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comparison test-data/rp_013_0001_with_thermo.xml @ 0:44e54b56328d draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 24 Nov 2021 09:48:18 +0000
parents
children 21a900eee812
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-1:000000000000 0:44e54b56328d
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="_2db93def850b5b412e9c6bfb2f3ae31a33b90fb03a3777278e0e69de0adbd9b8" id="RP_model_013_0001" name="013_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
4 <listOfCompartments>
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14 <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
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238 <brsynth:units value="kilojoule / mole"/>
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243 <brsynth:units value="kilojoule / mole"/>
244 </brsynth:thermo_dG_prime>
245 <brsynth:thermo_dG>
246 <brsynth:value value="-686.7138625418233"/>
247 <brsynth:error value="7.140374782195817"/>
248 <brsynth:units value="kilojoule / mole"/>
249 </brsynth:thermo_dG>
250 </brsynth:brsynth>
251 </rdf:BRSynth>
252 </rdf:RDF>
253 </annotation>
254 <listOfReactants>
255 <speciesReference species="MNXM1" stoichiometry="3" constant="true"/>
256 <speciesReference species="MNXM188" stoichiometry="1" constant="true"/>
257 <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
258 <speciesReference species="MNXM6" stoichiometry="1" constant="true"/>
259 </listOfReactants>
260 <listOfProducts>
261 <speciesReference species="CMPD_0000000003" stoichiometry="1" constant="true"/>
262 <speciesReference species="CMPD_0000000004" stoichiometry="1" constant="true"/>
263 <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
264 <speciesReference species="MNXM15" stoichiometry="1" constant="true"/>
265 <speciesReference species="MNXM5" stoichiometry="1" constant="true"/>
266 </listOfProducts>
267 </reaction>
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281 <brsynth:rp2_transfo_id value="TRS_0_1_3"/>
282 <brsynth:rule_ids/>
283 <brsynth:tmpl_rxn_ids/>
284 <brsynth:rule_score value="0.5683242688496836"/>
285 <brsynth:idx_in_path value="2"/>
286 <brsynth:thermo_dG0_prime>
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288 <brsynth:error value="9.81314488510582"/>
289 <brsynth:units value="kilojoule / mole"/>
290 </brsynth:thermo_dG0_prime>
291 <brsynth:thermo_dGm_prime>
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293 <brsynth:error value="9.81314488510582"/>
294 <brsynth:units value="kilojoule / mole"/>
295 </brsynth:thermo_dGm_prime>
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298 <brsynth:error value="9.81314488510582"/>
299 <brsynth:units value="kilojoule / mole"/>
300 </brsynth:thermo_dG_prime>
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302 <brsynth:value value="56.91941717742026"/>
303 <brsynth:error value="9.81314488510582"/>
304 <brsynth:units value="kilojoule / mole"/>
305 </brsynth:thermo_dG>
306 </brsynth:brsynth>
307 </rdf:BRSynth>
308 </rdf:RDF>
309 </annotation>
310 <listOfReactants>
311 <speciesReference species="CMPD_0000000003" stoichiometry="2" constant="true"/>
312 <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
313 </listOfReactants>
314 <listOfProducts>
315 <speciesReference species="MNXM1" stoichiometry="1" constant="true"/>
316 <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
317 </listOfProducts>
318 </reaction>
319 <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC__10000_0" fbc:upperFluxBound="BRS_FBC_10000_0">
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327 </bqbiol:is>
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332 <brsynth:rp2_transfo_id value="TRS_0_0_0"/>
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337 <brsynth:thermo_dG0_prime>
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339 <brsynth:error value="10.250976801552927"/>
340 <brsynth:units value="kilojoule / mole"/>
341 </brsynth:thermo_dG0_prime>
342 <brsynth:thermo_dGm_prime>
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344 <brsynth:error value="10.250976801552927"/>
345 <brsynth:units value="kilojoule / mole"/>
346 </brsynth:thermo_dGm_prime>
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350 <brsynth:units value="kilojoule / mole"/>
351 </brsynth:thermo_dG_prime>
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354 <brsynth:error value="10.250976801552927"/>
355 <brsynth:units value="kilojoule / mole"/>
356 </brsynth:thermo_dG>
357 </brsynth:brsynth>
358 </rdf:BRSynth>
359 </rdf:RDF>
360 </annotation>
361 <listOfReactants>
362 <speciesReference species="CMPD_0000000004" stoichiometry="3" constant="true"/>
363 <speciesReference species="MNXM4" stoichiometry="1" constant="true"/>
364 <speciesReference species="MNXM6" stoichiometry="1" constant="true"/>
365 </listOfReactants>
366 <listOfProducts>
367 <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
368 <speciesReference species="MNXM5" stoichiometry="1" constant="true"/>
369 </listOfProducts>
370 </reaction>
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372 <groups:listOfGroups>
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380 <brsynth:error value="22.459032062576664"/>
381 <brsynth:units value="kilojoule / mole"/>
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383 <brsynth:thermo_dGm_prime>
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386 <brsynth:units value="kilojoule / mole"/>
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388 <brsynth:thermo_dG_prime>
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391 <brsynth:units value="kilojoule / mole"/>
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393 <brsynth:thermo_dG>
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395 <brsynth:error value="22.459032062576664"/>
396 <brsynth:units value="kilojoule / mole"/>
397 </brsynth:thermo_dG>
398 <brsynth:global_score value="-1"/>
399 </brsynth:brsynth>
400 </rdf:BRSynth>
401 </rdf:RDF>
402 </annotation>
403 <groups:listOfMembers>
404 <groups:member groups:idRef="rxn_1"/>
405 <groups:member groups:idRef="rxn_2"/>
406 <groups:member groups:idRef="rxn_3"/>
407 </groups:listOfMembers>
408 </groups:group>
409 <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">
410 <annotation>
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415 </rdf:RDF>
416 </annotation>
417 <groups:listOfMembers>
418 <groups:member groups:idRef="CMPD_0000000004"/>
419 <groups:member groups:idRef="CMPD_0000000003"/>
420 </groups:listOfMembers>
421 </groups:group>
422 <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
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425 <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">
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428 </rdf:RDF>
429 </annotation>
430 <groups:listOfMembers>
431 <groups:member groups:idRef="MNXM4"/>
432 <groups:member groups:idRef="CMPD_0000000004"/>
433 <groups:member groups:idRef="MNXM6"/>
434 <groups:member groups:idRef="CMPD_0000000003"/>
435 <groups:member groups:idRef="MNXM164"/>
436 <groups:member groups:idRef="TARGET_0000000001"/>
437 </groups:listOfMembers>
438 </groups:group>
439 <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
440 <annotation>
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442 <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
443 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
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445 </rdf:RDF>
446 </annotation>
447 <groups:listOfMembers>
448 <groups:member groups:idRef="MNXM1"/>
449 <groups:member groups:idRef="MNXM13"/>
450 <groups:member groups:idRef="MNXM2"/>
451 <groups:member groups:idRef="MNXM5"/>
452 </groups:listOfMembers>
453 </groups:group>
454 <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
455 <annotation>
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457 <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
458 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
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460 </rdf:RDF>
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463 <groups:member groups:idRef="MNXM4"/>
464 <groups:member groups:idRef="MNXM6"/>
465 <groups:member groups:idRef="MNXM2"/>
466 <groups:member groups:idRef="MNXM1"/>
467 <groups:member groups:idRef="MNXM13"/>
468 <groups:member groups:idRef="MNXM164"/>
469 <groups:member groups:idRef="MNXM5"/>
470 </groups:listOfMembers>
471 </groups:group>
472 <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection">
473 <annotation>
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475 <rdf:BRSynth rdf:about="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8">
476 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
477 </rdf:BRSynth>
478 </rdf:RDF>
479 </annotation>
480 </groups:group>
481 </groups:listOfGroups>
482 </model>
483 </sbml>