| Previous changeset 0:98d925a75257 (2021-11-23) Next changeset 2:d5c53a916005 (2022-04-15) |
|
Commit message:
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty" |
|
modified:
rpcompletion.xml test-data/rp_001_0001.xml test-data/rp_001_0006.xml test-data/rp_001_0011.xml test-data/rp_002_0001.xml test-data/rp_002_0011.xml test-data/rp_002_0021.xml test-data/rp_003_0001.xml test-data/rp_003_0131.xml test-data/rp_003_0261.xml |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 rpcompletion.xml --- a/rpcompletion.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/rpcompletion.xml Wed Feb 09 16:05:48 2022 +0000 |
| b |
| @@ -1,7 +1,10 @@ -<tool id="rpCompletion" name="Complete Reactions" version="5.9.2"> +<tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="19.09"> <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description> + <macros> + <token name="@TOOL_VERSION@">5.12.1</token> + </macros> <requirements> - <requirement type="package" version="5.9.2">rptools</requirement> + <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" description="Could not Xref compartment_id" /> @@ -84,7 +87,7 @@ Version ---------- -5.9.2 +5.12.1 Authors ------- |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_001_0001.xml --- a/test-data/rp_001_0001.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_001_0001.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,78 +23,6 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n- <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)"/>\n- <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" h'..b'th.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -310,8 +310,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -323,11 +323,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n- <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n+ <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -339,8 +339,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n@@ -353,9 +353,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM132"/>\n+ <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_001_0006.xml --- a/test-data/rp_001_0006.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_001_0006.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,96 +23,6 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- '..b'/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n </listOfSpecies>\n <listOfParameters>\n <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>\n@@ -310,8 +310,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -323,11 +323,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n- <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n+ <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -339,9 +339,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM11"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -353,9 +353,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM132"/>\n+ <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_001_0011.xml --- a/test-data/rp_001_0011.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_001_0011.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,60 +23,6 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n- <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)"/>\n- <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="[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]"/>\n- <brs'..b'bout="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -310,8 +310,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -323,11 +323,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n- <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n+ <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -353,9 +353,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM132"/>\n <groups:member groups:idRef="MNXM11"/>\n- <groups:member groups:idRef="MNXM132"/>\n+ <groups:member groups:idRef="MNXM83"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_002_0001.xml --- a/test-data/rp_002_0001.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_002_0001.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,19 +23,19 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n+ <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n+ <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n+ <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -59,19 +59,19 @@\n </rdf:RDF>\n </annotation>\n </species>\n- <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n+ <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n- <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)"/>\n- <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ <brsynth:smiles/>\n+ <brsynth:inchi/>\n+ <brsynth:inchikey/>\n </brsynth:brsynth>\n '..b' <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n+ <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -313,8 +313,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -326,11 +326,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -342,8 +342,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n@@ -356,9 +356,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM100"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="MNXM100"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_002_0011.xml --- a/test-data/rp_002_0011.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_002_0011.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,37 +23,19 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">\n+ <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">\n+ <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n+ <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n+ <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n+ <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -77,24 +59,6 @@\n </rdf:RDF>\n </annotation>\n </species>\n- <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211d'..b'brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n </listOfSpecies>\n <listOfParameters>\n <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>\n@@ -313,8 +313,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -326,11 +326,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -342,9 +342,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM11"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -356,9 +356,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM100"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="MNXM100"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_002_0021.xml --- a/test-data/rp_002_0021.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_002_0021.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,37 +23,19 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n- <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)"/>\n- <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n+ <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n+ <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -77,19 +59,55 @@\n </rdf:RDF>\n </annotation>\n </species>\n- <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n '..b't="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n+ <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]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -313,8 +313,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -326,11 +326,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="MNXM100"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -356,9 +356,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM100"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="MNXM100"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_003_0001.xml --- a/test-data/rp_003_0001.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_003_0001.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,19 +23,19 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n+ <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n+ <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n+ <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -59,6 +59,60 @@\n </rdf:RDF>\n </annotation>\n </species>\n+ <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles/>\n+ <brsynth:inchi/>\n+ <brsynth:inchikey/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f30093'..b'([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]"/>\n- <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"/>\n- <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n </listOfSpecies>\n <listOfParameters>\n <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>\n@@ -351,8 +351,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -364,11 +364,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM34"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -380,8 +380,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM24"/>\n </groups:listOfMembers>\n </groups:group>\n@@ -394,9 +394,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM34"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM34"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_003_0131.xml --- a/test-data/rp_003_0131.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_003_0131.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,6 +23,96 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n+ <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n+ <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n+ <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles/>\n+ <brsynth:inchi/>\n+ <brsynth:inchikey/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="[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]"/>\n+ <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"/>\n+ <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" init'..b' <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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"/>\n- <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n </listOfSpecies>\n <listOfParameters>\n <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>\n@@ -351,8 +351,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -364,11 +364,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM34"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -380,9 +380,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM36"/>\n <groups:member groups:idRef="MNXM8975"/>\n- <groups:member groups:idRef="MNXM11"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n@@ -394,9 +394,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM34"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM34"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |
| b |
| diff -r 98d925a75257 -r b8242cf18cc0 test-data/rp_003_0261.xml --- a/test-data/rp_003_0261.xml Tue Nov 23 13:45:45 2021 +0000 +++ b/test-data/rp_003_0261.xml Wed Feb 09 16:05:48 2022 +0000 |
| [ |
| b'@@ -23,37 +23,19 @@\n </compartment>\n </listOfCompartments>\n <listOfSpecies>\n- <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n <annotation>\n <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <bqbiol:is>\n <rdf:Bag/>\n </bqbiol:is>\n </rdf:Description>\n- <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <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]"/>\n- <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)"/>\n- <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n- </brsynth:brsynth>\n- </rdf:BRSynth>\n- </rdf:RDF>\n- </annotation>\n- </species>\n- <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n- <annotation>\n- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n- <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <bqbiol:is>\n- <rdf:Bag/>\n- </bqbiol:is>\n- </rdf:Description>\n- <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">\n- <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>\n- <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)"/>\n- <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>\n+ <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>\n+ <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>\n+ <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -77,37 +59,37 @@\n </rdf:RDF>\n </annotation>\n </species>\n- <species metaid="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="(2E,6E)-farnesyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" const'..b':about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n- <brsynth:smiles/>\n- <brsynth:inchi/>\n- <brsynth:inchikey/>\n+ <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]"/>\n+ <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)"/>\n+ <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="(2E,6E)-farnesyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <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])[H]"/>\n+ <brsynth:inchi value="InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)"/>\n+ <brsynth:inchikey value="VWFJDQUYCIWHTN-UHFFFAOYSA-N"/>\n </brsynth:brsynth>\n </rdf:BRSynth>\n </rdf:RDF>\n@@ -351,8 +351,8 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="CMPD_0000000001"/>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n@@ -364,11 +364,11 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000001"/>\n <groups:member groups:idRef="MNXM83"/>\n- <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n <groups:member groups:idRef="MNXM34"/>\n- <groups:member groups:idRef="CMPD_0000000001"/>\n </groups:listOfMembers>\n </groups:group>\n <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n@@ -394,9 +394,9 @@\n </rdf:RDF>\n </annotation>\n <groups:listOfMembers>\n- <groups:member groups:idRef="MNXM34"/>\n <groups:member groups:idRef="MNXM11"/>\n <groups:member groups:idRef="MNXM83"/>\n+ <groups:member groups:idRef="MNXM34"/>\n </groups:listOfMembers>\n </groups:group>\n </groups:listOfGroups>\n' |