| Next changeset 1:ceab7bc46740 (2022-01-03) |
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Commit message:
Uploaded rpextractsink v5.9.2 |
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added:
rpextractsink/rpextractsink.xml rpextractsink/test-data/E.coli.sbml rpextractsink/test-data/sink.csv |
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| diff -r 000000000000 -r f664f3c3aca8 rpextractsink/rpextractsink.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpextractsink/rpextractsink.xml Fri Nov 19 13:56:03 2021 +0000 |
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| @@ -0,0 +1,142 @@ +<tool id="rpExtractSink" name="Sink from SBML" version="5.9.2"> + <description>Generate the RetroPath2.0 sink file from an SBML input</description> + <requirements> + <requirement type="package" version="5.9.2">rptools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python -m rptools.rpextractsink + '$input' + '$sink' + --compartment_id '$adv.compartment_id' + #if str($remove_dead_end) == "true": + --remove_dead_end + #end if + ]]></command> + <inputs> + <param name="input" type="data" format="sbml" optional="false" label="SBML model" /> + <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="compartment_id" type="text" value="MNXC3" label="SBML compartment ID" /> + </section> + </inputs> + <outputs> + <data name="sink" format="csv" label="${tool.name} - ${input.name}" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with default parameters --> + <param name="input" value="E.coli.sbml" /> + <output name="sink" file="sink.csv" ftype="csv" compare="diff"/> + </test> + </tests> + <help><![CDATA[ + +Sink from SBML +================= + +Sink refers to the collection of chemical species used by the restrosynthesis algorithm of RetroPath2.0 to finish metabolic route exploration. This tool uses an SBML file of the desired chassis organism, parses all the molecules within a specified compartment (example: cytoplasm, Golgi apparatus, nucleus, etc) and uses its MIRIAM annotation to find their InChI structures. You can use "Remove dead-end metabolites using FVA evaluation? to conduct Flux Variability Analysis to remove metabolites that lack the requisite flux that would account for their production or consumption within the metabolic network. + +In the advanced options, one can specify the compartment from which the tool will extract the chemical species. The default is MNXC3, the MetaNetX code for the cytoplasm. If the user wishes to upload an SBML file from another source, then this value must be changed. + +The results are written to a RetroPath2.0 friendly CSV file format that can be used as sink input. + + +Input +----- + +Required: + +* **input_sbml**\ : (string) Path to the input SBML file + +Advanced options: + +* **remove_dead_end**\ : (boolean, default: True) Perform FVA evaluation to remove dead end metabolites +* **compartment_id**\ : (string, default: MNXC3) Specify the compartment from which to extract the sink molecules. The default are for MetaNetX files + +Output +------ + +* **output_sink**\ : (string) Path to the output csv file + + +Project Links +--------------------- + +* `GitHub <https://github.com/brsynth/rptools>`_ + +Version +---------- + +5.9.2 + + +Authors +------- + + +* **Melchior du Lac** +* Joan Hérisson + +License +------- + +`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ + +Acknowledgments +--------------- + + +* Thomas Duigou + + + + ]]></help> + <citations> + <citation type="bibtex"> +@article{le2005minimum, + title={Minimum information requested in the annotation of biochemical models (MIRIAM)}, + author={Le Nov{\`e}re, Nicolas and Finney, Andrew and Hucka, Michael and Bhalla, Upinder S and Campagne, Fabien and Collado-Vides, Julio and Crampin, Edmund J and Halstead, Matt and Klipp, Edda and Mendes, Pedro and others}, + journal={Nature biotechnology}, + volume={23}, + number={12}, + pages={1509--1515}, + year={2005}, + publisher={Nature Publishing Group} +} + </citation> + <citation type="bibtex"> +@article{delepine2018retropath2, + title={RetroPath2. 0: a retrosynthesis workflow for metabolic engineers}, + author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup}, + journal={Metabolic engineering}, + volume={45}, + pages={158--170}, + year={2018}, + publisher={Elsevier}} + </citation> + <citation type="bibtex"> +@article{ebrahim2013cobrapy, + title={COBRApy: COnstraints-based reconstruction and analysis for python}, + author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R}, + journal={BMC systems biology}, + volume={7}, + number={1}, + pages={74}, + year={2013}, + publisher={Springer} +} + </citation> + <citation type="bibtex"> +@article{bornstein2008libsbml, + title={LibSBML: an API library for SBML}, + author={Bornstein, Benjamin J and Keating, Sarah M and Jouraku, Akiya and Hucka, Michael}, + journal={Bioinformatics}, + volume={24}, + number={6}, + pages={880--881}, + year={2008}, + publisher={Oxford University Press} +} + </citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r f664f3c3aca8 rpextractsink/test-data/E.coli.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpextractsink/test-data/E.coli.sbml Fri Nov 19 13:56:03 2021 +0000 |
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| b'@@ -0,0 +1,132876 @@\n+<?xml version=\'1.0\' encoding=\'UTF-8\' standalone=\'no\'?>\n+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false" level="3" version="1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:html="http://www.w3.org/1999/xhtml">\n+ <model fbc:strict="true" id="bigg_iAF1260" metaid="_533bc6ed-544a-488c-bad6-6a5f38656d9c" name="Escherichia coli str. K-12 substr. MG1655" sboTerm="SBO:0000624">\n+ <notes>\n+ <html:p>ID: bigg_iAF1260</html:p><html:p>Description: Escherichia coli str. K-12 substr. MG1655</html:p><html:p>LB: -999999.0</html:p><html:p>UB: 999999.0</html:p><html:p>MNXref Version: 2018/09/14</html:p><html:p>Processed Date: 2018/09/20</html:p><html:p>Source ID: iAF1260</html:p><html:p>Source Reference: PMID:26476456</html:p><html:p>Source Link: http://bigg.ucsd.edu</html:p><html:p>Taxid: 83333</html:p>\n+ </notes>\n+ <annotation>\n+\t<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+\t<rdf:Description rdf:about="#_533bc6ed-544a-488c-bad6-6a5f38656d9c">\n+\t<bqbiol:hasTaxon>\n+\t<rdf:Bag>\n+\t<rdf:li rdf:resource="http://identifiers.org/taxonomy/83333"/>\n+\t</rdf:Bag>\n+\t</bqbiol:hasTaxon>\n+\t</rdf:Description>\n+\t</rdf:RDF>\n+\t</annotation>\n+ <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" fbc:activeObjective="obj_biomass">\n+ <fbc:objective fbc:id="obj_biomass" fbc:type="maximize">\n+ <fbc:listOfFluxObjectives>\n+ <fbc:fluxObjective fbc:coefficient="1" fbc:reaction="biomass"/>\n+ </fbc:listOfFluxObjectives>\n+ </fbc:objective>\n+ </fbc:listOfObjectives>\n+ <fbc:listOfGeneProducts xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2">\n+ <fbc:geneProduct fbc:id="G_OMPC_ECOLI" fbc:label="OMPC_ECOLI" fbc:name="OMPC_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_OMPF_ECOLI" fbc:label="OMPF_ECOLI" fbc:name="OMPF_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_OMPN_ECOLI" fbc:label="OMPN_ECOLI" fbc:name="OMPN_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_PHOE_ECOLI" fbc:label="PHOE_ECOLI" fbc:name="PHOE_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_TSX_ECOLI" fbc:label="TSX_ECOLI" fbc:name="TSX_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_PDXK_ECOLI" fbc:label="PDXK_ECOLI" fbc:name="PDXK_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_THID_ECOLI" fbc:label="THID_ECOLI" fbc:name="THID_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_FABB_ECOLI" fbc:label="FABB_ECOLI" fbc:name="FABB_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_FABF_ECOLI" fbc:label="FABF_ECOLI" fbc:name="FABF_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_PA1_ECOLI" fbc:label="PA1_ECOLI" fbc:name="PA1_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_TRPGD_ECOLI" fbc:label="TRPGD_ECOLI" fbc:name="TRPGD_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_MANC_ECOLI" fbc:label="MANC_ECOLI" fbc:name="MANC_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_FABA_ECOLI" fbc:label="FABA_ECOLI" fbc:name="FABA_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_FABZ_ECOLI" fbc:label="FABZ_ECOLI" fbc:name="FABZ_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_HIS1_ECOLI" fbc:label="HIS1_ECOLI" fbc:name="HIS1_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_PGSA_ECOLI" fbc:label="PGSA_ECOLI" fbc:name="PGSA_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_ACTP_ECOLI" fbc:label="ACTP_ECOLI" fbc:name="ACTP_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_LPLT_ECOLI" fbc:label="LPLT_ECOLI" fbc:name="LPLT_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_INGK_ECOLI" fbc:label="INGK_ECOLI" fbc:name="INGK_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_MSBA_ECOLI" fbc:label="MSBA_ECOLI" fbc:name="MSBA_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_TESA_ECOLI" fbc:label="TESA_ECOLI" fbc:name="TESA_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_FSAA_ECOLI" fbc:label="FSAA_ECOLI" fbc:name="FSAA_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_FSAB_ECOLI" fbc:label="FSAB_ECOLI" fbc:name="FSAB_ECOLI"/>\n+ <fbc:geneProduct fbc:id="G_PUUA_ECOLI" fbc:label="PUUA_ECOLI" fbc:name'..b'\n+\t</bqbiol:is>\n+\t</rdf:Description>\n+\t</rdf:RDF>\n+\t</annotation>\n+ <fbc:geneProductAssociation xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2">\n+ <fbc:geneProductRef fbc:geneProduct="G_DAPD_ECOLI"/>\n+ </fbc:geneProductAssociation>\n+ <listOfReactants>\n+ <speciesReference constant="true" species="MNXM2__64__MNXC3" stoichiometry="1"/>\n+ <speciesReference constant="true" species="MNXM480__64__MNXC3" stoichiometry="1"/>\n+ <speciesReference constant="true" species="MNXM92__64__MNXC3" stoichiometry="1"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference constant="true" species="MNXM12__64__MNXC3" stoichiometry="1"/>\n+ <speciesReference constant="true" species="MNXM1563__64__MNXC3" stoichiometry="1"/>\n+ </listOfProducts>\n+ </reaction>\n+ <reaction fast="false" fbc:lowerFluxBound="B_0" fbc:upperFluxBound="B_999999" id="RFFF0833A" metaid="_8b229e2e-f244-4e35-aa3b-4b6df47ea582" reversible="false" sboTerm="SBO:0000375">\n+ <notes>\n+ <html:p>SOURCE: R_RNTR3c</html:p><html:p>REACTION: MNXR104077</html:p><html:p>XREFS: bigg:RNTR3c;bigg:R_RNTR3c;deprecated:MNXR32351</html:p><html:p>GENE ASSOCIATION: (bact:FENR_ECOLI and bact:FLAV_ECOLI and bact:NRDD_ECOLI and bact:NRDG_ECOLI) or (bact:FENR_ECOLI and bact:FLAW_ECOLI and bact:NRDD_ECOLI and bact:NRDG_ECOLI) or (bact:FLAV_ECOLI and bact:NRDD_ECOLI) or (bact:FLAW_ECOLI and bact:NRDD_ECOLI)</html:p><html:p>PROP BC-b: oned</html:p><html:p>PROP BC-p: asso</html:p><html:p>PROP BC-t: enzy</html:p>\n+ </notes>\n+ <annotation>\n+\t<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+\t<rdf:Description rdf:about="#_8b229e2e-f244-4e35-aa3b-4b6df47ea582">\n+\t<bqbiol:is>\n+\t<rdf:Bag>\n+\t<rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR104077"/>\n+\t<rdf:li rdf:resource="http://identifiers.org/bigg.reaction/RNTR3c"/>\n+\t<rdf:li rdf:resource="http://identifiers.org/bigg.reaction/R_RNTR3c"/>\n+\t</rdf:Bag>\n+\t</bqbiol:is>\n+\t</rdf:Description>\n+\t</rdf:RDF>\n+\t</annotation>\n+ <fbc:geneProductAssociation xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2">\n+ <fbc:or>\n+ <fbc:and>\n+ <fbc:geneProductRef fbc:geneProduct="G_FENR_ECOLI"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_FLAV_ECOLI"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_NRDD_ECOLI"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_NRDG_ECOLI"/>\n+ </fbc:and>\n+ <fbc:and>\n+ <fbc:geneProductRef fbc:geneProduct="G_FENR_ECOLI"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_FLAW_ECOLI"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_NRDD_ECOLI"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_NRDG_ECOLI"/>\n+ </fbc:and>\n+ <fbc:and>\n+ <fbc:geneProductRef fbc:geneProduct="G_FLAV_ECOLI"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_NRDD_ECOLI"/>\n+ </fbc:and>\n+ <fbc:and>\n+ <fbc:geneProductRef fbc:geneProduct="G_FLAW_ECOLI"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_NRDD_ECOLI"/>\n+ </fbc:and>\n+ </fbc:or>\n+ </fbc:geneProductAssociation>\n+ <listOfReactants>\n+ <speciesReference constant="true" species="MNXM3707__64__MNXC3" stoichiometry="1"/>\n+ <speciesReference constant="true" species="MNXM63__64__MNXC3" stoichiometry="1"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference constant="true" species="MNXM2__64__MNXC3" stoichiometry="1"/>\n+ <speciesReference constant="true" species="MNXM360__64__MNXC3" stoichiometry="1"/>\n+ <speciesReference constant="true" species="MNXM4076__64__MNXC3" stoichiometry="1"/>\n+ </listOfProducts>\n+ </reaction>\n+ </listOfReactions>\n+ </model>\n+</sbml>\n' |
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| diff -r 000000000000 -r f664f3c3aca8 rpextractsink/test-data/sink.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpextractsink/test-data/sink.csv Fri Nov 19 13:56:03 2021 +0000 |
| b |
| b'@@ -0,0 +1,630 @@\n+"Name","InChI"\n+"MNXM3","InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)"\n+"MNXM1","InChI=1S/p+1"\n+"MNXM7","InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)"\n+"MNXM790","InChI=1S/C6H10N3O4P/c1-4-8-2-5(6(7)9-4)3-13-14(10,11)12/h2H,3H2,1H3,(H2,7,8,9)(H2,10,11,12)"\n+"MNXM13","InChI=1S/CO2/c2-1-3"\n+"MNXM188","InChI=1S/C7H7NO2/c8-6-4-2-1-3-5(6)7(9)10/h1-4H,8H2,(H,9,10)"\n+"MNXM91","InChI=1S/C5H13O14P3/c6-3-2(1-16-20(8,9)10)17-5(4(3)7)18-22(14,15)19-21(11,12)13/h2-7H,1H2,(H,14,15)(H2,8,9,10)(H2,11,12,13)"\n+"MNXM11","InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"\n+"MNXM1489","InChI=1S/C12H16NO9P/c14-9-8(5-21-23(18,19)20)22-11(10(9)15)13-7-4-2-1-3-6(7)12(16)17/h1-4,8-11,13-15H,5H2,(H,16,17)(H2,18,19,20)"\n+"MNXM30","InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)"\n+"MNXM82","InChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)"\n+"MNXM9","InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)"\n+"MNXM2","InChI=1S/H2O/h1H2"\n+"MNXM1351","InChI=1S/C15H25N5O20P4/c16-12-7-13(18-4-19(12)14-10(23)8(21)5(37-14)1-35-41(25,26)27)20(3-17-7)15-11(24)9(22)6(38-15)2-36-43(31,32)40-44(33,34)39-42(28,29)30/h3-6,8-11,14-16,21-24H,1-2H2,(H,31,32)(H,33,34)(H2,25,26,27)(H2,28,29,30)"\n+"MNXM66","InChI=1S/C3H9O6P/c4-1-3(5)2-9-10(6,7)8/h3-5H,1-2H2,(H2,6,7,8)"\n+"MNXM31","InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)"\n+"MNXM26","InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)"\n+"MNXM27","InChI=1S/Na/q+1"\n+"MNXM334","InChI=1S/C10H12N4O5/c15-1-4-6(16)7(17)10(19-4)14-3-13-5-8(14)11-2-12-9(5)18/h2-4,6-7,10,15-17H,1H2,(H,11,12,18)"\n+"MNXM125","InChI=1S/C10H13N4O8P/c15-6-4(1-21-23(18,19)20)22-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,11,12,17)(H2,18,19,20)"\n+"MNXM32180","InChI=1S/C38H76O13P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-37(40)47-33-36(34-50-53(45,46)49-32-35(39)31-48-52(42,43)44)51-38(41)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h35-36,39H,3-34H2,1-2H3,(H,45,46)(H2,42,43,44)"\n+"MNXM460","InChI=1S/C3H6O3/c4-1-3(6)2-5/h4-5H,1-2H2"\n+"MNXM74","InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h1,3,5H,2H2,(H2,6,7,8)"\n+"MNXM118","InChI=1S/C4H12N2/c5-3-1-2-4-6/h1-6H2"\n+"MNXM89557","InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)"\n+"MNXM1668","InChI=1S/C9H19N3O3/c10-5-1-2-6-12-8(13)4-3-7(11)9(14)15/h7H,1-6,10-11H2,(H,12,13)(H,14,15)"\n+"MNXM38","InChI=1S/C27H35N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,32,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H2,33,34,42,43)"\n+"MNXM7354","InChI=1S/C30H27N3O15/c34-19-7-1-4-13(22(19)37)25(40)31-16-10-46-29(44)18(33-27(42)15-6-3-9-21(36)24(15)39)12-48-30(45)17(11-47-28(16)43)32-26(41)14-5-2-8-20(35)23(14)38/h1-9,16-18,34-39H,10-12H2,(H,31,40)(H,32,41)(H,33,42)"\n+"MNXM111","InChI=1S/Fe/q+2"\n+"MNXM33","InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H5,28,29,30,34,42,43,44,45,46,47)/p+1"\n+"MNXM883","InChI=1S/C30H27N3O15/c34-19-7-1-4-13(22(19)37)25(40)31-16-10-46-29(44)18(33-27(42)15-6-3-9-21(36)24(15)39)12-48-30(45)17(11-47-28(16)43)32-26(41)14-5-2-8-20(35)23(14)38/h1-9,16-18,34-39H,10-12H2,(H,31,40)(H,32,41)(H,33,42)"\n+"MNXM164143","InChI=1S/C7H12O5/c1-4(2'..b',10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)"\n+"MNXM2403","InChI=1S/C8H15NO6/c1-4(12)9-5(2-10)7(14)8(15)6(13)3-11/h2,5-8,11,13-15H,3H2,1H3,(H,9,12)"\n+"MNXM730","InChI=1S/C7H11NO5/c1-4(9)8-5(7(12)13)2-3-6(10)11/h5H,2-3H2,1H3,(H,8,9)(H,10,11)(H,12,13)"\n+"MNXM1954","InChI=1S/C41H65N9O28P2/c1-15(32(58)45-17(3)37(62)63)44-35(61)21(8-6-7-20(42)38(64)65)47-25(53)10-9-22(39(66)67)48-33(59)16(2)43-34(60)18(4)74-31-27(46-19(5)52)40(76-23(13-51)29(31)56)77-80(71,72)78-79(69,70)73-14-24-28(55)30(57)36(75-24)50-12-11-26(54)49-41(50)68/h11-12,15-18,20-24,27-31,36,40,51,55-57H,6-10,13-14,42H2,1-5H3,(H,43,60)(H,44,61)(H,45,58)(H,46,52)(H,47,53)(H,48,59)(H,62,63)(H,64,65)(H,66,67)(H,69,70)(H,71,72)(H,49,54,68)"\n+"MNXM1608","InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)"\n+"MNXM1329","InChI=1S/C17H34N6O5S/c18-6-1-2-7-20-8-3-9-21-15(25)10-22-16(26)13(11-29)23-14(24)5-4-12(19)17(27)28/h12-13,20,29H,1-11,18-19H2,(H,21,25)(H,22,26)(H,23,24)(H,27,28)"\n+"MNXM1407","InChI=1S/C4H9O8P/c5-2(3(6)4(7)8)1-12-13(9,10)11/h2-3,5-6H,1H2,(H,7,8)(H2,9,10,11)"\n+"MNXM1734","InChI=1S/C6H12O7/c7-1-2(8)3(9)4(10)5(11)6(12)13/h2-5,7-11H,1H2,(H,12,13)"\n+"MNXM1750","InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h3,5-8,10-11H,2H2,1H3"\n+"MNXM1403","InChI=1S/C9H10O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-5H,6-7H2,(H,10,11)"\n+"MNXM2112","InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)"\n+"MNXM608","InChI=1S/C25H40N7O19P3S/c1-12(23(37)38)24(39)55-7-6-27-14(33)4-5-28-21(36)18(35)25(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)32-11-31-15-19(26)29-10-30-20(15)32/h10-13,16-18,22,34-35H,4-9H2,1-3H3,(H,27,33)(H,28,36)(H,37,38)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)"\n+"MNXM114390","InChI=1S/C13H19N6O9P/c14-5(1-20)13(23)28-29(24,25)26-2-6-8(21)9(22)12(27-6)19-4-18-7-10(15)16-3-17-11(7)19/h3-6,8-9,12,20-22H,1-2,14H2,(H,24,25)(H2,15,16,17)"\n+"MNXM1482","InChI=1S/C6H12N3O4P/c7-5(3-13-14(10,11)12)1-6-2-8-4-9-6/h2,4-5H,1,3,7H2,(H,8,9)(H2,10,11,12)"\n+"MNXM1922","InChI=1S/C10H13N4O7P/c15-5-1-7(21-6(5)2-20-22(17,18)19)14-4-13-8-9(14)11-3-12-10(8)16/h3-7,15H,1-2H2,(H,11,12,16)(H2,17,18,19)"\n+"MNXM435","InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2"\n+"MNXM4232","InChI=1S/C15H31O7P/c1-2-3-4-5-6-7-8-9-10-11-15(17)21-12-14(16)13-22-23(18,19)20/h14,16H,2-13H2,1H3,(H2,18,19,20)"\n+"MNXM154","InChI=1S/C4H6O3/c1-3(5)2-4(6)7/h2H2,1H3,(H,6,7)"\n+"MNXM1886","InChI=1S/C46H70O/c1-37(2)19-12-20-38(3)21-13-22-39(4)23-14-24-40(5)25-15-26-41(6)27-16-28-42(7)29-17-30-43(8)31-18-32-44(9)35-36-45-33-10-11-34-46(45)47/h10-11,19,21,23,25,27,29,31,33-35,47H,12-18,20,22,24,26,28,30,32,36H2,1-9H3"\n+"MNXM1870","InChI=1S/C96H176N2O38P2/c1-6-11-16-21-26-31-36-41-46-51-66(101)56-76(107)97-81-89(130-79(110)57-67(102)52-47-42-37-32-27-22-17-12-7-2)85(114)74(128-92(81)136-138(122,123)124)64-125-91-82(98-77(108)59-69(54-49-44-39-34-29-24-19-14-9-4)127-78(109)55-50-45-40-35-30-25-20-15-10-5)90(131-80(111)58-68(103)53-48-43-38-33-28-23-18-13-8-3)88(135-137(119,120)121)75(129-91)65-126-95(93(115)116)61-73(84(113)87(133-95)72(106)63-100)132-96(94(117)118)60-70(104)83(112)86(134-96)71(105)62-99/h66-75,81-92,99-106,112-114H,6-65H2,1-5H3,(H,97,107)(H,98,108)(H,115,116)(H,117,118)(H2,119,120,121)(H2,122,123,124)"\n+"MNXM1080","InChI=1S/C6H10O8/c7-1(3(9)5(11)12)2(8)4(10)6(13)14/h1-4,7-10H,(H,11,12)(H,13,14)"\n+"MNXM1334","InChI=1S/C4H10NO6P/c5-3(4(6)7)1-2-11-12(8,9)10/h3H,1-2,5H2,(H,6,7)(H2,8,9,10)"\n+"MNXM495","InChI=1S/C10H14N4O11P2/c15-6-4(1-23-27(21,22)25-26(18,19)20)24-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,21,22)(H,11,12,17)(H2,18,19,20)"\n+"MNXM309","InChI=1S/C21H26N6O15P2/c22-17-12-18(24-7-23-17)27(8-25-12)20-16(31)14(29)11(41-20)6-39-44(36,37)42-43(34,35)38-5-10-13(28)15(30)19(40-10)26-3-1-2-9(4-26)21(32)33/h1-4,7-8,10-11,13-16,19-20,28-31H,5-6H2,(H4-,22,23,24,32,33,34,35,36,37)/p+1"\n+"MNXM182","InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2"\n+"MNXM241","InChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)"\n' |