Mercurial > repos > tduigou > rptools_rpranker

comparison test-data/rp_001_0011.xml @ 0:8b05775f6c16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Wed, 16 Nov 2022 11:10:47 +0000
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-1:000000000000 0:8b05775f6c16
1 <?xml version="1.0" encoding="UTF-8"?>
2 <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">
3 <model metaid="_2eda565339ba8b09cce4d7e7775c0cdc48d2829ace3c6b73d4eb3136afc453a4" id="RP_model_001_0011" name="001_0011" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
4 <listOfCompartments>
5 <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
6 <annotation>
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8 <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
9 <bqbiol:is>
10 <rdf:Bag>
11 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
12 <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
13 <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
14 <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
15 <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
16 <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
17 <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
18 </rdf:Bag>
19 </bqbiol:is>
20 </rdf:Description>
21 </rdf:RDF>
22 </annotation>
23 </compartment>
24 </listOfCompartments>
25 <listOfSpecies>
26 <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
27 <annotation>
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37 <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
38 <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
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42 <brsynth:fba_fraction_shadow_price>
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44 </brsynth:fba_fraction_shadow_price>
45 <brsynth:thermo_standard_dg_formation>
46 <brsynth:value value="936.7141451846444"/>
47 <brsynth:units value="kilojoule / mole"/>
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49 </brsynth:brsynth>
50 </rdf:BRSynth>
51 </rdf:RDF>
52 </annotation>
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65 <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
66 <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
67 <brsynth:fba_biomass_shadow_price>
68 <brsynth:value value="-0.2304026738597042"/>
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70 <brsynth:fba_fraction_shadow_price>
71 <brsynth:value value="-0.9919678714859437"/>
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73 <brsynth:thermo_standard_dg_formation>
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75 <brsynth:units value="kilojoule / mole"/>
76 </brsynth:thermo_standard_dg_formation>
77 </brsynth:brsynth>
78 </rdf:BRSynth>
79 </rdf:RDF>
80 </annotation>
81 </species>
82 <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
83 <annotation>
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90 <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
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93 <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"/>
94 <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
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98 <brsynth:fba_fraction_shadow_price>
99 <brsynth:value value="-1.0"/>
100 </brsynth:fba_fraction_shadow_price>
101 <brsynth:thermo_standard_dg_formation>
102 <brsynth:value value="1245.5794452419402"/>
103 <brsynth:units value="kilojoule / mole"/>
104 </brsynth:thermo_standard_dg_formation>
105 </brsynth:brsynth>
106 </rdf:BRSynth>
107 </rdf:RDF>
108 </annotation>
109 </species>
110 <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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119 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
120 <brsynth:smiles/>
121 <brsynth:inchi/>
122 <brsynth:inchikey/>
123 <brsynth:fba_biomass_shadow_price>
124 <brsynth:value value="None"/>
125 </brsynth:fba_biomass_shadow_price>
126 <brsynth:fba_fraction_shadow_price>
127 <brsynth:value value="None"/>
128 </brsynth:fba_fraction_shadow_price>
129 <brsynth:thermo_standard_dg_formation>
130 <brsynth:value value="-2256.1898491337233"/>
131 <brsynth:units value="kilojoule / mole"/>
132 </brsynth:thermo_standard_dg_formation>
133 </brsynth:brsynth>
134 </rdf:BRSynth>
135 </rdf:RDF>
136 </annotation>
137 </species>
138 <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="MNXM11" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
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142 <bqbiol:is>
143 <rdf:Bag/>
144 </bqbiol:is>
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146 <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
147 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
148 <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
149 <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
150 <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
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154 <brsynth:fba_fraction_shadow_price>
155 <brsynth:value value="None"/>
156 </brsynth:fba_fraction_shadow_price>
157 <brsynth:thermo_standard_dg_formation>
158 <brsynth:value value="-1966.8036657706114"/>
159 <brsynth:units value="kilojoule / mole"/>
160 </brsynth:thermo_standard_dg_formation>
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162 </rdf:BRSynth>
163 </rdf:RDF>
164 </annotation>
165 </species>
166 <species metaid="_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc" id="MNXM132" name="MNXM132" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
167 <annotation>
168 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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176 <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]"/>
177 <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)"/>
178 <brsynth:inchikey value="CBIDRCWHNCKSTO-UHFFFAOYSA-N"/>
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182 <brsynth:fba_fraction_shadow_price>
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184 </brsynth:fba_fraction_shadow_price>
185 <brsynth:thermo_standard_dg_formation>
186 <brsynth:value value="-1833.2298341488033"/>
187 <brsynth:units value="kilojoule / mole"/>
188 </brsynth:thermo_standard_dg_formation>
189 </brsynth:brsynth>
190 </rdf:BRSynth>
191 </rdf:RDF>
192 </annotation>
193 </species>
194 <species metaid="_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb" id="MNXM35" name="MNXM35" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
195 <annotation>
196 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
197 <rdf:Description rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
198 <bqbiol:is>
199 <rdf:Bag/>
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201 </rdf:Description>
202 <rdf:BRSynth rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
203 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
204 <brsynth:smiles/>
205 <brsynth:inchi/>
206 <brsynth:inchikey/>
207 <brsynth:fba_biomass_shadow_price>
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209 </brsynth:fba_biomass_shadow_price>
210 <brsynth:fba_fraction_shadow_price>
211 <brsynth:value value="None"/>
212 </brsynth:fba_fraction_shadow_price>
213 <brsynth:thermo_standard_dg_formation>
214 <brsynth:value value="-2172.1728715236113"/>
215 <brsynth:units value="kilojoule / mole"/>
216 </brsynth:thermo_standard_dg_formation>
217 </brsynth:brsynth>
218 </rdf:BRSynth>
219 </rdf:RDF>
220 </annotation>
221 </species>
222 <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="MNXM83" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
223 <annotation>
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233 <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)"/>
234 <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
235 <brsynth:fba_biomass_shadow_price>
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238 <brsynth:fba_fraction_shadow_price>
239 <brsynth:value value="None"/>
240 </brsynth:fba_fraction_shadow_price>
241 <brsynth:thermo_standard_dg_formation>
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243 <brsynth:units value="kilojoule / mole"/>
244 </brsynth:thermo_standard_dg_formation>
245 </brsynth:brsynth>
246 </rdf:BRSynth>
247 </rdf:RDF>
248 </annotation>
249 </species>
250 </listOfSpecies>
251 <listOfParameters>
252 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
253 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
254 </listOfParameters>
255 <listOfReactions>
256 <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">
257 <annotation>
258 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
259 <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
260 <bqbiol:is>
261 <rdf:Bag>
262 <rdf:li rdf:resource="http://identifiers.org/ec-code/2.5.1.29"/>
263 </rdf:Bag>
264 </bqbiol:is>
265 </rdf:Description>
266 <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
267 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
268 <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].[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]&gt;&gt;[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.O=P(O)(O)OP(=O)(O)O"/>
269 <brsynth:rp2_transfo_id value="TRS_0_2_739"/>
270 <brsynth:rule_ids>
271 <brsynth:RR-02-90bcfd187709eb1b-14-F/>
272 </brsynth:rule_ids>
273 <brsynth:tmpl_rxn_ids>
274 <brsynth:MNXR132232/>
275 </brsynth:tmpl_rxn_ids>
276 <brsynth:rule_score value="0.5706379442030705"/>
277 <brsynth:idx_in_path value="1"/>
278 <brsynth:selenzy/>
279 <brsynth:fba_biomass>
280 <brsynth:value value="0.0"/>
281 <brsynth:units value="gDW / gDW / hour"/>
282 </brsynth:fba_biomass>
283 <brsynth:fba_fraction>
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285 <brsynth:units value="milimole / gDW / hour"/>
286 </brsynth:fba_fraction>
287 <brsynth:thermo_dG0_prime>
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289 <brsynth:error value="7.250256007547839"/>
290 <brsynth:units value="kilojoule / mole"/>
291 </brsynth:thermo_dG0_prime>
292 <brsynth:thermo_dGm_prime>
293 <brsynth:value value="-3050.151185208441"/>
294 <brsynth:error value="7.250256007547839"/>
295 <brsynth:units value="kilojoule / mole"/>
296 </brsynth:thermo_dGm_prime>
297 <brsynth:thermo_dG_prime>
298 <brsynth:value value="-3015.9215101389987"/>
299 <brsynth:error value="7.250256007547839"/>
300 <brsynth:units value="kilojoule / mole"/>
301 </brsynth:thermo_dG_prime>
302 <brsynth:thermo_dG>
303 <brsynth:value value="-3734.681829188674"/>
304 <brsynth:error value="7.250256007547839"/>
305 <brsynth:units value="kilojoule / mole"/>
306 </brsynth:thermo_dG>
307 </brsynth:brsynth>
308 </rdf:BRSynth>
309 </rdf:RDF>
310 </annotation>
311 <listOfReactants>
312 <speciesReference species="MNXM132" stoichiometry="1" constant="true"/>
313 <speciesReference species="MNXM83" stoichiometry="1" constant="true"/>
314 </listOfReactants>
315 <listOfProducts>
316 <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
317 <speciesReference species="MNXM11" stoichiometry="3" constant="true"/>
318 </listOfProducts>
319 </reaction>
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341 <brsynth:MNXR111499/>
342 <brsynth:MNXR113543/>
343 <brsynth:MNXR118024/>
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353 <brsynth:fba_fraction>
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355 <brsynth:units value="milimole / gDW / hour"/>
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357 <brsynth:thermo_dG0_prime>
358 <brsynth:value value="-119.13360567395966"/>
359 <brsynth:error value="11.000567449695138"/>
360 <brsynth:units value="kilojoule / mole"/>
361 </brsynth:thermo_dG0_prime>
362 <brsynth:thermo_dGm_prime>
363 <brsynth:value value="-153.36328074340173"/>
364 <brsynth:error value="11.000567449695138"/>
365 <brsynth:units value="kilojoule / mole"/>
366 </brsynth:thermo_dGm_prime>
367 <brsynth:thermo_dG_prime>
368 <brsynth:value value="-119.13360567395966"/>
369 <brsynth:error value="11.000567449695138"/>
370 <brsynth:units value="kilojoule / mole"/>
371 </brsynth:thermo_dG_prime>
372 <brsynth:thermo_dG>
373 <brsynth:value value="-1501.0650763644926"/>
374 <brsynth:error value="11.000567449695138"/>
375 <brsynth:units value="kilojoule / mole"/>
376 </brsynth:thermo_dG>
377 </brsynth:brsynth>
378 </rdf:BRSynth>
379 </rdf:RDF>
380 </annotation>
381 <listOfReactants>
382 <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
383 </listOfReactants>
384 <listOfProducts>
385 <speciesReference species="CMPD_0000000001" stoichiometry="1" constant="true"/>
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442 </rdf:RDF>
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447 </listOfReactants>
448 <listOfProducts>
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450 <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
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452 </reaction>
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523 <groups:member groups:idRef="TARGET_0000000001"/>
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525 <groups:member groups:idRef="MNXM83"/>
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580 <groups:member groups:idRef="TARGET_0000000001"/>
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582 </groups:group>
583 </groups:listOfGroups>
584 </model>
585 </sbml>