Mercurial > repos > tduigou > rptools_rpthermo

comparison test-data/pathway.xml @ 0:e9d05fc83186 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
author tduigou
date Tue, 28 Mar 2023 12:08:14 +0000
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-1:000000000000 0:e9d05fc83186
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="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" 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>
7 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
27 <annotation>
28 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
29 <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
30 <bqbiol:is>
31 <rdf:Bag/>
32 </bqbiol:is>
33 </rdf:Description>
34 <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
35 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
36 <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
37 <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/>
38 <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/>
39 <brsynth:fba_biomass_shadow_price>
40 <brsynth:value value="-0.0"/>
41 </brsynth:fba_biomass_shadow_price>
42 <brsynth:fba_fraction_shadow_price>
43 <brsynth:value value="-1.0"/>
44 </brsynth:fba_fraction_shadow_price>
45 <brsynth:thermo_standard_dg_formation>
46 <brsynth:value value="208.92559504464236"/>
47 <brsynth:units value="kilojoule / mole"/>
48 </brsynth:thermo_standard_dg_formation>
49 </brsynth:brsynth>
50 </rdf:BRSynth>
51 </rdf:RDF>
52 </annotation>
53 </species>
54 <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
55 <annotation>
56 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
57 <rdf:Description rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
58 <bqbiol:is>
59 <rdf:Bag/>
60 </bqbiol:is>
61 </rdf:Description>
62 <rdf:BRSynth rdf:about="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
63 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
64 <brsynth:smiles value="[H+]"/>
65 <brsynth:inchi value="InChI=1S/p+1"/>
66 <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
67 <brsynth:fba_biomass_shadow_price>
68 <brsynth:value value="None"/>
69 </brsynth:fba_biomass_shadow_price>
70 <brsynth:fba_fraction_shadow_price>
71 <brsynth:value value="None"/>
72 </brsynth:fba_fraction_shadow_price>
73 <brsynth:thermo_standard_dg_formation>
74 <brsynth:value value="NaN"/>
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="_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16" id="CMPD_0000000002" name="CMPD_0000000002" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
83 <annotation>
84 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
85 <rdf:Description rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16">
86 <bqbiol:is>
87 <rdf:Bag/>
88 </bqbiol:is>
89 </rdf:Description>
90 <rdf:BRSynth rdf:about="#_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16">
91 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
92 <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
93 <brsynth:inchi value="InChI=1S/C9H8O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-7H,(H,10,11)"/>
94 <brsynth:inchikey value="WBYWAXJHAXSJNI-UHFFFAOYSA-N"/>
95 <brsynth:fba_biomass_shadow_price>
96 <brsynth:value value="-0.0009404190769783985"/>
97 </brsynth:fba_biomass_shadow_price>
98 <brsynth:fba_fraction_shadow_price>
99 <brsynth:value value="-1.0057339449541285"/>
100 </brsynth:fba_fraction_shadow_price>
101 <brsynth:thermo_standard_dg_formation>
102 <brsynth:value value="-127.1962856224608"/>
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="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
111 <annotation>
112 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
113 <rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
114 <bqbiol:is>
115 <rdf:Bag/>
116 </bqbiol:is>
117 </rdf:Description>
118 <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
119 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
120 <brsynth:smiles value="N"/>
121 <brsynth:inchi value="InChI=1S/H3N/h1H3"/>
122 <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
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="-81.91776181003092"/>
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="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
139 <annotation>
140 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
141 <rdf:Description rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
142 <bqbiol:is>
143 <rdf:Bag/>
144 </bqbiol:is>
145 </rdf:Description>
146 <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
147 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
148 <brsynth:smiles value="O=C=O"/>
149 <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
150 <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
151 <brsynth:fba_biomass_shadow_price>
152 <brsynth:value value="None"/>
153 </brsynth:fba_biomass_shadow_price>
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="-386.0000000000019"/>
159 <brsynth:units value="kilojoule / mole"/>
160 </brsynth:thermo_standard_dg_formation>
161 </brsynth:brsynth>
162 </rdf:BRSynth>
163 </rdf:RDF>
164 </annotation>
165 </species>
166 <species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" 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/">
169 <rdf:Description rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
170 <bqbiol:is>
171 <rdf:Bag/>
172 </bqbiol:is>
173 </rdf:Description>
174 <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
175 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
176 <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
177 <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)"/>
178 <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/>
179 <brsynth:fba_biomass_shadow_price>
180 <brsynth:value value="None"/>
181 </brsynth:fba_biomass_shadow_price>
182 <brsynth:fba_fraction_shadow_price>
183 <brsynth:value value="None"/>
184 </brsynth:fba_fraction_shadow_price>
185 <brsynth:thermo_standard_dg_formation>
186 <brsynth:value value="-207.07052002003908"/>
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 </listOfSpecies>
195 <listOfParameters>
196 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
197 <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
198 </listOfParameters>
199 <listOfReactions>
200 <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">
201 <annotation>
202 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
203 <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
204 <bqbiol:is>
205 <rdf:Bag>
206 <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.25"/>
207 <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.24"/>
208 </rdf:Bag>
209 </bqbiol:is>
210 </rdf:Description>
211 <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
212 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
213 <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]&gt;&gt;[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].N"/>
214 <brsynth:rp2_transfo_id value="TRS_0_1_1"/>
215 <brsynth:rule_id value="RR-02-3545d6ed74034d56-16-F"/>
216 <brsynth:tmpl_rxn_ids>
217 <brsynth:MNXR106649/>
218 <brsynth:MNXR131345/>
219 </brsynth:tmpl_rxn_ids>
220 <brsynth:rule_score value="0.5869134225065102"/>
221 <brsynth:idx_in_path value="1"/>
222 <brsynth:selenzy/>
223 <brsynth:fba_biomass>
224 <brsynth:value value="0.0"/>
225 <brsynth:units value="gDW / gDW / hour"/>
226 </brsynth:fba_biomass>
227 <brsynth:fba_fraction>
228 <brsynth:value value="1.3666677776240859"/>
229 <brsynth:units value="milimole / gDW / hour"/>
230 </brsynth:fba_fraction>
231 <brsynth:thermo_dG0_prime>
232 <brsynth:value value="-3.619165315209898"/>
233 <brsynth:error value="0.5540714922475698"/>
234 <brsynth:units value="kilojoule / mole"/>
235 </brsynth:thermo_dG0_prime>
236 <brsynth:thermo_dGm_prime>
237 <brsynth:value value="-20.73400284993093"/>
238 <brsynth:error value="0.5540714922475698"/>
239 <brsynth:units value="kilojoule / mole"/>
240 </brsynth:thermo_dGm_prime>
241 <brsynth:thermo_dG_prime>
242 <brsynth:value value="-3.619165315209898"/>
243 <brsynth:error value="0.5540714922475698"/>
244 <brsynth:units value="kilojoule / mole"/>
245 </brsynth:thermo_dG_prime>
246 <brsynth:thermo_dG>
247 <brsynth:value value="-2.0435274124526472"/>
248 <brsynth:error value="0.5540714922475698"/>
249 <brsynth:units value="kilojoule / mole"/>
250 </brsynth:thermo_dG>
251 </brsynth:brsynth>
252 </rdf:BRSynth>
253 </rdf:RDF>
254 </annotation>
255 <listOfReactants>
256 <speciesReference species="MNXM97" stoichiometry="1" constant="true"/>
257 </listOfReactants>
258 <listOfProducts>
259 <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/>
260 <speciesReference species="MNXM15" stoichiometry="1" constant="true"/>
261 </listOfProducts>
262 </reaction>
263 <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">
264 <annotation>
265 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
266 <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
267 <bqbiol:is>
268 <rdf:Bag>
269 <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.102"/>
270 </rdf:Bag>
271 </bqbiol:is>
272 </rdf:Description>
273 <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
274 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
275 <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].[H+]&gt;&gt;O=C=O.[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
276 <brsynth:rp2_transfo_id value="TRS_0_0_0"/>
277 <brsynth:rule_id value="RR-02-caf68bc1dcd9ce0f-16-F"/>
278 <brsynth:tmpl_rxn_ids>
279 <brsynth:MNXR114372/>
280 </brsynth:tmpl_rxn_ids>
281 <brsynth:rule_score value="1.0"/>
282 <brsynth:idx_in_path value="2"/>
283 <brsynth:selenzy/>
284 <brsynth:fba_biomass>
285 <brsynth:value value="0.0"/>
286 <brsynth:units value="gDW / gDW / hour"/>
287 </brsynth:fba_biomass>
288 <brsynth:fba_fraction>
289 <brsynth:value value="1.3666677776240859"/>
290 <brsynth:units value="milimole / gDW / hour"/>
291 </brsynth:fba_fraction>
292 <brsynth:thermo_dG0_prime>
293 <brsynth:value value="-5.570411694686811"/>
294 <brsynth:error value="5.365139708628456"/>
295 <brsynth:units value="kilojoule / mole"/>
296 </brsynth:thermo_dG0_prime>
297 <brsynth:thermo_dGm_prime>
298 <brsynth:value value="-22.685249229407844"/>
299 <brsynth:error value="5.365139708628456"/>
300 <brsynth:units value="kilojoule / mole"/>
301 </brsynth:thermo_dGm_prime>
302 <brsynth:thermo_dG_prime>
303 <brsynth:value value="-5.570411694686811"/>
304 <brsynth:error value="5.365139708628456"/>
305 <brsynth:units value="kilojoule / mole"/>
306 </brsynth:thermo_dG_prime>
307 <brsynth:thermo_dG>
308 <brsynth:value value="-49.87811933289868"/>
309 <brsynth:error value="5.365139708628456"/>
310 <brsynth:units value="kilojoule / mole"/>
311 </brsynth:thermo_dG>
312 </brsynth:brsynth>
313 </rdf:BRSynth>
314 </rdf:RDF>
315 </annotation>
316 <listOfReactants>
317 <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/>
318 <speciesReference species="MNXM1" stoichiometry="1" constant="true"/>
319 </listOfReactants>
320 <listOfProducts>
321 <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
322 <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
323 </listOfProducts>
324 </reaction>
325 </listOfReactions>
326 <groups:listOfGroups>
327 <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
328 <annotation>
329 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
330 <rdf:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">
331 <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
332 <brsynth:fba_biomass>
333 <brsynth:value value="0.8769972144269752"/>
334 <brsynth:units value="gDW / gDW / hour"/>
335 </brsynth:fba_biomass>
336 <brsynth:fba_fraction>
337 <brsynth:value value="1.3666677776240859"/>
338 <brsynth:units value="milimole / gDW / hour"/>
339 </brsynth:fba_fraction>
340 <brsynth:thermo_dG0_prime>
341 <brsynth:value value="-9.189577009896766"/>
342 <brsynth:error value="5.336452836371218"/>
343 <brsynth:units value="kilojoule / mole"/>
344 </brsynth:thermo_dG0_prime>
345 <brsynth:thermo_dGm_prime>
346 <brsynth:value value="-43.41925207933883"/>
347 <brsynth:error value="5.336452836371218"/>
348 <brsynth:units value="kilojoule / mole"/>
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444 </sbml>