tue Dec 07 15:53:15 2021 +0000 @@ -0,0 +1,383 @@ +<?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="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true"> + <listOfCompartments> + <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/> + <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/> + <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/> + <rdf:li rdf:resource="http://identifiers.org/seed/c"/> + <rdf:li rdf:resource="http://identifiers.org/seed/c0"/> + <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/> + <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </compartment> + </listOfCompartments> + <listOfSpecies> + <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" 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="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="O=C=O"/> + <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/> + <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16" id="CMPD_0000000002" name="CMPD_0000000002" 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="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:inchi value="InChI=1S/C9H8O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-7H,(H,10,11)"/> + <brsynth:inchikey value="WBYWAXJHAXSJNI-UHFFFAOYSA-N"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" 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="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="N"/> + <brsynth:inchi value="InChI=1S/H3N/h1H3"/> + <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/> + </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/"> + <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/> + <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" 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="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/> + <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </species> + <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> + <bqbiol:is> + <rdf:Bag/> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H+]"/> + <brsynth:inchi value="InChI=1S/p+1"/> + <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </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/4.3.1.24"/> + <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.25"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]>>[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].N"/> + <brsynth:rp2_transfo_id value="TRS_0_1_1"/> + <brsynth:rule_ids/> + <brsynth:tmpl_rxn_ids> + <brsynth:MNXR106649/> + <brsynth:MNXR131345/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="0.5869134225065102"/> + <brsynth:idx_in_path value="1"/> + <brsynth:fba_biomass> + <brsynth:value value="0.0"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="1.3666677776240859"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-3.619165315209898"/> + <brsynth:error value="0.5540714922475698"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-20.73400284993093"/> + <brsynth:error value="0.5540714922475698"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-3.619165315209898"/> + <brsynth:error value="0.5540714922475698"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-2.0435274124526472"/> + <brsynth:error value="0.5540714922475698"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="MNXM97" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM15" stoichiometry="1" 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/4.1.1.102"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"> + <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].[H+]>>O=C=O.[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/> + <brsynth:rp2_transfo_id value="TRS_0_0_0"/> + <brsynth:rule_ids/> + <brsynth:tmpl_rxn_ids> + <brsynth:MNXR114372/> + </brsynth:tmpl_rxn_ids> + <brsynth:rule_score value="1.0"/> + <brsynth:idx_in_path value="2"/> + <brsynth:fba_biomass> + <brsynth:value value="0.0"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="1.3666677776240859"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-5.570411694686811"/> + <brsynth:error value="5.365139708628456"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-22.685249229407844"/> + <brsynth:error value="5.365139708628456"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-5.570411694686811"/> + <brsynth:error value="5.365139708628456"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-49.87811933289868"/> + <brsynth:error value="5.365139708628456"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <listOfReactants> + <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/> + <speciesReference species="MNXM1" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="MNXM13" stoichiometry="1" 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="0.8769972144269752"/> + <brsynth:units value="gDW / gDW / hour"/> + </brsynth:fba_biomass> + <brsynth:fba_fraction> + <brsynth:value value="1.3666677776240859"/> + <brsynth:units value="milimole / gDW / hour"/> + </brsynth:fba_fraction> + <brsynth:thermo_dG0_prime> + <brsynth:value value="-9.189577009896766"/> + <brsynth:error value="5.336452836371218"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG0_prime> + <brsynth:thermo_dGm_prime> + <brsynth:value value="-43.41925207933883"/> + <brsynth:error value="5.336452836371218"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dGm_prime> + <brsynth:thermo_dG_prime> + <brsynth:value value="-9.189577009896766"/> + <brsynth:error value="5.336452836371218"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG_prime> + <brsynth:thermo_dG> + <brsynth:value value="-51.92164674535138"/> + <brsynth:error value="5.336452836371218"/> + <brsynth:units value="kilojoule / mole"/> + </brsynth:thermo_dG> + <brsynth:global_score value="0.9923127055168152"/> + </brsynth:brsynth> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="rxn_1"/> + <groups:member groups:idRef="rxn_2"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="CMPD_0000000002"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="TARGET_0000000001"/> + <groups:member groups:idRef="CMPD_0000000002"/> + <groups:member groups:idRef="MNXM97"/> + </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="MNXM13"/> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM15"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="MNXM13"/> + <groups:member groups:idRef="MNXM1"/> + <groups:member groups:idRef="MNXM15"/> + <groups:member groups:idRef="MNXM97"/> + </groups:listOfMembers> + </groups:group> + <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_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="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </groups:group> + <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wrap.xml Tue Dec 07 15:53:15 2021 +0000 @@ -0,0 +1,71 @@ +<tool id="rpscore" name="Score Pathway" version="5.9.2"> + <description>Computes a global score for a heterologous pathway.</description> + <requirements> + <requirement type="package" version="5.9.2">rptools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python -m rptools.rpscore '$pathway' '$scored_pathway' + --no_of_rxns_thres '$adv.no_of_rxns_thres' + --log '$adv.log_level' + ]]></command> + <inputs> + <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" /> + <param name="log_level" type="select" label="Log level"> + <option value="debug" >debug</option> + <option value="info" >info</option> + <option value="warning" >warning</option> + <option value="error" selected="true">error</option> + <option value="critical" >critical</option> + </param> + </section> + </inputs> + <outputs> + <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with default parameters --> + <param name="pathway" value="pathway.xml" /> + <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/> + </test> + </tests> + <help><![CDATA[ +rpscore +========= + + +Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway. + + +Input +----- + +Required: + +* **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...) +* **outfile**\ : (string) Path to write pathway file (rpSBML) with global score + +Advanced options: + +* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long) +* **--log**: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical' + +Version +---------- + +5.9.2 + +Authors +------- + +* **Jean-Loup Faulon** +* **Joan Hérisson** + +Acknowledgments +--------------- + +* Thomas Duigou + ]]></help> +</tool> \ No newline at end of file