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Merge pull request #1744 from rmtfleming/develop
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merger of updated submodules and repaired vonB
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@rmtfleming
rmtfleming authored Mar 31, 2021
2 parents 8456d32 + 3b44a68 commit b66ab31
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Showing 78 changed files with 5,002 additions and 343 deletions.
2 changes: 1 addition & 1 deletion binary
Submodule binary updated 4 files
+ − all/CplexFVA.class
+ − all/CplexFVARunnable.class
+ − all/EscherConverter-1.2.1.jar
+ − all/SignedTaskCounter.class
2 changes: 1 addition & 1 deletion external/analysis/Volume-and-Sampling
Submodule Volume-and-Sampling updated 1 files
+6 −1 preprocess.m
9 changes: 9 additions & 0 deletions initCobraToolbox.m
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Original file line number Diff line number Diff line change
Expand Up @@ -630,6 +630,15 @@ function initCobraToolbox(updateToolbox)
% set up the COBRA System path
addCOBRABinaryPathToSystemPath();

%remove /new thermo folders from path
%TODO resolve issues with new file versions
aPath = which('initVonBertalanffy');
basePath = strrep(aPath,'vonBertalanffy/initVonBertalanffy.m','');
addpath(genpath(basePath))
folderPattern=[filesep 'new'];
method = 'remove';
editCobraToolboxPath(basePath,folderPattern,method)

% change back to the current directory
cd(currentDir);

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2 changes: 1 addition & 1 deletion papers
Submodule papers updated 144 files
7 changes: 7 additions & 0 deletions src/analysis/exploration/printRxnFormula.m
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Expand Up @@ -73,6 +73,13 @@

end

if ~isfield(model,'lb')
model.lb=ones(size(model.S,2),1)*-inf;
end
if ~isfield(model,'ub')
model.lb=ones(size(model.S,2),1)*inf;
end

parser = inputParser();
parser.addRequired('model',@isstruct) % we only check, whether its a struct, no details for speed
parser.addParamValue('rxnAbbrList',model.rxns,@(x) iscell(x) || ischar(x))
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1 change: 0 additions & 1 deletion src/analysis/thermo/componentContribution/data/.~lock.TECRDB.tsv#
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This file was deleted.

1 change: 0 additions & 1 deletion src/analysis/thermo/componentContribution/data/.~lock.formation_energies_transformed.tsv#
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72 changes: 72 additions & 0 deletions src/analysis/thermo/componentContribution/data/kegg_inchi_additions.csv
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C00225,"InChI=1S/C12H14N2/c1-13-7-3-11(4-8-13)12-5-9-14(2)10-6-12/h3-10H,1-2H3/q+2"
C01041,"InChI=1S/C6H7O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-8,10H,1H2/t2-,5+/m0/s1"
C02022,"InChI=1S/C4H8O4/c5-1-3(7)4(8)2-6/h3,5-7H,1-2H2/t3-/m1/s1"
C02045,"InChI=1S/C4H8O4/c5-1-3(7)4(8)2-6/h3,5-7H,1-2H2/t3-/m0/s1"
C04446,"InChI=1S/C8H10N2O4/c9-5(8(13)14)3-10-2-1-6(11)7(12)4-10/h1-2,4-5,12H,3,9H2,(H,13,14)/p+1"
C06397,"InChI=1S/C17H27N5O16P2/c18-14-7-15(20-3-19-14)22(4-21-7)16-11(28)8(25)6(35-16)2-34-39(30,31)38-40(32,33)37-17-12(29)9(26)10(27)13(36-17)5(24)1-23/h3-6,8-13,16-17,23-29H,1-2H2,(H,30,31)(H,32,33)(H2,18,19,20)/t5-,6-,8-,9+,10+,11-,12+,13-,16-,17?/m1/s1"
C06398,"InChI=1S/C17H27N5O16P2/c18-14-7-15(20-3-19-14)22(4-21-7)16-11(28)8(25)6(35-16)2-34-39(30,31)38-40(32,33)37-17-12(29)9(26)10(27)13(36-17)5(24)1-23/h3-6,8-13,16-17,23-29H,1-2H2,(H,30,31)(H,32,33)(H2,18,19,20)/t5-,6+,8+,9-,10-,11+,12-,13+,16+,17?/m0/s1"
C80001,"InChI=1S/C7H11N3O2/c1-10-3-5(9-4-10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12)/p+1/t6-/m0/s1"
C80002,"InChI=1S/C6H5Cl/c7-6-4-2-1-3-5-6/h1-5H"
C80003,"InChI=1S/C6H4Cl2/c7-5-3-1-2-4-6(5)8/h1-4H"
C80004,"InChI=1S/C6H4Cl2/c7-5-2-1-3-6(8)4-5/h1-4H"
C80005,"InChI=1S/C6H4Cl2/c7-5-1-2-6(8)4-3-5/h1-4H"
C80006,"InChI=1S/C6H3Cl3/c7-4-2-1-3-5(8)6(4)9/h1-3H"
C80007,"InChI=1S/C6H3Cl3/c7-4-1-2-5(8)6(9)3-4/h1-3H"
C80008,"InChI=1S/C6H3Cl3/c7-4-1-5(8)3-6(9)2-4/h1-3H"
C80009,"InChI=1S/C6H2Cl4/c7-3-1-2-4(8)6(10)5(3)9/h1-2H"
C80010,"InChI=1S/C6H2Cl4/c7-3-1-4(8)6(10)5(9)2-3/h1-2H"
C80011,"InChI=1S/C6H2Cl4/c7-3-1-4(8)6(10)2-5(3)9/h1-2H"
C80012,"InChI=1S/C6HCl5/c7-2-1-3(8)5(10)6(11)4(2)9/h1H"
C80013,"InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9"
C80014,"InChI=1S/C7H5ClO2/c8-6-3-1-2-5(4-6)7(9)10/h1-4H,(H,9,10)"
C80015,"InChI=1S/C7H4Cl2O2/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3H,(H,10,11)"
C80016,"InChI=1S/C7H4Cl2O2/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3H,(H,10,11)"
C80017,"InChI=1S/C7H4Cl2O2/c8-4-2-1-3-5(9)6(4)7(10)11/h1-3H,(H,10,11)"
C80018,"InChI=1S/C7H4Cl2O2/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3H,(H,10,11)"
C80019,"InChI=1S/C7H4Cl2O2/c8-5-1-4(7(10)11)2-6(9)3-5/h1-3H,(H,10,11)"
C80020,"InChI=1S/C7H3Cl3O2/c8-3-1-4(7(11)12)6(10)5(9)2-3/h1-2H,(H,11,12)"
C80021,"InChI=1S/C7H3Cl3O2/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1-2H,(H,11,12)"
C80022,"InChI=1S/C7H5BrO2/c8-6-4-2-1-3-5(6)7(9)10/h1-4H,(H,9,10)"
C80023,"InChI=1S/C7H5BrO2/c8-6-3-1-2-5(4-6)7(9)10/h1-4H,(H,9,10)"
C80024,"InChI=1S/C7H5BrO2/c8-6-3-1-5(2-4-6)7(9)10/h1-4H,(H,9,10)"
C80025,"InChI=1S/C7H5IO2/c8-6-4-2-1-3-5(6)7(9)10/h1-4H,(H,9,10)"
C80026,"InChI=1S/C7H5IO2/c8-6-3-1-2-5(4-6)7(9)10/h1-4H,(H,9,10)"
C80027,"InChI=1S/C7H5IO2/c8-6-3-1-5(2-4-6)7(9)10/h1-4H,(H,9,10)"
C80028,"InChI=1S/C7H6ClNO2/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3H,9H2,(H,10,11)"
C80029,"InChI=1S/C7H5ClO3/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3,9H,(H,10,11)"
C80030,"InChI=1S/C8H7ClO2/c1-5-2-3-6(9)4-7(5)8(10)11/h2-4H,1H3,(H,10,11)"
C80031,"InChI=1S/C6H4Cl2O/c7-4-2-1-3-5(9)6(4)8/h1-3,9H"
C80032,"InChI=1S/C6H4Cl2O/c7-4-1-5(8)3-6(9)2-4/h1-3,9H"
C80033,"InChI=1S/C6H3Cl3O/c7-3-1-2-4(10)6(9)5(3)8/h1-2,10H"
C80034,"InChI=1S/C6H3Cl3O/c7-3-1-5(9)6(10)2-4(3)8/h1-2,10H"
C80035,"InChI=1S/C6H3Cl3O/c7-3-1-4(8)6(10)5(9)2-3/h1-2,10H"
C80036,"InChI=1S/C6H3Cl3O/c7-3-1-4(8)6(9)5(10)2-3/h1-2,10H"
C80037,"InChI=1S/C6H3Cl3O/c7-3-1-2-4(8)6(10)5(3)9/h1-2,10H"
C80038,"InChI=1S/C6H3Cl3O/c7-4-1-3(10)2-5(8)6(4)9/h1-2,10H"
C80039,"InChI=1S/C6H2Cl4O/c7-2-1-3(11)5(9)6(10)4(2)8/h1,11H"
C80040,"InChI=1S/C6H2Cl4O/c7-2-1-3(8)6(11)5(10)4(2)9/h1,11H"
C80041,"InChI=1S/C6H2Cl4O/c7-2-1-3(8)5(10)6(11)4(2)9/h1,11H"
C80042,"InChI=1S/C6HCl5O/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H"
C80043,"InChI=1S/CH3Cl/c1-2/h1H3"
C80045,"InChI=1S/C2H6/c1-2/h1-2H3"
C80046,"InChI=1S/C2H2Cl4/c3-1(4)2(5)6/h1-2H"
C80047,"InChI=1S/C3H8/c1-3-2/h3H2,1-2H3"
C80048,"InChI=1S/C3H7Cl/c1-2-3-4/h2-3H2,1H3"
C80049,"InChI=1S/C3H6Cl2/c4-2-1-3-5/h1-3H2"
C80050,"InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3"
C80051,"InChI=1S/C4H9Cl/c1-2-3-4-5/h2-4H2,1H3"
C80052,"InChI=1S/C4H9Cl/c1-3-4(2)5/h4H,3H2,1-2H3"
C80053,"InChI=1S/C5H12/c1-3-5-4-2/h3-5H2,1-2H3"
C80054,"InChI=1S/C5H11Cl/c1-2-3-4-5-6/h2-5H2,1H3"
C80055,"InChI=1S/C3H10NO/c1-4(2,3)5/h5H,1-3H3/q+1"
C80056,"InChI=1/C9H19NO2S2/c10-7-14-6-5-8(13)3-1-2-4-9(11)12/h8,13H,1-7,10H2,(H,11,12)"
C80057,"InChI=1S/C22H28N6O14P2/c1-10(29)11-3-2-4-27(5-11)21-17(32)15(30)12(40-21)6-38-43(34,35)42-44(36,37)39-7-13-16(31)18(33)22(41-13)28-9-26-14-19(23)24-8-25-20(14)28/h2-5,8-9,12-13,15-18,21-22,30-33H,6-7H2,1H3,(H3-,23,24,25,34,35,36,37)/p+1"
C80058,"InChI=1S/C22H30N6O14P2/c1-10(29)11-3-2-4-27(5-11)21-17(32)15(30)12(40-21)6-38-43(34,35)42-44(36,37)39-7-13-16(31)18(33)22(41-13)28-9-26-14-19(23)24-8-25-20(14)28/h2,4-5,8-9,12-13,15-18,21-22,30-33H,3,6-7H2,1H3,(H,34,35)(H,36,37)(H2,23,24,25)"
C80061,"InChI=1S/C4H8O/c1-4(2)3-5/h3-4H,1-2H3"
C80062,"InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3-4,6-9H,1-2H2"
C80063,"InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3-4,6-7H,1-2H2,(H2,9,10,11)(H2,12,13,14)"
C80064,"InChI=1S/C6H10O7/c7-1-3(9)4(10)6(13,2-8)5(11)12/h3,7-9,13H,1-2H2,(H,11,12)"
C80065,"InChI=1S/C6H12O13P2/c7-3(1-18-20(12,13)14)4(8)6(11,5(9)10)2-19-21(15,16)17/h3,7,11H,1-2H2,(H,9,10)(H2,12,13,14)(H2,15,16,17)"
C80066,"InChI=1S/C3H7O7P/c4-1-2(5)3(6)10-11(7,8)9/h2,4-5H,1H2,(H2,7,8,9)"
C80068,"InChI=1S/C8H16O9/c9-1-2(10)3(11)4(12)5(13)6(14)7(15)8(16)17/h2-7,9-15H,1H2,(H,16,17)"
C80069,"InChI=1S/C9H19NO2S2/c10-7-14-6-5-8(13)3-1-2-4-9(11)12/h8,13H,1-7,10H2,(H,11,12)"
72 changes: 72 additions & 0 deletions src/analysis/thermo/componentContribution/data/kegg_inchi_additions.txt
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InChI=1S/C12H14N2/c1-13-7-3-11(4-8-13)12-5-9-14(2)10-6-12/h3-10H,1-2H3/q+2 C00225
InChI=1S/C6H7O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2,5,7-8,10H,1H2/t2-,5+/m0/s1 C01041
InChI=1S/C4H8O4/c5-1-3(7)4(8)2-6/h3,5-7H,1-2H2/t3-/m1/s1 C02022
InChI=1S/C4H8O4/c5-1-3(7)4(8)2-6/h3,5-7H,1-2H2/t3-/m0/s1 C02045
InChI=1S/C8H10N2O4/c9-5(8(13)14)3-10-2-1-6(11)7(12)4-10/h1-2,4-5,12H,3,9H2,(H,13,14)/p+1 C04446
InChI=1S/C17H27N5O16P2/c18-14-7-15(20-3-19-14)22(4-21-7)16-11(28)8(25)6(35-16)2-34-39(30,31)38-40(32,33)37-17-12(29)9(26)10(27)13(36-17)5(24)1-23/h3-6,8-13,16-17,23-29H,1-2H2,(H,30,31)(H,32,33)(H2,18,19,20)/t5-,6-,8-,9+,10+,11-,12+,13-,16-,17?/m1/s1 C06397
InChI=1S/C17H27N5O16P2/c18-14-7-15(20-3-19-14)22(4-21-7)16-11(28)8(25)6(35-16)2-34-39(30,31)38-40(32,33)37-17-12(29)9(26)10(27)13(36-17)5(24)1-23/h3-6,8-13,16-17,23-29H,1-2H2,(H,30,31)(H,32,33)(H2,18,19,20)/t5-,6+,8+,9-,10-,11+,12-,13+,16+,17?/m0/s1 C06398
InChI=1S/C7H11N3O2/c1-10-3-5(9-4-10)2-6(8)7(11)12/h3-4,6H,2,8H2,1H3,(H,11,12)/p+1/t6-/m0/s1 C80001
InChI=1S/C6H5Cl/c7-6-4-2-1-3-5-6/h1-5H C80002
InChI=1S/C6H4Cl2/c7-5-3-1-2-4-6(5)8/h1-4H C80003
InChI=1S/C6H4Cl2/c7-5-2-1-3-6(8)4-5/h1-4H C80004
InChI=1S/C6H4Cl2/c7-5-1-2-6(8)4-3-5/h1-4H C80005
InChI=1S/C6H3Cl3/c7-4-2-1-3-5(8)6(4)9/h1-3H C80006
InChI=1S/C6H3Cl3/c7-4-1-2-5(8)6(9)3-4/h1-3H C80007
InChI=1S/C6H3Cl3/c7-4-1-5(8)3-6(9)2-4/h1-3H C80008
InChI=1S/C6H2Cl4/c7-3-1-2-4(8)6(10)5(3)9/h1-2H C80009
InChI=1S/C6H2Cl4/c7-3-1-4(8)6(10)5(9)2-3/h1-2H C80010
InChI=1S/C6H2Cl4/c7-3-1-4(8)6(10)2-5(3)9/h1-2H C80011
InChI=1S/C6HCl5/c7-2-1-3(8)5(10)6(11)4(2)9/h1H C80012
InChI=1S/C6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9 C80013
InChI=1S/C7H5ClO2/c8-6-3-1-2-5(4-6)7(9)10/h1-4H,(H,9,10) C80014
InChI=1S/C7H4Cl2O2/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3H,(H,10,11) C80015
InChI=1S/C7H4Cl2O2/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3H,(H,10,11) C80016
InChI=1S/C7H4Cl2O2/c8-4-2-1-3-5(9)6(4)7(10)11/h1-3H,(H,10,11) C80017
InChI=1S/C7H4Cl2O2/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3H,(H,10,11) C80018
InChI=1S/C7H4Cl2O2/c8-5-1-4(7(10)11)2-6(9)3-5/h1-3H,(H,10,11) C80019
InChI=1S/C7H3Cl3O2/c8-3-1-4(7(11)12)6(10)5(9)2-3/h1-2H,(H,11,12) C80020
InChI=1S/C7H3Cl3O2/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1-2H,(H,11,12) C80021
InChI=1S/C7H5BrO2/c8-6-4-2-1-3-5(6)7(9)10/h1-4H,(H,9,10) C80022
InChI=1S/C7H5BrO2/c8-6-3-1-2-5(4-6)7(9)10/h1-4H,(H,9,10) C80023
InChI=1S/C7H5BrO2/c8-6-3-1-5(2-4-6)7(9)10/h1-4H,(H,9,10) C80024
InChI=1S/C7H5IO2/c8-6-4-2-1-3-5(6)7(9)10/h1-4H,(H,9,10) C80025
InChI=1S/C7H5IO2/c8-6-3-1-2-5(4-6)7(9)10/h1-4H,(H,9,10) C80026
InChI=1S/C7H5IO2/c8-6-3-1-5(2-4-6)7(9)10/h1-4H,(H,9,10) C80027
InChI=1S/C7H6ClNO2/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3H,9H2,(H,10,11) C80028
InChI=1S/C7H5ClO3/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3,9H,(H,10,11) C80029
InChI=1S/C8H7ClO2/c1-5-2-3-6(9)4-7(5)8(10)11/h2-4H,1H3,(H,10,11) C80030
InChI=1S/C6H4Cl2O/c7-4-2-1-3-5(9)6(4)8/h1-3,9H C80031
InChI=1S/C6H4Cl2O/c7-4-1-5(8)3-6(9)2-4/h1-3,9H C80032
InChI=1S/C6H3Cl3O/c7-3-1-2-4(10)6(9)5(3)8/h1-2,10H C80033
InChI=1S/C6H3Cl3O/c7-3-1-5(9)6(10)2-4(3)8/h1-2,10H C80034
InChI=1S/C6H3Cl3O/c7-3-1-4(8)6(10)5(9)2-3/h1-2,10H C80035
InChI=1S/C6H3Cl3O/c7-3-1-4(8)6(9)5(10)2-3/h1-2,10H C80036
InChI=1S/C6H3Cl3O/c7-3-1-2-4(8)6(10)5(3)9/h1-2,10H C80037
InChI=1S/C6H3Cl3O/c7-4-1-3(10)2-5(8)6(4)9/h1-2,10H C80038
InChI=1S/C6H2Cl4O/c7-2-1-3(11)5(9)6(10)4(2)8/h1,11H C80039
InChI=1S/C6H2Cl4O/c7-2-1-3(8)6(11)5(10)4(2)9/h1,11H C80040
InChI=1S/C6H2Cl4O/c7-2-1-3(8)5(10)6(11)4(2)9/h1,11H C80041
InChI=1S/C6HCl5O/c7-1-2(8)4(10)6(12)5(11)3(1)9/h12H C80042
InChI=1S/CH3Cl/c1-2/h1H3 C80043
InChI=1S/C2H6/c1-2/h1-2H3 C80045
InChI=1S/C2H2Cl4/c3-1(4)2(5)6/h1-2H C80046
InChI=1S/C3H8/c1-3-2/h3H2,1-2H3 C80047
InChI=1S/C3H7Cl/c1-2-3-4/h2-3H2,1H3 C80048
InChI=1S/C3H6Cl2/c4-2-1-3-5/h1-3H2 C80049
InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3 C80050
InChI=1S/C4H9Cl/c1-2-3-4-5/h2-4H2,1H3 C80051
InChI=1S/C4H9Cl/c1-3-4(2)5/h4H,3H2,1-2H3 C80052
InChI=1S/C5H12/c1-3-5-4-2/h3-5H2,1-2H3 C80053
InChI=1S/C5H11Cl/c1-2-3-4-5-6/h2-5H2,1H3 C80054
InChI=1S/C3H10NO/c1-4(2,3)5/h5H,1-3H3/q+1 C80055
InChI=1/C9H19NO2S2/c10-7-14-6-5-8(13)3-1-2-4-9(11)12/h8,13H,1-7,10H2,(H,11,12) C80056
InChI=1S/C22H28N6O14P2/c1-10(29)11-3-2-4-27(5-11)21-17(32)15(30)12(40-21)6-38-43(34,35)42-44(36,37)39-7-13-16(31)18(33)22(41-13)28-9-26-14-19(23)24-8-25-20(14)28/h2-5,8-9,12-13,15-18,21-22,30-33H,6-7H2,1H3,(H3-,23,24,25,34,35,36,37)/p+1 C80057
InChI=1S/C22H30N6O14P2/c1-10(29)11-3-2-4-27(5-11)21-17(32)15(30)12(40-21)6-38-43(34,35)42-44(36,37)39-7-13-16(31)18(33)22(41-13)28-9-26-14-19(23)24-8-25-20(14)28/h2,4-5,8-9,12-13,15-18,21-22,30-33H,3,6-7H2,1H3,(H,34,35)(H,36,37)(H2,23,24,25) C80058
InChI=1S/C4H8O/c1-4(2)3-5/h3-4H,1-2H3 C80061
InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3-4,6-9H,1-2H2 C80062
InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3-4,6-7H,1-2H2,(H2,9,10,11)(H2,12,13,14) C80063
InChI=1S/C6H10O7/c7-1-3(9)4(10)6(13,2-8)5(11)12/h3,7-9,13H,1-2H2,(H,11,12) C80064
InChI=1S/C6H12O13P2/c7-3(1-18-20(12,13)14)4(8)6(11,5(9)10)2-19-21(15,16)17/h3,7,11H,1-2H2,(H,9,10)(H2,12,13,14)(H2,15,16,17) C80065
InChI=1S/C3H7O7P/c4-1-2(5)3(6)10-11(7,8)9/h2,4-5H,1H2,(H2,7,8,9) C80066
InChI=1S/C8H16O9/c9-1-2(10)3(11)4(12)5(13)6(14)7(15)8(16)17/h2-7,9-15H,1H2,(H,16,17) C80068
InChI=1S/C9H19NO2S2/c10-7-14-6-5-8(13)3-1-2-4-9(11)12/h8,13H,1-7,10H2,(H,11,12) C80069
0 ...tribution/createGroupContributionStruct.m → ...jankowski/createGroupContributionStruct.m
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0 ...upContribution/webCGMtoTabDelimitedFile.m → ...tion/jankowski/webCGMtoTabDelimitedFile.m
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56 changes: 56 additions & 0 deletions src/analysis/thermo/componentContribution/new/checkForMissingStereo.m
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Original file line number Diff line number Diff line change
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function missingStereo = checkForMissingStereo(model, trainingModel)
% USAGE:
%
% missingStereo = checkForMissingStereo(model, trainingModel)
%
% INPUTS:
% model: structure with fields:
%
% * .mets
% * .inchi.standard
% * .inchi.standardWithStereo
%
% trainingModel: structure with fields:
%
% *.inchi.standard
% *.inchi.standardWithStereo
%
% OUTPUTS:
% missingStereo:

nistStdBool = false(length(trainingModel.inchi.standard));
for n = 1:length(trainingModel.inchi.standard)
if ~isempty(trainingModel.inchi.standard{n})
if ~any(nistStdBool(:,n))
nistStdBool(n,n) = true;
nistStdBool(n,strcmp(trainingModel.inchi.standard{n},trainingModel.inchi.standard)) = true;
end
end
end

nistStdStereoBool = false(length(trainingModel.inchi.standardWithStereo));
for n = 1:length(trainingModel.inchi.standardWithStereo)
if ~isempty(trainingModel.inchi.standardWithStereo{n})
if ~any(nistStdStereoBool(:,n))
nistStdStereoBool(n,n) = true;
nistStdStereoBool(n,strcmp(trainingModel.inchi.standardWithStereo{n},trainingModel.inchi.standardWithStereo)) = true;
end
end
end

nistStdStereoBool(diag(true(size(nistStdStereoBool,1),1))) = false;
nistBool = nistStdBool & ~nistStdStereoBool;
nistBool = nistBool(sum(nistBool,2)>1,:);

nistStdInchi = trainingModel.inchi.standard(any(nistBool));
modelStdInchi = model.inchi.standard;
modelStdInchi(cellfun(@isempty,modelStdInchi)) = {'N/A'};

modelStdInchiStereo = model.inchi.standardWithStereo(ismember(modelStdInchi,nistStdInchi));
modelMets = model.mets(ismember(modelStdInchi,nistStdInchi));
modelMets = regexprep(modelMets,'\[\w\]','');
[modelMets,crossi] = unique(modelMets);
modelStdInchiStereo = modelStdInchiStereo(crossi);
missingStereo = modelMets(cellfun('isempty',regexp(modelStdInchiStereo,'[tms]')));

end
0 ...onentContribution/componentContribution.m → ...tContribution/new/componentContribution.m
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