Merge pull request #1748 from opencobra/develop

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opencobra · Apr 1, 2021 · 9478adc · 9478adc
2 parents ac29c75 + f959908
commit 9478adc
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Showing 121 changed files with 6,562 additions and 1,977 deletions.
diff --git a/binary b/binary
diff --git a/external/analysis/Volume-and-Sampling b/external/analysis/Volume-and-Sampling
diff --git a/initCobraToolbox.m b/initCobraToolbox.m
@@ -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);
 

diff --git a/papers b/papers
diff --git a/src/analysis/exploration/printRxnFormula.m b/src/analysis/exploration/printRxnFormula.m
@@ -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))

diff --git a/...analysis/multiSpecies/microbiomeModelingToolbox/additionalAnalysis/analyzeMgPipeResults.m b/...analysis/multiSpecies/microbiomeModelingToolbox/additionalAnalysis/analyzeMgPipeResults.m
@@ -113,7 +113,7 @@ function analyzeMgPipeResults(infoFilePath,resPath,varargin)
             cd(violinPath)
 
             % create violin plots for net uptake and secretion files
-            if any(strcmp(fileList{i,1},{'net_uptake_fluxes.csv','net_secretion_fluxes.csv'}))
+            if any(contains(fileList{i,1},{'net_uptake_fluxes.csv','net_secretion_fluxes.csv'}))
                 makeViolinPlots(sampleData, infoFile, 'stratification',sampleGroupHeaders{j}, 'plottedFeature', filename, 'unit', 'mmol/person/day')
             end
             cd(currentDir)

diff --git a/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/createPanModels.m b/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/createPanModels.m
@@ -40,6 +40,8 @@ function createPanModels(agoraPath, panPath, taxonLevel, numWorkers, taxTable)
     numWorkers = 0;
 end
 
+mkdir(panPath)
+
 % initialize parallel pool
 if numWorkers > 0
     % with parallelization
@@ -79,12 +81,24 @@ function createPanModels(agoraPath, panPath, taxonLevel, numWorkers, taxTable)
 % Remove unclassified organisms
 allTaxa(strncmp('unclassified', allTaxa, 12)) = [];
 allTaxa(~cellfun(@isempty, strfind(allTaxa, 'bacteri')))
-built = ls(panPath);
 
 % Remove models that have already been assembled from the list of models to create
-built = cellstr(built);
+dInfo = dir(panPath);
+dInfo = dInfo(~[dInfo.isdir]);
+built={dInfo.name};
+built=built';
 built = strrep(built, '.mat', '');
-toCreate = setdiff(allTaxa, built);
+built=regexprep(built,'pan','','once');
+translTaxa=strrep(allTaxa,'[','');
+translTaxa=strrep(translTaxa,' ','_');
+translTaxa=strrep(translTaxa,']','');
+translTaxa=strrep(translTaxa,'(','_');
+translTaxa=strrep(translTaxa,')','');
+translTaxa=strrep(translTaxa,'/','_');
+translTaxa=strrep(translTaxa,'-','_');
+translTaxa=strrep(translTaxa,'.','');
+[C,IA] = setdiff(translTaxa, built);
+toCreate=allTaxa(IA);
 
 % Build pan-models
 % define the intervals in which the testing and regular saving will be
@@ -233,7 +247,7 @@ function createPanModels(agoraPath, panPath, taxonLevel, numWorkers, taxTable)
     'GLYC3Pt AND GLYC3Pti','GLYC3Pt',[]
     'FA180ACPHrev AND STCOATA AND FACOAL180','FACOAL180','FACOAL180i'
     'CITt2 AND CAt4i AND CITCAt','CITCAt','CITCAti'
-    'CITt2ipp AND CAt4i AND CITCAt','CITCAt','CITCAti'
+    'CITt2pp AND CAt4i AND CITCAt','CITCAt','CITCAti'
     'AHCYSNS_r AND AHCYSNS','AHCYSNS_r',[]
     'FDOXR AND GLFRDO AND OOR2r AND FRDOr','FRDOr','FRDO'
     'GNOX AND GNOXy AND GNOXuq AND GNOXmq','GNOXmq','GNOXmqi'
@@ -381,7 +395,7 @@ function createPanModels(agoraPath, panPath, taxonLevel, numWorkers, taxTable)
             go = true;
             for k = 1:size(rxns, 2)
                 RxForm = database.reactions{find(ismember(database.reactions(:, 1), rxns{k})), 3};
-                if contains(RxForm,'[e]')
+                if contains(RxForm,'[e]') && any(contains(model.mets,'[p]'))
                     newName=[rxns{k} 'pp'];
                     % make sure we get the correct reaction
                     newForm=strrep(RxForm,'[e]','[p]');
@@ -446,8 +460,7 @@ function createPanModels(agoraPath, panPath, taxonLevel, numWorkers, taxTable)
                     % account for periplasmatic versions
                     % fix some special cases
                     if ~isempty(intersect(model.rxns,'CITt2ipp'))
-                        model.rxns=strrep(model.rxns,'CITt2ipp','CITt2pp');
-
+                        model.rxns=strrep(model.rxns,'CITt2ipp','CITt2pp');      
                     end
                     if ~isempty(intersect(model.rxns,'CITCAtiipp'))
                         model.rxns=strrep(model.rxns,'CITCAtiipp','CITCAtipp');

diff --git a/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/rebuildModel.m b/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/rebuildModel.m
@@ -53,7 +53,6 @@
 for i=1:length(model.rxns)
     if ~strncmp('bio',model.rxns{i,1},3)
         % find reaction index
-try
     rInd=find(ismember(database.reactions(:, 1), model.rxns{i,1}));
         model.rxns{i,1}=database.reactions{rInd, 1};
         model.grRules{i,1}=model.grRules{i};
@@ -67,10 +66,6 @@
             model.ub(i,1)=1000;
         end
         model.formulas{i,1}=database.reactions{rInd, 3};
-catch
-    errorR{i}=model.rxns{i,1};
-    save errorRxns errorR
-end
     else
         model.rxns{i,1}=model.rxns{i};
         model.grRules{i,1}=model.grRules{i};
@@ -105,7 +100,7 @@
 rbio.data(:,14)=model.rxnKEGGID(oldInd);
 end
 rbio.description=cell(7,1);
-try
+
 % build model with rBioNet
 bInd = find(strncmp('bio',rbio.data(:,2),3));
 bAbb = rbio.data{bInd,2};
@@ -118,7 +113,7 @@
 model.rxnECNumbers{end+1,1} = '';
 model.rxnKEGGID{end+1,1} = '';
 model.rxnConfidenceScores{end+1,1} = '';
-end
+
 % fix incorrect format of PubChemID, metChEBIID, and metKEGGID
 if isfield(model,'metPubChemID')
 for i=1:length(model.metPubChemID)
@@ -134,6 +129,11 @@
 model.description.date=date;
 end
 
+% adapt model.subSystems to current standard
+for i=1:length(model.subSystems)
+    model.subSystems{i,1}=char(model.subSystems{i,1});
+end
+
 % set biomass reaction as objective function
 model=changeObjective(model,bAbb);
 

diff --git a/...pecies/microbiomeModelingToolbox/pairwiseInteractionModeling/joinModelsPairwiseFromList.m b/...pecies/microbiomeModelingToolbox/pairwiseInteractionModeling/joinModelsPairwiseFromList.m
@@ -68,23 +68,24 @@ function joinModelsPairwiseFromList(modelList, modelFolder, varargin)
 
 % then join all models in modelList
 for i = 1:size(modelList, 1)
+
+    % Load the reconstructions to be joined
+    inputModels={};
+    model=readCbModel([modelFolder filesep modelList{i,1} '.mat']);
+    inputModels{i}=model;
+    for k = i + 1:size(modelList, 1)
+        model=readCbModel([modelFolder filesep modelList{k,1} '.mat']);
+        inputModels{k}=model;
+    end
+
     if numWorkers > 0
         % with parallelization
         poolobj = gcp('nocreate');
         if isempty(poolobj)
             parpool(numWorkers)
         end
         pairedModelsTemp = {};
-
-        % Load the reconstructions to be joined
-        inputModels={};
-        model=readCbModel([modelFolder filesep modelList{i,1} '.mat']);
-        inputModels{i}=model;
-        for k = i + 1:size(modelList, 1)
-            model=readCbModel([modelFolder filesep modelList{k,1} '.mat']);
-            inputModels{k}=model;
-        end
-
+
         parfor k = i + 1:size(modelList, 1)
             model1 = inputModels{i};
             model2 = inputModels{k};

diff --git a/src/analysis/thermo/componentContribution/data/.~lock.TECRDB.tsv# b/src/analysis/thermo/componentContribution/data/.~lock.TECRDB.tsv#
diff --git a/src/analysis/thermo/componentContribution/data/.~lock.formation_energies_transformed.tsv# b/src/analysis/thermo/componentContribution/data/.~lock.formation_energies_transformed.tsv#
diff --git a/src/analysis/thermo/componentContribution/data/kegg_inchi_additions.csv b/src/analysis/thermo/componentContribution/data/kegg_inchi_additions.csv
@@ -0,0 +1,72 @@
+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)"
diff --git a/src/analysis/thermo/componentContribution/data/kegg_inchi_additions.txt b/src/analysis/thermo/componentContribution/data/kegg_inchi_additions.txt
@@ -0,0 +1,72 @@
+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
+ −		all/CplexFVA.class
+ −		all/CplexFVARunnable.class
+ −		all/EscherConverter-1.2.1.jar
+ −		all/SignedTaskCounter.class