From 5dcec1cddddee4757bdb517ec7a811a8f97aa74a Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Mon, 14 Oct 2024 17:48:42 +0200 Subject: [PATCH] refactor: identifier prefixes (#566) * refactor: default behaviour add/remove prefixes * fix: filenames * fix: update test result importExport --- core/checkModelStruct.m | 19 +- doc/core/checkModelStruct.html | 399 ++- doc/index.html | 6 +- doc/io/SBMLFromExcel.html | 4 +- doc/io/checkFileExistence.html | 2 +- doc/io/exportForGit.html | 4 +- doc/io/exportModel.html | 1542 ++++++----- doc/io/importModel.html | 2339 ++++++++--------- doc/io/sortIdentifiers.html | 2 +- .../addCOBRAstylePrefixes.html | 125 - .../addIdentifierPrefix.html | 128 + doc/struct_conversion/index.html | 2 +- .../removeCOBRAstylePrefixes.html | 133 - .../removeIdentifierPrefix.html | 143 + io/exportModel.m | 37 +- io/importModel.m | 48 +- struct_conversion/addCOBRAstylePrefixes.m | 58 - struct_conversion/addIdentifierPrefix.m | 60 + ...ylePrefixes.m => removeIdentifierPrefix.m} | 21 +- .../test_data/importExportResults.mat | Bin 1411 -> 1400 bytes 20 files changed, 2522 insertions(+), 2550 deletions(-) delete mode 100644 doc/struct_conversion/addCOBRAstylePrefixes.html create mode 100644 doc/struct_conversion/addIdentifierPrefix.html delete mode 100644 doc/struct_conversion/removeCOBRAstylePrefixes.html create mode 100644 doc/struct_conversion/removeIdentifierPrefix.html delete mode 100644 struct_conversion/addCOBRAstylePrefixes.m create mode 100644 struct_conversion/addIdentifierPrefix.m rename struct_conversion/{removeCOBRAstylePrefixes.m => removeIdentifierPrefix.m} (71%) diff --git a/core/checkModelStruct.m b/core/checkModelStruct.m index 21b1b461..139c43d8 100755 --- a/core/checkModelStruct.m +++ b/core/checkModelStruct.m @@ -250,22 +250,17 @@ function checkModelStruct(model,throwErrors,trimWarnings) fieldPrefix = {'R_';'M_';'C_';'G_'}; for i=1:numel(fields) try - numIDs = startsWith(model.(fields{i}),digitsPattern(1)); + numIDs = ~startsWith(model.(fields{i}),regexpPattern('^[a-zA-Z_]')); catch numIDs = []; end if any(numIDs) - EM = ['The following ' fieldNames{i} ' identifiers start with a ' ... - 'digit, which does not comply with SBML specifications. This ' ... - 'does not impact RAVEN functionality, but before exporting ' ... - 'the model to SBML you should either (a) correct these ' ... - 'identifiers directly; or (b) run "model = addCOBRAstylePrefixes ' ... - '(model,''' fields{i} ''');" to have COBRA style "' fieldPrefix{i} ... - '" prefixes added to all ' fieldNames{i} ' identifiers; or (c) ' ... - 'let exportModel add COBRA style prefixes to all identifiers ' ... - 'in the model by setting COBRAstyle as true. Example: ' ... - '"exportModel(model, ''filename.xml'', true);"']; - dispEM(EM,throwErrors,{model.(fields{i}){numIDs}},trimWarnings); + EM = ['The following ' fieldNames{i} ' identifiers do not start '... + 'with a letter or _ (conflicting with SBML specifications). '... + 'This does not impact RAVEN functionality, but be aware that '... + 'exportModel will automatically add ' fieldPrefix{i} ... + ' prefixes to all ' fieldNames{i} ' identifiers:']; + dispEM(EM,false,{model.(fields{i}){numIDs}},trimWarnings); end end diff --git a/doc/core/checkModelStruct.html b/doc/core/checkModelStruct.html index 2a39d781..288a1ff0 100644 --- a/doc/core/checkModelStruct.html +++ b/doc/core/checkModelStruct.html @@ -309,212 +309,207 @@

SOURCE CODE ^'R_';'M_';'C_';'G_'}; 0251 for i=1:numel(fields) 0252 try -0253 numIDs = startsWith(model.(fields{i}),digitsPattern(1)); +0253 numIDs = ~startsWith(model.(fields{i}),regexpPattern('^[a-zA-Z_]')); 0254 catch 0255 numIDs = []; 0256 end 0257 if any(numIDs) -0258 EM = ['The following ' fieldNames{i} ' identifiers start with a ' ... -0259 'digit, which does not comply with SBML specifications. This ' ... -0260 'does not impact RAVEN functionality, but before exporting ' ... -0261 'the model to SBML you should either (a) correct these ' ... -0262 'identifiers directly; or (b) run "model = addCOBRAstylePrefixes ' ... -0263 '(model,''' fields{i} ''');" to have COBRA style "' fieldPrefix{i} ... -0264 '" prefixes added to all ' fieldNames{i} ' identifiers; or (c) ' ... -0265 'let exportModel add COBRA style prefixes to all identifiers ' ... -0266 'in the model by setting COBRAstyle as true. Example: ' ... -0267 '"exportModel(model, ''filename.xml'', true);"']; -0268 dispEM(EM,throwErrors,{model.(fields{i}){numIDs}},trimWarnings); -0269 end -0270 end -0271 -0272 %Duplicates -0273 EM='The following reaction IDs are duplicates:'; -0274 dispEM(EM,throwErrors,model.rxns(duplicates(model.rxns)),trimWarnings); -0275 EM='The following metabolite IDs are duplicates:'; -0276 dispEM(EM,throwErrors,model.mets(duplicates(model.mets)),trimWarnings); -0277 EM='The following compartment IDs are duplicates:'; -0278 dispEM(EM,throwErrors,model.comps(duplicates(model.comps)),trimWarnings); -0279 if isfield(model,'genes') -0280 EM='The following genes are duplicates:'; -0281 dispEM(EM,throwErrors,model.genes(duplicates(model.genes)),trimWarnings); -0282 end -0283 metInComp=strcat(model.metNames,'[',model.comps(model.metComps),']'); -0284 EM='The following metabolites already exist in the same compartment:'; -0285 dispEM(EM,throwErrors,metInComp(duplicates(metInComp)),trimWarnings); -0286 -0287 %Elements never used (print only as warnings -0288 EM='The following reactions are empty (no involved metabolites):'; -0289 dispEM(EM,false,model.rxns(~any(model.S,1)),trimWarnings); -0290 EM='The following metabolites are never used in a reaction:'; -0291 dispEM(EM,false,model.mets(~any(model.S,2)),trimWarnings); -0292 if isfield(model,'genes') -0293 EM='The following genes are not associated to a reaction:'; -0294 dispEM(EM,false,model.genes(~any(model.rxnGeneMat,1)),trimWarnings); -0295 end -0296 I=true(numel(model.comps),1); -0297 I(model.metComps)=false; -0298 EM='The following compartments contain no metabolites:'; -0299 dispEM(EM,false,model.comps(I),trimWarnings); -0300 -0301 %Contradicting bounds -0302 EM='The following reactions have contradicting bounds (lower bound is higher than upper bound):'; -0303 dispEM(EM,throwErrors,model.rxns(model.lb>model.ub),trimWarnings); -0304 EM='The following reactions have lower and upper bounds that indicate reversibility, but are indicated as irreversible in model.rev:'; -0305 dispEM(EM,false,model.rxns(model.lb < 0 & model.ub > 0 & model.rev==0),trimWarnings); -0306 -0307 %Multiple or no objective functions not allowed in SBML L3V1 FBCv2 -0308 if numel(find(model.c))>1 -0309 EM='Multiple objective functions found. This might be intended, but results in FBCv2 non-compliant SBML file when exported'; -0310 dispEM(EM,false,model.rxns(find(model.c)),trimWarnings); -0311 elseif ~any(model.c) -0312 EM='No objective function found. This might be intended, but results in FBCv2 non-compliant SBML file when exported'; -0313 dispEM(EM,false); -0314 end -0315 -0316 %Mapping of compartments -0317 if isfield(model,'compOutside') -0318 EM='The following compartments are in "compOutside" but not in "comps":'; -0319 dispEM(EM,throwErrors,setdiff(model.compOutside,[{''};model.comps]),trimWarnings); -0320 end -0321 -0322 %Met names which start with number -0323 I=false(numel(model.metNames),1); -0324 for i=1:numel(model.metNames) -0325 index=strfind(model.metNames{i},' '); -0326 if any(index) -0327 if any(str2double(model.metNames{i}(1:index(1)-1))) -0328 I(i)=true; -0329 end -0330 end -0331 end -0332 EM='The following metabolite names begin with a number directly followed by space, which could potentially cause problems:'; -0333 dispEM(EM,false,model.metNames(I),trimWarnings); -0334 -0335 %Non-parseable composition -0336 if isfield(model,'metFormulas') -0337 [~, ~, exitFlag]=parseFormulas(model.metFormulas,true,false); -0338 EM='The composition for the following metabolites could not be parsed:'; -0339 dispEM(EM,false,model.mets(exitFlag==-1),trimWarnings); -0340 end -0341 -0342 %Check if there are metabolites with different names but the same MIRIAM -0343 %codes -0344 if isfield(model,'metMiriams') -0345 miriams=containers.Map(); -0346 for i=1:numel(model.mets) -0347 if ~isempty(model.metMiriams{i}) -0348 %Loop through and add for each miriam -0349 for j=1:numel(model.metMiriams{i}.name) -0350 %Get existing metabolite indexes -0351 current=strcat(model.metMiriams{i}.name{j},'/',model.metMiriams{i}.value{j}); -0352 if isKey(miriams,current) -0353 existing=miriams(current); -0354 else -0355 existing=[]; -0356 end -0357 miriams(current)=[existing;i]; -0358 end -0359 end -0360 end -0361 -0362 %Get all keys -0363 allMiriams=keys(miriams); -0364 -0365 hasMultiple=false(numel(allMiriams),1); -0366 for i=1:numel(allMiriams) -0367 if numel(miriams(allMiriams{i}))>1 -0368 %Check if they all have the same name -0369 if numel(unique(model.metNames(miriams(allMiriams{i}))))>1 -0370 if ~regexp(allMiriams{i},'^sbo\/SBO:') % SBO terms are expected to be multiple -0371 hasMultiple(i)=true; -0372 end -0373 end -0374 end -0375 end -0376 -0377 %Print output -0378 EM='The following MIRIAM strings are associated to more than one unique metabolite name:'; -0379 dispEM(EM,false,allMiriams(hasMultiple),trimWarnings); -0380 end -0381 -0382 %Check if there are metabolites with different names but the same InChI -0383 %codes -0384 if isfield(model,'inchis') -0385 inchis=containers.Map(); -0386 for i=1:numel(model.mets) -0387 if ~isempty(model.inchis{i}) -0388 %Get existing metabolite indexes -0389 if isKey(inchis,model.inchis{i}) -0390 existing=inchis(model.inchis{i}); -0391 else -0392 existing=[]; -0393 end -0394 inchis(model.inchis{i})=[existing;i]; -0395 end -0396 end -0397 -0398 %Get all keys -0399 allInchis=keys(inchis); -0400 -0401 hasMultiple=false(numel(allInchis),1); -0402 for i=1:numel(allInchis) -0403 if numel(inchis(allInchis{i}))>1 -0404 %Check if they all have the same name -0405 if numel(unique(model.metNames(inchis(allInchis{i}))))>1 -0406 hasMultiple(i)=true; -0407 end -0408 end -0409 end -0410 -0411 %Print output -0412 EM='The following InChI strings are associated to more than one unique metabolite name:'; -0413 dispEM(EM,false,allInchis(hasMultiple),trimWarnings); -0414 end -0415 -0416 % %Check if there are metabolites with different names but the same SMILES -0417 % if isfield(model,'metSmiles') -0418 % metSmiles=containers.Map(); -0419 % for i=1:numel(model.mets) -0420 % if ~isempty(model.metSmiles{i}) -0421 % %Get existing metabolite indexes -0422 % if isKey(metSmiles,model.metSmiles{i}) -0423 % existing=metSmiles(model.metSmiles{i}); -0424 % else -0425 % existing=[]; -0426 % end -0427 % metSmiles(model.metSmiles{i})=[existing;i]; -0428 % end -0429 % end -0430 % -0431 % %Get all keys -0432 % allmetSmiles=keys(metSmiles); -0433 % -0434 % hasMultiple=false(numel(metSmiles),1); -0435 % for i=1:numel(metSmiles) -0436 % if numel(metSmiles(metSmiles{i}))>1 -0437 % %Check if they all have the same name -0438 % if numel(unique(model.metNames(metSmiles(allmetSmiles{i}))))>1 -0439 % hasMultiple(i)=true; -0440 % end -0441 % end -0442 % end -0443 % -0444 % %Print output -0445 % EM='The following metSmiles strings are associated to more than one unique metabolite name:'; -0446 % dispEM(EM,false,allmetSmiles(hasMultiple),trimWarnings); -0447 % end -0448 end -0449 -0450 function I=duplicates(strings) -0451 I=false(numel(strings),1); -0452 [J, K]=unique(strings); -0453 if numel(J)~=numel(strings) -0454 L=1:numel(strings); -0455 L(K)=[]; -0456 I(L)=true; -0457 end -0458 end +0258 EM = ['The following ' fieldNames{i} ' identifiers do not start '... +0259 'with a letter or _ (conflicting with SBML specifications). '... +0260 'This does not impact RAVEN functionality, but be aware that '... +0261 'exportModel will automatically add ' fieldPrefix{i} ... +0262 ' prefixes to all ' fieldNames{i} ' identifiers:']; +0263 dispEM(EM,false,{model.(fields{i}){numIDs}},trimWarnings); +0264 end +0265 end +0266 +0267 %Duplicates +0268 EM='The following reaction IDs are duplicates:'; +0269 dispEM(EM,throwErrors,model.rxns(duplicates(model.rxns)),trimWarnings); +0270 EM='The following metabolite IDs are duplicates:'; +0271 dispEM(EM,throwErrors,model.mets(duplicates(model.mets)),trimWarnings); +0272 EM='The following compartment IDs are duplicates:'; +0273 dispEM(EM,throwErrors,model.comps(duplicates(model.comps)),trimWarnings); +0274 if isfield(model,'genes') +0275 EM='The following genes are duplicates:'; +0276 dispEM(EM,throwErrors,model.genes(duplicates(model.genes)),trimWarnings); +0277 end +0278 metInComp=strcat(model.metNames,'[',model.comps(model.metComps),']'); +0279 EM='The following metabolites already exist in the same compartment:'; +0280 dispEM(EM,throwErrors,metInComp(duplicates(metInComp)),trimWarnings); +0281 +0282 %Elements never used (print only as warnings +0283 EM='The following reactions are empty (no involved metabolites):'; +0284 dispEM(EM,false,model.rxns(~any(model.S,1)),trimWarnings); +0285 EM='The following metabolites are never used in a reaction:'; +0286 dispEM(EM,false,model.mets(~any(model.S,2)),trimWarnings); +0287 if isfield(model,'genes') +0288 EM='The following genes are not associated to a reaction:'; +0289 dispEM(EM,false,model.genes(~any(model.rxnGeneMat,1)),trimWarnings); +0290 end +0291 I=true(numel(model.comps),1); +0292 I(model.metComps)=false; +0293 EM='The following compartments contain no metabolites:'; +0294 dispEM(EM,false,model.comps(I),trimWarnings); +0295 +0296 %Contradicting bounds +0297 EM='The following reactions have contradicting bounds (lower bound is higher than upper bound):'; +0298 dispEM(EM,throwErrors,model.rxns(model.lb>model.ub),trimWarnings); +0299 EM='The following reactions have lower and upper bounds that indicate reversibility, but are indicated as irreversible in model.rev:'; +0300 dispEM(EM,false,model.rxns(model.lb < 0 & model.ub > 0 & model.rev==0),trimWarnings); +0301 +0302 %Multiple or no objective functions not allowed in SBML L3V1 FBCv2 +0303 if numel(find(model.c))>1 +0304 EM='Multiple objective functions found. This might be intended, but results in FBCv2 non-compliant SBML file when exported'; +0305 dispEM(EM,false,model.rxns(find(model.c)),trimWarnings); +0306 elseif ~any(model.c) +0307 EM='No objective function found. This might be intended, but results in FBCv2 non-compliant SBML file when exported'; +0308 dispEM(EM,false); +0309 end +0310 +0311 %Mapping of compartments +0312 if isfield(model,'compOutside') +0313 EM='The following compartments are in "compOutside" but not in "comps":'; +0314 dispEM(EM,throwErrors,setdiff(model.compOutside,[{''};model.comps]),trimWarnings); +0315 end +0316 +0317 %Met names which start with number +0318 I=false(numel(model.metNames),1); +0319 for i=1:numel(model.metNames) +0320 index=strfind(model.metNames{i},' '); +0321 if any(index) +0322 if any(str2double(model.metNames{i}(1:index(1)-1))) +0323 I(i)=true; +0324 end +0325 end +0326 end +0327 EM='The following metabolite names begin with a number directly followed by space, which could potentially cause problems:'; +0328 dispEM(EM,false,model.metNames(I),trimWarnings); +0329 +0330 %Non-parseable composition +0331 if isfield(model,'metFormulas') +0332 [~, ~, exitFlag]=parseFormulas(model.metFormulas,true,false); +0333 EM='The composition for the following metabolites could not be parsed:'; +0334 dispEM(EM,false,model.mets(exitFlag==-1),trimWarnings); +0335 end +0336 +0337 %Check if there are metabolites with different names but the same MIRIAM +0338 %codes +0339 if isfield(model,'metMiriams') +0340 miriams=containers.Map(); +0341 for i=1:numel(model.mets) +0342 if ~isempty(model.metMiriams{i}) +0343 %Loop through and add for each miriam +0344 for j=1:numel(model.metMiriams{i}.name) +0345 %Get existing metabolite indexes +0346 current=strcat(model.metMiriams{i}.name{j},'/',model.metMiriams{i}.value{j}); +0347 if isKey(miriams,current) +0348 existing=miriams(current); +0349 else +0350 existing=[]; +0351 end +0352 miriams(current)=[existing;i]; +0353 end +0354 end +0355 end +0356 +0357 %Get all keys +0358 allMiriams=keys(miriams); +0359 +0360 hasMultiple=false(numel(allMiriams),1); +0361 for i=1:numel(allMiriams) +0362 if numel(miriams(allMiriams{i}))>1 +0363 %Check if they all have the same name +0364 if numel(unique(model.metNames(miriams(allMiriams{i}))))>1 +0365 if ~regexp(allMiriams{i},'^sbo\/SBO:') % SBO terms are expected to be multiple +0366 hasMultiple(i)=true; +0367 end +0368 end +0369 end +0370 end +0371 +0372 %Print output +0373 EM='The following MIRIAM strings are associated to more than one unique metabolite name:'; +0374 dispEM(EM,false,allMiriams(hasMultiple),trimWarnings); +0375 end +0376 +0377 %Check if there are metabolites with different names but the same InChI +0378 %codes +0379 if isfield(model,'inchis') +0380 inchis=containers.Map(); +0381 for i=1:numel(model.mets) +0382 if ~isempty(model.inchis{i}) +0383 %Get existing metabolite indexes +0384 if isKey(inchis,model.inchis{i}) +0385 existing=inchis(model.inchis{i}); +0386 else +0387 existing=[]; +0388 end +0389 inchis(model.inchis{i})=[existing;i]; +0390 end +0391 end +0392 +0393 %Get all keys +0394 allInchis=keys(inchis); +0395 +0396 hasMultiple=false(numel(allInchis),1); +0397 for i=1:numel(allInchis) +0398 if numel(inchis(allInchis{i}))>1 +0399 %Check if they all have the same name +0400 if numel(unique(model.metNames(inchis(allInchis{i}))))>1 +0401 hasMultiple(i)=true; +0402 end +0403 end +0404 end +0405 +0406 %Print output +0407 EM='The following InChI strings are associated to more than one unique metabolite name:'; +0408 dispEM(EM,false,allInchis(hasMultiple),trimWarnings); +0409 end +0410 +0411 % %Check if there are metabolites with different names but the same SMILES +0412 % if isfield(model,'metSmiles') +0413 % metSmiles=containers.Map(); +0414 % for i=1:numel(model.mets) +0415 % if ~isempty(model.metSmiles{i}) +0416 % %Get existing metabolite indexes +0417 % if isKey(metSmiles,model.metSmiles{i}) +0418 % existing=metSmiles(model.metSmiles{i}); +0419 % else +0420 % existing=[]; +0421 % end +0422 % metSmiles(model.metSmiles{i})=[existing;i]; +0423 % end +0424 % end +0425 % +0426 % %Get all keys +0427 % allmetSmiles=keys(metSmiles); +0428 % +0429 % hasMultiple=false(numel(metSmiles),1); +0430 % for i=1:numel(metSmiles) +0431 % if numel(metSmiles(metSmiles{i}))>1 +0432 % %Check if they all have the same name +0433 % if numel(unique(model.metNames(metSmiles(allmetSmiles{i}))))>1 +0434 % hasMultiple(i)=true; +0435 % end +0436 % end +0437 % end +0438 % +0439 % %Print output +0440 % EM='The following metSmiles strings are associated to more than one unique metabolite name:'; +0441 % dispEM(EM,false,allmetSmiles(hasMultiple),trimWarnings); +0442 % end +0443 end +0444 +0445 function I=duplicates(strings) +0446 I=false(numel(strings),1); +0447 [J, K]=unique(strings); +0448 if numel(J)~=numel(strings) +0449 L=1:numel(strings); +0450 L(K)=[]; +0451 I(L)=true; +0452 end +0453 end
Generated by m2html © 2005
\ No newline at end of file diff --git a/doc/index.html b/doc/index.html index dc5ea880..25c6ef92 100644 --- a/doc/index.html +++ b/doc/index.html @@ -23,9 +23,9 @@

Matlab Files found in these Directories

INITStepDesc expandModel getObjectiveString randomSampling ManualINITTests exportForGit getPathwayDimensions ravenCobraWrapper SBMLFromExcel exportModel getPhylDist readYAMLmodel - addCOBRAstylePrefixes exportModelToSIF getRxnsFromKEGG removeBadRxns - addExchangeRxns exportToExcelFormat getRxnsFromMetaCyc removeCOBRAstylePrefixes - addGenesRaven exportToTabDelimited getRxnsInComp removeGenes + addExchangeRxns exportModelToSIF getRxnsFromKEGG removeBadRxns + addGenesRaven exportToExcelFormat getRxnsFromMetaCyc removeGenes + addIdentifierPrefix exportToTabDelimited getRxnsInComp removeIdentifierPrefix addJavaPaths extractMiriam getToolboxVersion removeLowScoreGenes addMets fillGaps getTransportRxns removeMets addRavenToUserPath fillGapsLargeTests getWSLpath removeRavenFromPath diff --git a/doc/io/SBMLFromExcel.html b/doc/io/SBMLFromExcel.html index d54c5188..4565e925 100644 --- a/doc/io/SBMLFromExcel.html +++ b/doc/io/SBMLFromExcel.html @@ -49,7 +49,7 @@

DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

This function calls: +
  • exportModel exportModel
  • importExcelModel importExcelModel
    • This function is called by: @@ -87,7 +87,7 @@

    SOURCE CODE ^importExcelModel(fileName,false,printWarnings); 0029 printModelStats(model,printWarnings,false); -0030 exportModel(model,outputFileName,toCOBRA,true); +0030 exportModel(model,outputFileName,toCOBRA,true); 0031 end
    Generated by m2html © 2005
    diff --git a/doc/io/checkFileExistence.html b/doc/io/checkFileExistence.html index bc22e113..d17fbfcd 100644 --- a/doc/io/checkFileExistence.html +++ b/doc/io/checkFileExistence.html @@ -61,7 +61,7 @@

    CROSS-REFERENCE INFORMATION ^ </ul> This function is called by: <ul style= -
  • exportModel exportModel
  • getMD5Hash getMD5Hash
  • importModel importModel
    • +
  • exportModel exportModel
  • getMD5Hash getMD5Hash
  • importModel importModel
    • diff --git a/doc/io/exportForGit.html b/doc/io/exportForGit.html index ecb194ad..74a90f62 100644 --- a/doc/io/exportForGit.html +++ b/doc/io/exportForGit.html @@ -69,7 +69,7 @@

    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

    This function calls: +
  • exportModel exportModel
  • exportToExcelFormat exportToExcelFormat
  • getToolboxVersion getToolboxVersion
  • sortIdentifiers exportModel
  • writeYAMLmodel writeYAMLmodel
    • This function is called by: @@ -222,7 +222,7 @@

    SOURCE CODE ^% Write XML format 0144 if ismember('xml', formats) -0145 exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')),COBRAstyle); +0145 exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')),COBRAstyle); 0146 end 0147 0148 %Save file with versions: diff --git a/doc/io/exportModel.html b/doc/io/exportModel.html index ff9eea03..34b6f359 100644 --- a/doc/io/exportModel.html +++ b/doc/io/exportModel.html @@ -24,7 +24,7 @@

    PURPOSE ^exportModel

    SYNOPSIS ^

    -
    function exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
    +
    function exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)

    DESCRIPTION ^

     exportModel
@@ -34,12 +34,9 @@ 
    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • checkFileExistence	checkFileExistence
  • exportModel	exportModel
  • sortIdentifiers	exportModel
    • 
 This function is called by:
 
+
  • SBMLFromExcel	SBMLFromExcel
  • exportForGit	exportForGit
  • exportModel	exportModel
    • 
 
 
 
    SUBFUNCTIONS ^
    
@@ -64,7 +61,7 @@ 
    SUBFUNCTIONS ^function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
  • function miriamString=getMiriam(miriamStruct)
  • function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
  • function vecT = columnVector(vec)
    • 
 
 
    SOURCE CODE ^
    
-
    0001 function exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
+
    0001 function exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)
 0002 % exportModel
 0003 %   Exports a constraint-based model to an SBML file (L3V1 FBCv2)
 0004 %
@@ -72,793 +69,788 @@ 
    SOURCE CODE ^%   model               a model structure
 0007 %   fileName            filename to export the model to. A dialog window
 0008 %                       will open if no file name is specified.
-0009 %   COBRAstyle          true if COBRA-style prefixes should be added to all
-0010 %                       identifiers: R_ for reactions, M_ for metabolites,
-0011 %                       G_ for genes and C_ for compartments. If all
-0012 %                       identifiers of a particular field already have the
-0013 %                       prefix, then no additional prefixes are added.
-0014 %                       (optional, default false)
-0015 %   supressWarnings     true if warnings should be supressed. This might
-0016 %                       results in invalid SBML files, as no checks are
-0017 %                       performed (optional, default false)
-0018 %   sortIds             logical whether metabolites, reactions and genes
-0019 %                       should be sorted alphabetically by their
-0020 %                       identifiers (optional, default false)
-0021 %
-0022 % Usage: exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
-0023 
-0024 if nargin<2 || isempty(fileName)
-0025     [fileName, pathName] = uiputfile({'*.xml;*.sbml'}, 'Select file for model export',[model.id '.xml']);
-0026     if fileName == 0
-0027         error('You should provide a file location')
-0028     else
-0029         fileName = fullfile(pathName,fileName);
-0030     end
-0031 end
-0032 fileName=char(fileName);
-0033 if nargin<3
-0034     COBRAstyle=false;
-0035 elseif ~islogical(COBRAstyle)
-0036     error("COBRAstyle should be either true or false")
-0037 end
-0038 if nargin<4
-0039     supressWarnings=false;
-0040 end
-0041 if nargin<5
-0042     sortIds=false;
-0043 end
-0044 if sortIds==true
-0045     model=sortIdentifiers(model);
-0046 end
-0047 
-0048 if isfield(model,'ec')
-0049     warning("exportModel does not store information from the 'model.ec' structure. Use 'writeYAMLmodel(model)' to export all content from a GECKO model.")
-0050 end
-0051 
-0052 %If no subSystems are defined, then no need to use groups package
-0053 if isfield(model,'subSystems')
-0054     modelHasSubsystems=true;
-0055 else
-0056     modelHasSubsystems=false;
-0057 end
-0058 
-0059 %The default SBML format settings, which are used as input for appropriate
-0060 %libSBML functions to generate the blank SBML model structure before using
-0061 %exporting in with OutputSBML to xml file
-0062 sbmlLevel=3;
-0063 sbmlVersion=1;
-0064 sbmlPackages={'fbc'};
-0065 sbmlPackageVersions=2;
-0066 if modelHasSubsystems
-0067     sbmlPackages={sbmlPackages,'groups'};
-0068     sbmlPackageVersions=[sbmlPackageVersions,1];
-0069 end
-0070 
-0071 %Check if the "unconstrained" field is still present. This shows if
-0072 %exchange metabolites have been removed
-0073 if ~isfield(model,'unconstrained')
-0074     model.unconstrained=zeros(numel(model.mets),1);
-0075 end
-0076 
-0077 %If model id and name do not exist, make sure that default
-0078 %strings are included
-0079 if ~isfield(model,'id')
-0080     fprintf('WARNING: The model is missing the "id" field. Uses "blankID". \n');
-0081     model.id='blankID';
-0082 end
-0083 if ~isfield(model,'name')
-0084     fprintf('WARNING: The model is missing the "name" field. Uses "blankName". \n');
-0085     model.name='blankName';
-0086 end
-0087 
-0088 % Add prefixes if desired
-0089 if COBRAstyle
-0090     if isfield(model,'ec')
-0091         error('ecModels cannot be exported with COBRAstyle flag, manually correct any non-compliant identifiers if needed.')
-0092     end
-0093     model = addCOBRAstylePrefixes(model,[],false);
+0009 %   neverPrefix         true if prefixes are never added to identifiers,
+0010 %                       even if start with e.g. digits. This might result
+0011 %                       in invalid SBML files (optional, default false)
+0012 %   supressWarnings     true if warnings should be supressed. This might
+0013 %                       results in invalid SBML files, as no checks are
+0014 %                       performed (optional, default false)
+0015 %   sortIds             logical whether metabolites, reactions and genes
+0016 %                       should be sorted alphabetically by their
+0017 %                       identifiers (optional, default false)
+0018 %
+0019 % Usage: exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)
+0020 
+0021 if nargin<2 || isempty(fileName)
+0022     [fileName, pathName] = uiputfile({'*.xml;*.sbml'}, 'Select file for model export',[model.id '.xml']);
+0023     if fileName == 0
+0024         error('You should provide a file location')
+0025     else
+0026         fileName = fullfile(pathName,fileName);
+0027     end
+0028 end
+0029 fileName=char(fileName);
+0030 if nargin<3 || isempty(neverPrefix)
+0031     neverPrefix=false;
+0032 end
+0033 if nargin<4 || isempty(supressWarnings)
+0034     supressWarnings=false;
+0035 end
+0036 if nargin<5 || isempty(sortIds)
+0037     sortIds=false;
+0038 end
+0039 if sortIds==true
+0040     model=sortIdentifiers(model);
+0041 end
+0042 
+0043 if isfield(model,'ec')
+0044     warning("exportModel does not store information from the 'model.ec' structure. Use 'writeYAMLmodel(model)' to export all content from a GECKO model.")
+0045 end
+0046 
+0047 %If no subSystems are defined, then no need to use groups package
+0048 if isfield(model,'subSystems')
+0049     modelHasSubsystems=true;
+0050 else
+0051     modelHasSubsystems=false;
+0052 end
+0053 
+0054 %The default SBML format settings, which are used as input for appropriate
+0055 %libSBML functions to generate the blank SBML model structure before using
+0056 %exporting in with OutputSBML to xml file
+0057 sbmlLevel=3;
+0058 sbmlVersion=1;
+0059 sbmlPackages={'fbc'};
+0060 sbmlPackageVersions=2;
+0061 if modelHasSubsystems
+0062     sbmlPackages={sbmlPackages,'groups'};
+0063     sbmlPackageVersions=[sbmlPackageVersions,1];
+0064 end
+0065 
+0066 %Check if the "unconstrained" field is still present. This shows if
+0067 %exchange metabolites have been removed
+0068 if ~isfield(model,'unconstrained')
+0069     model.unconstrained=zeros(numel(model.mets),1);
+0070 end
+0071 
+0072 %If model id and name do not exist, make sure that default
+0073 %strings are included
+0074 if ~isfield(model,'id')
+0075     fprintf('WARNING: The model is missing the "id" field. Uses "blankID". \n');
+0076     model.id='blankID';
+0077 end
+0078 if ~isfield(model,'name')
+0079     fprintf('WARNING: The model is missing the "name" field. Uses "blankName". \n');
+0080     model.name='blankName';
+0081 end
+0082 
+0083 % Add prefixes if required
+0084 if ~neverPrefix
+0085     [model,hasChanged] = addIdentifierPrefix(model);
+0086     dispEM(['The following fields have one or more entries that do not start '...
+0087         'with a letter or _ (conflicting with SBML specifications). Prefixes '...
+0088         'are added to all entries in those fields:'],false,hasChanged)
+0089 end
+0090 
+0091 %Check the model structure
+0092 if supressWarnings==false
+0093     checkModelStruct(model);
 0094 end
 0095 
-0096 %Check the model structure
-0097 if supressWarnings==false
-0098     checkModelStruct(model,false);
-0099 end
-0100 
-0101 %Add several blank fields, if they do not exist already. This is to reduce
-0102 %the number of conditions below
-0103 if ~isfield(model,'compMiriams')
-0104     model.compMiriams=cell(numel(model.comps),1);
-0105 end
-0106 if ~isfield(model,'inchis')
-0107     model.inchis=cell(numel(model.mets),1);
-0108 end
-0109 if ~isfield(model,'metFormulas')
-0110     model.metFormulas=cell(numel(model.mets),1);
-0111 end
-0112 if ~isfield(model,'metMiriams')
-0113     model.metMiriams=cell(numel(model.mets),1);
-0114 end
-0115 if ~isfield(model,'geneMiriams') && isfield(model,'genes')
-0116     model.geneMiriams=cell(numel(model.genes),1);
-0117 end
-0118 if ~isfield(model,'geneShortNames') && isfield(model,'genes')
-0119     model.geneShortNames=cell(numel(model.genes),1);
-0120 end
-0121 if ~isfield(model,'proteins') && isfield(model,'genes')
-0122     model.proteins=cell(numel(model.genes),1);
-0123 end
-0124 if ~isfield(model,'subSystems')
-0125     model.subSystems=cell(numel(model.rxns),1);
-0126 end
-0127 if ~isfield(model,'eccodes')
-0128     model.eccodes=cell(numel(model.rxns),1);
-0129 end
-0130 if ~isfield(model,'rxnReferences')
-0131     model.rxnReferences=cell(numel(model.rxns),1);
-0132 end
-0133 if ~isfield(model,'rxnConfidenceScores')
-0134     model.rxnConfidenceScores=NaN(numel(model.rxns),1);
-0135 end
-0136 if ~isfield(model,'rxnNotes')
-0137     model.rxnNotes=cell(numel(model.rxns),1);
-0138 end
-0139 if ~isfield(model,'rxnMiriams')
-0140     model.rxnMiriams=cell(numel(model.rxns),1);
-0141 end
-0142 
-0143 if sbmlLevel<3
-0144     %Check if genes have associated compartments
-0145     if ~isfield(model,'geneComps') && isfield(model,'genes')
-0146         if supressWarnings==false
-0147             EM='There are no compartments specified for genes. All genes will be assigned to the first compartment. This is because the SBML structure requires all elements to be assigned to a compartment';
-0148             dispEM(EM,false);
-0149         end
-0150         model.geneComps=ones(numel(model.genes),1);
-0151     end
-0152 end
-0153 
-0154 %Convert ids to SBML-convenient format. This is to avoid the data loss when
-0155 %unsupported characters are included in ids. Here we are using part from
-0156 %convertSBMLID, originating from the COBRA Toolbox
-0157 model.rxns=regexprep(model.rxns,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0158 model.mets=regexprep(model.mets,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0159 model.comps=regexprep(model.comps,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0160 if isfield(model,'genes')
-0161     problemGenes=find(~cellfun('isempty',regexp(model.genes,'([^0-9_a-zA-Z])')));
-0162     originalGenes=model.genes(problemGenes);
-0163     replacedGenes=regexprep(model.genes(problemGenes),'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0164     model.genes(problemGenes)=replacedGenes;
-0165     for i=1:numel(problemGenes)
-0166         model.grRules = regexprep(model.grRules, ['(^|\s|\()' originalGenes{i} '($|\s|\))'], ['$1' replacedGenes{i} '$2']);
-0167     end
-0168 end
-0169 
-0170 %Generate an empty SBML structure
-0171 modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0172 modelSBML.metaid=model.id;
-0173 modelSBML.id=regexprep(model.id,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0174 modelSBML.name=model.name;
-0175 
-0176 if isfield(model,'annotation')
-0177     if isfield(model.annotation,'note')
-0178         modelSBML.notes=['<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>',regexprep(model.annotation.note,'<p>|</p>',''),'</p></body></notes>'];
-0179     end
-0180 else
-0181     modelSBML.notes='<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>This file was generated using the exportModel function in RAVEN Toolbox 2 and OutputSBML in libSBML </p></body></notes>';
-0182 end
-0183 
-0184 if isfield(model,'annotation')
-0185     nameString='';
-0186     if isfield(model.annotation,'familyName')
-0187         if ~isempty(model.annotation.familyName)
-0188             nameString=['<vCard:Family>' model.annotation.familyName '</vCard:Family>'];
+0096 %Add several blank fields, if they do not exist already. This is to reduce
+0097 %the number of conditions below
+0098 if ~isfield(model,'compMiriams')
+0099     model.compMiriams=cell(numel(model.comps),1);
+0100 end
+0101 if ~isfield(model,'inchis')
+0102     model.inchis=cell(numel(model.mets),1);
+0103 end
+0104 if ~isfield(model,'metFormulas')
+0105     model.metFormulas=cell(numel(model.mets),1);
+0106 end
+0107 if ~isfield(model,'metMiriams')
+0108     model.metMiriams=cell(numel(model.mets),1);
+0109 end
+0110 if ~isfield(model,'geneMiriams') && isfield(model,'genes')
+0111     model.geneMiriams=cell(numel(model.genes),1);
+0112 end
+0113 if ~isfield(model,'geneShortNames') && isfield(model,'genes')
+0114     model.geneShortNames=cell(numel(model.genes),1);
+0115 end
+0116 if ~isfield(model,'proteins') && isfield(model,'genes')
+0117     model.proteins=cell(numel(model.genes),1);
+0118 end
+0119 if ~isfield(model,'subSystems')
+0120     model.subSystems=cell(numel(model.rxns),1);
+0121 end
+0122 if ~isfield(model,'eccodes')
+0123     model.eccodes=cell(numel(model.rxns),1);
+0124 end
+0125 if ~isfield(model,'rxnReferences')
+0126     model.rxnReferences=cell(numel(model.rxns),1);
+0127 end
+0128 if ~isfield(model,'rxnConfidenceScores')
+0129     model.rxnConfidenceScores=NaN(numel(model.rxns),1);
+0130 end
+0131 if ~isfield(model,'rxnNotes')
+0132     model.rxnNotes=cell(numel(model.rxns),1);
+0133 end
+0134 if ~isfield(model,'rxnMiriams')
+0135     model.rxnMiriams=cell(numel(model.rxns),1);
+0136 end
+0137 
+0138 if sbmlLevel<3
+0139     %Check if genes have associated compartments
+0140     if ~isfield(model,'geneComps') && isfield(model,'genes')
+0141         if supressWarnings==false
+0142             EM='There are no compartments specified for genes. All genes will be assigned to the first compartment. This is because the SBML structure requires all elements to be assigned to a compartment';
+0143             dispEM(EM,false);
+0144         end
+0145         model.geneComps=ones(numel(model.genes),1);
+0146     end
+0147 end
+0148 
+0149 %Convert ids to SBML-convenient format. This is to avoid the data loss when
+0150 %unsupported characters are included in ids. Here we are using part from
+0151 %convertSBMLID, originating from the COBRA Toolbox
+0152 model.rxns=regexprep(model.rxns,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0153 model.mets=regexprep(model.mets,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0154 model.comps=regexprep(model.comps,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0155 if isfield(model,'genes')
+0156     problemGenes=find(~cellfun('isempty',regexp(model.genes,'([^0-9_a-zA-Z])')));
+0157     originalGenes=model.genes(problemGenes);
+0158     replacedGenes=regexprep(model.genes(problemGenes),'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0159     model.genes(problemGenes)=replacedGenes;
+0160     for i=1:numel(problemGenes)
+0161         model.grRules = regexprep(model.grRules, ['(^|\s|\()' originalGenes{i} '($|\s|\))'], ['$1' replacedGenes{i} '$2']);
+0162     end
+0163 end
+0164 
+0165 %Generate an empty SBML structure
+0166 modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0167 modelSBML.metaid=model.id;
+0168 modelSBML.id=regexprep(model.id,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0169 modelSBML.name=model.name;
+0170 
+0171 if isfield(model,'annotation')
+0172     if isfield(model.annotation,'note')
+0173         modelSBML.notes=['<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>',regexprep(model.annotation.note,'<p>|</p>',''),'</p></body></notes>'];
+0174     end
+0175 else
+0176     modelSBML.notes='<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>This file was generated using the exportModel function in RAVEN Toolbox 2 and OutputSBML in libSBML </p></body></notes>';
+0177 end
+0178 
+0179 if isfield(model,'annotation')
+0180     nameString='';
+0181     if isfield(model.annotation,'familyName')
+0182         if ~isempty(model.annotation.familyName)
+0183             nameString=['<vCard:Family>' model.annotation.familyName '</vCard:Family>'];
+0184         end
+0185     end
+0186     if isfield(model.annotation,'givenName')
+0187         if ~isempty(model.annotation.givenName)
+0188             nameString=[nameString '<vCard:Given>' model.annotation.givenName '</vCard:Given>'];
 0189         end
 0190     end
-0191     if isfield(model.annotation,'givenName')
-0192         if ~isempty(model.annotation.givenName)
-0193             nameString=[nameString '<vCard:Given>' model.annotation.givenName '</vCard:Given>'];
-0194         end
-0195     end
-0196     email='';
-0197     if isfield(model.annotation,'email')
-0198         if ~isempty(model.annotation.email)
-0199             email=['<vCard:EMAIL>' model.annotation.email '</vCard:EMAIL>'];
-0200         end
-0201     end
-0202     org='';
-0203     if isfield(model.annotation,'organization')
-0204         if ~isempty(model.annotation.organization)
-0205             org=['<vCard:ORG rdf:parseType="Resource"><vCard:Orgname>' model.annotation.organization '</vCard:Orgname></vCard:ORG>'];
-0206         end
-0207     end
-0208     if ~isempty(nameString) || ~isempty(email) || ~isempty(org) % Only fill .annotation if ownership data is provided
-0209         modelSBML.annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.id '">'];
-0210         modelSBML.annotation=[modelSBML.annotation '<dc:creator><rdf:Bag><rdf:li rdf:parseType="Resource">'];
-0211         if ~isempty(nameString)
-0212             modelSBML.annotation=[modelSBML.annotation '<vCard:N rdf:parseType="Resource">' nameString '</vCard:N>'];
-0213         end
-0214         modelSBML.annotation=[modelSBML.annotation email org '</rdf:li></rdf:Bag></dc:creator>'];
-0215         modelSBML.annotation=[modelSBML.annotation '<dcterms:created rdf:parseType="Resource">'...
-0216             '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF></dcterms:created><dcterms:modified rdf:parseType="Resource">'...
-0217             '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF></dcterms:modified>'];
-0218         if isfield(model.annotation,'taxonomy')
-0219             modelSBML.annotation=[modelSBML.annotation '<bqbiol:is><rdf:Bag><rdf:li rdf:resource="https://identifiers.org/taxonomy/' regexprep(model.annotation.taxonomy,'taxonomy/','') '"/></rdf:Bag></bqbiol:is>'];
-0220         end
-0221         modelSBML.annotation=[modelSBML.annotation '</rdf:Description></rdf:RDF></annotation>'];
-0222     end
-0223 end
-0224 
-0225 %Prepare compartments
-0226 for i=1:numel(model.comps)
-0227     %Add the default values, as these will be the same in all entries
-0228     if i==1
-0229         if isfield(modelSBML.compartment, 'sboTerm')
-0230             modelSBML.compartment(i).sboTerm=290;
-0231         end
-0232         if isfield(modelSBML.compartment, 'spatialDimensions')
-0233             modelSBML.compartment(i).spatialDimensions=3;
-0234         end
-0235         if isfield(modelSBML.compartment, 'size')
-0236             modelSBML.compartment(i).size=1;
-0237         end
-0238         if isfield(modelSBML.compartment, 'constant')
-0239             modelSBML.compartment(i).constant=1;
-0240         end
-0241         if isfield(modelSBML.compartment, 'isSetSize')
-0242             modelSBML.compartment(i).isSetSize=1;
-0243         end
-0244         if isfield(modelSBML.compartment, 'isSetSpatialDimensions')
-0245             modelSBML.compartment(i).isSetSpatialDimensions=1;
-0246         end
+0191     email='';
+0192     if isfield(model.annotation,'email')
+0193         if ~isempty(model.annotation.email)
+0194             email=['<vCard:EMAIL>' model.annotation.email '</vCard:EMAIL>'];
+0195         end
+0196     end
+0197     org='';
+0198     if isfield(model.annotation,'organization')
+0199         if ~isempty(model.annotation.organization)
+0200             org=['<vCard:ORG rdf:parseType="Resource"><vCard:Orgname>' model.annotation.organization '</vCard:Orgname></vCard:ORG>'];
+0201         end
+0202     end
+0203     if ~isempty(nameString) || ~isempty(email) || ~isempty(org) % Only fill .annotation if ownership data is provided
+0204         modelSBML.annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.id '">'];
+0205         modelSBML.annotation=[modelSBML.annotation '<dc:creator><rdf:Bag><rdf:li rdf:parseType="Resource">'];
+0206         if ~isempty(nameString)
+0207             modelSBML.annotation=[modelSBML.annotation '<vCard:N rdf:parseType="Resource">' nameString '</vCard:N>'];
+0208         end
+0209         modelSBML.annotation=[modelSBML.annotation email org '</rdf:li></rdf:Bag></dc:creator>'];
+0210         modelSBML.annotation=[modelSBML.annotation '<dcterms:created rdf:parseType="Resource">'...
+0211             '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF></dcterms:created><dcterms:modified rdf:parseType="Resource">'...
+0212             '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF></dcterms:modified>'];
+0213         if isfield(model.annotation,'taxonomy')
+0214             modelSBML.annotation=[modelSBML.annotation '<bqbiol:is><rdf:Bag><rdf:li rdf:resource="https://identifiers.org/taxonomy/' regexprep(model.annotation.taxonomy,'taxonomy/','') '"/></rdf:Bag></bqbiol:is>'];
+0215         end
+0216         modelSBML.annotation=[modelSBML.annotation '</rdf:Description></rdf:RDF></annotation>'];
+0217     end
+0218 end
+0219 
+0220 %Prepare compartments
+0221 for i=1:numel(model.comps)
+0222     %Add the default values, as these will be the same in all entries
+0223     if i==1
+0224         if isfield(modelSBML.compartment, 'sboTerm')
+0225             modelSBML.compartment(i).sboTerm=290;
+0226         end
+0227         if isfield(modelSBML.compartment, 'spatialDimensions')
+0228             modelSBML.compartment(i).spatialDimensions=3;
+0229         end
+0230         if isfield(modelSBML.compartment, 'size')
+0231             modelSBML.compartment(i).size=1;
+0232         end
+0233         if isfield(modelSBML.compartment, 'constant')
+0234             modelSBML.compartment(i).constant=1;
+0235         end
+0236         if isfield(modelSBML.compartment, 'isSetSize')
+0237             modelSBML.compartment(i).isSetSize=1;
+0238         end
+0239         if isfield(modelSBML.compartment, 'isSetSpatialDimensions')
+0240             modelSBML.compartment(i).isSetSpatialDimensions=1;
+0241         end
+0242     end
+0243     %Copy the default values to the next entry as long as it is not the
+0244     %last one
+0245     if i<numel(model.comps)
+0246         modelSBML.compartment(i+1)=modelSBML.compartment(i);
 0247     end
-0248     %Copy the default values to the next entry as long as it is not the
-0249     %last one
-0250     if i<numel(model.comps)
-0251         modelSBML.compartment(i+1)=modelSBML.compartment(i);
-0252     end
-0253     
-0254     if isfield(modelSBML.compartment,'metaid')
-0255         modelSBML.compartment(i).metaid=model.comps{i};
-0256     end
-0257     %Prepare Miriam strings
-0258     if ~isempty(model.compMiriams{i})
-0259         [~,sbo_ind] = ismember('sbo',model.compMiriams{i}.name);
-0260         if sbo_ind > 0
-0261             modelSBML.compartment(i).sboTerm=str2double(regexprep(model.compMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0262             % remove the SBO term from compMiriams so the information is
-0263             % not duplicated in the "annotation" field later on
-0264             model.compMiriams{i}.name(sbo_ind) = [];
-0265             model.compMiriams{i}.value(sbo_ind) = [];
-0266         end
+0248     
+0249     if isfield(modelSBML.compartment,'metaid')
+0250         modelSBML.compartment(i).metaid=model.comps{i};
+0251     end
+0252     %Prepare Miriam strings
+0253     if ~isempty(model.compMiriams{i})
+0254         [~,sbo_ind] = ismember('sbo',model.compMiriams{i}.name);
+0255         if sbo_ind > 0
+0256             modelSBML.compartment(i).sboTerm=str2double(regexprep(model.compMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0257             % remove the SBO term from compMiriams so the information is
+0258             % not duplicated in the "annotation" field later on
+0259             model.compMiriams{i}.name(sbo_ind) = [];
+0260             model.compMiriams{i}.value(sbo_ind) = [];
+0261         end
+0262     end
+0263     if ~isempty(model.compMiriams{i}) && isfield(modelSBML.compartment(i),'annotation')
+0264         modelSBML.compartment(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.comps{i} '">'];
+0265         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation '<bqbiol:is><rdf:Bag>'];
+0266         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation getMiriam(model.compMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
 0267     end
-0268     if ~isempty(model.compMiriams{i}) && isfield(modelSBML.compartment(i),'annotation')
-0269         modelSBML.compartment(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.comps{i} '">'];
-0270         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation '<bqbiol:is><rdf:Bag>'];
-0271         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation getMiriam(model.compMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0272     end
-0273     if isfield(modelSBML.compartment, 'name')
-0274         modelSBML.compartment(i).name=model.compNames{i};
-0275     end
-0276     if isfield(modelSBML.compartment, 'id')
-0277         modelSBML.compartment(i).id=model.comps{i};
-0278     end
-0279     
-0280 end
-0281 
-0282 %Begin writing species
-0283 for i=1:numel(model.mets)
-0284     %Add the default values, as these will be the same in all entries
-0285     if i==1
-0286         if isfield(modelSBML.species, 'sboTerm')
-0287             modelSBML.species(i).sboTerm=247;
-0288         end
-0289         if isfield(modelSBML.species, 'initialAmount')
-0290             modelSBML.species(i).initialAmount=1;
-0291         end
-0292         if isfield(modelSBML.species, 'initialConcentration')
-0293             modelSBML.species(i).initialConcentration=0;
-0294         end
-0295         if isfield(modelSBML.species, 'isSetInitialAmount')
-0296             modelSBML.species(i).isSetInitialAmount=1;
-0297         end
-0298         if isfield(modelSBML.species, 'isSetInitialConcentration')
-0299             modelSBML.species(i).isSetInitialConcentration=1;
-0300         end
+0268     if isfield(modelSBML.compartment, 'name')
+0269         modelSBML.compartment(i).name=model.compNames{i};
+0270     end
+0271     if isfield(modelSBML.compartment, 'id')
+0272         modelSBML.compartment(i).id=model.comps{i};
+0273     end
+0274     
+0275 end
+0276 
+0277 %Begin writing species
+0278 for i=1:numel(model.mets)
+0279     %Add the default values, as these will be the same in all entries
+0280     if i==1
+0281         if isfield(modelSBML.species, 'sboTerm')
+0282             modelSBML.species(i).sboTerm=247;
+0283         end
+0284         if isfield(modelSBML.species, 'initialAmount')
+0285             modelSBML.species(i).initialAmount=1;
+0286         end
+0287         if isfield(modelSBML.species, 'initialConcentration')
+0288             modelSBML.species(i).initialConcentration=0;
+0289         end
+0290         if isfield(modelSBML.species, 'isSetInitialAmount')
+0291             modelSBML.species(i).isSetInitialAmount=1;
+0292         end
+0293         if isfield(modelSBML.species, 'isSetInitialConcentration')
+0294             modelSBML.species(i).isSetInitialConcentration=1;
+0295         end
+0296     end
+0297     %Copy the default values to the next entry as long as it is not the
+0298     %last one
+0299     if i<numel(model.mets)
+0300         modelSBML.species(i+1)=modelSBML.species(i);
 0301     end
-0302     %Copy the default values to the next entry as long as it is not the
-0303     %last one
-0304     if i<numel(model.mets)
-0305         modelSBML.species(i+1)=modelSBML.species(i);
-0306     end
-0307     
-0308     if isfield(modelSBML.species,'metaid')
-0309         modelSBML.species(i).metaid=model.mets{i};
-0310     end
-0311     if isfield(modelSBML.species, 'name')
-0312         modelSBML.species(i).name=model.metNames{i};
-0313     end
-0314     if isfield(modelSBML.species, 'id')
-0315         modelSBML.species(i).id=model.mets{i};
-0316     end
-0317     if isfield(modelSBML.species, 'compartment')
-0318         modelSBML.species(i).compartment=model.comps{model.metComps(i)};
+0302     
+0303     if isfield(modelSBML.species,'metaid')
+0304         modelSBML.species(i).metaid=model.mets{i};
+0305     end
+0306     if isfield(modelSBML.species, 'name')
+0307         modelSBML.species(i).name=model.metNames{i};
+0308     end
+0309     if isfield(modelSBML.species, 'id')
+0310         modelSBML.species(i).id=model.mets{i};
+0311     end
+0312     if isfield(modelSBML.species, 'compartment')
+0313         modelSBML.species(i).compartment=model.comps{model.metComps(i)};
+0314     end
+0315     if isfield(model,'unconstrained')
+0316         if model.unconstrained(i)
+0317             modelSBML.species(i).boundaryCondition=1;
+0318         end
 0319     end
-0320     if isfield(model,'unconstrained')
-0321         if model.unconstrained(i)
-0322             modelSBML.species(i).boundaryCondition=1;
-0323         end
-0324     end
-0325     if isfield(modelSBML.species, 'fbc_charge') && isfield(model,'metCharges')
-0326         if ~isnan(model.metCharges(i))
-0327             modelSBML.species(i).fbc_charge=model.metCharges(i);
-0328             modelSBML.species(i).isSetfbc_charge=1;
-0329         else
-0330             modelSBML.species(i).isSetfbc_charge=0;
-0331         end
-0332     end
-0333     if ~isempty(model.metMiriams{i})
-0334         [~,sbo_ind] = ismember('sbo',model.metMiriams{i}.name);
-0335         if sbo_ind > 0
-0336             modelSBML.species(i).sboTerm=str2double(regexprep(model.metMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0337             % remove the SBO term from metMiriams so the information is
-0338             % not duplicated in the "annotation" field later on
-0339             model.metMiriams{i}.name(sbo_ind) = [];
-0340             model.metMiriams{i}.value(sbo_ind) = [];
-0341         end
-0342     end
-0343     if isfield(modelSBML.species,'annotation')
-0344         if ~isempty(model.metMiriams{i}) || ~isempty(model.metFormulas{i})
-0345             hasInchi=false;
-0346             if ~isempty(model.metFormulas{i})
-0347                 %Only export formula if there is no InChI. This is because
-0348                 %the metFormulas field is populated by InChIs if available
-0349                 if ~isempty(model.inchis{i})
-0350                     hasInchi=true;
-0351                 end
-0352                 if hasInchi==false
-0353                     modelSBML.species(i).fbc_chemicalFormula=model.metFormulas{i};
-0354                 end
-0355             end
-0356             if ~isempty(model.metMiriams{i}) || hasInchi==true
-0357                 modelSBML.species(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.mets{i} '">'];
-0358                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<bqbiol:is><rdf:Bag>'];
-0359                 if ~isempty(model.metMiriams{i})
-0360                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation getMiriam(model.metMiriams{i})];
-0361                 end
-0362                 if hasInchi==true
-0363                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<rdf:li rdf:resource="https://identifiers.org/inchi/InChI=' regexprep(model.inchis{i},'^InChI=','') '"/>'];
-0364                     modelSBML.species(i).fbc_chemicalFormula=char(regexp(model.inchis{i}, '/(\w+)/', 'tokens', 'once'));
-0365                 end
-0366                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0367             end
-0368         end
-0369     end
-0370 end
-0371 
-0372 if isfield(model,'genes')
-0373     for i=1:numel(model.genes)
-0374         %Add the default values, as these will be the same in all entries
-0375         if i==1
-0376             if isfield(modelSBML.fbc_geneProduct, 'sboTerm')
-0377                 modelSBML.fbc_geneProduct(i).sboTerm=243;
-0378             end
+0320     if isfield(modelSBML.species, 'fbc_charge') && isfield(model,'metCharges')
+0321         if ~isnan(model.metCharges(i))
+0322             modelSBML.species(i).fbc_charge=model.metCharges(i);
+0323             modelSBML.species(i).isSetfbc_charge=1;
+0324         else
+0325             modelSBML.species(i).isSetfbc_charge=0;
+0326         end
+0327     end
+0328     if ~isempty(model.metMiriams{i})
+0329         [~,sbo_ind] = ismember('sbo',model.metMiriams{i}.name);
+0330         if sbo_ind > 0
+0331             modelSBML.species(i).sboTerm=str2double(regexprep(model.metMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0332             % remove the SBO term from metMiriams so the information is
+0333             % not duplicated in the "annotation" field later on
+0334             model.metMiriams{i}.name(sbo_ind) = [];
+0335             model.metMiriams{i}.value(sbo_ind) = [];
+0336         end
+0337     end
+0338     if isfield(modelSBML.species,'annotation')
+0339         if ~isempty(model.metMiriams{i}) || ~isempty(model.metFormulas{i})
+0340             hasInchi=false;
+0341             if ~isempty(model.metFormulas{i})
+0342                 %Only export formula if there is no InChI. This is because
+0343                 %the metFormulas field is populated by InChIs if available
+0344                 if ~isempty(model.inchis{i})
+0345                     hasInchi=true;
+0346                 end
+0347                 if hasInchi==false
+0348                     modelSBML.species(i).fbc_chemicalFormula=model.metFormulas{i};
+0349                 end
+0350             end
+0351             if ~isempty(model.metMiriams{i}) || hasInchi==true
+0352                 modelSBML.species(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.mets{i} '">'];
+0353                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<bqbiol:is><rdf:Bag>'];
+0354                 if ~isempty(model.metMiriams{i})
+0355                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation getMiriam(model.metMiriams{i})];
+0356                 end
+0357                 if hasInchi==true
+0358                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<rdf:li rdf:resource="https://identifiers.org/inchi/InChI=' regexprep(model.inchis{i},'^InChI=','') '"/>'];
+0359                     modelSBML.species(i).fbc_chemicalFormula=char(regexp(model.inchis{i}, '/(\w+)/', 'tokens', 'once'));
+0360                 end
+0361                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0362             end
+0363         end
+0364     end
+0365 end
+0366 
+0367 if isfield(model,'genes')
+0368     for i=1:numel(model.genes)
+0369         %Add the default values, as these will be the same in all entries
+0370         if i==1
+0371             if isfield(modelSBML.fbc_geneProduct, 'sboTerm')
+0372                 modelSBML.fbc_geneProduct(i).sboTerm=243;
+0373             end
+0374         end
+0375         %Copy the default values to the next index as long as it is not the
+0376         %last one
+0377         if i<numel(model.genes)
+0378             modelSBML.fbc_geneProduct(i+1)=modelSBML.fbc_geneProduct(i);
 0379         end
-0380         %Copy the default values to the next index as long as it is not the
-0381         %last one
-0382         if i<numel(model.genes)
-0383             modelSBML.fbc_geneProduct(i+1)=modelSBML.fbc_geneProduct(i);
-0384         end
-0385         
-0386         if isfield(modelSBML.fbc_geneProduct,'metaid')
-0387             modelSBML.fbc_geneProduct(i).metaid=model.genes{i};
-0388         end
-0389         if ~isempty(model.geneMiriams{i})
-0390             [~,sbo_ind] = ismember('sbo',model.geneMiriams{i}.name);
-0391             if sbo_ind > 0
-0392                 modelSBML.fbc_geneProduct(i).sboTerm=str2double(regexprep(model.geneMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0393                 % remove the SBO term from compMiriams so the information is
-0394                 % not duplicated in the "annotation" field later on
-0395                 model.geneMiriams{i}.name(sbo_ind) = [];
-0396                 model.geneMiriams{i}.value(sbo_ind) = [];
-0397             end
+0380         
+0381         if isfield(modelSBML.fbc_geneProduct,'metaid')
+0382             modelSBML.fbc_geneProduct(i).metaid=model.genes{i};
+0383         end
+0384         if ~isempty(model.geneMiriams{i})
+0385             [~,sbo_ind] = ismember('sbo',model.geneMiriams{i}.name);
+0386             if sbo_ind > 0
+0387                 modelSBML.fbc_geneProduct(i).sboTerm=str2double(regexprep(model.geneMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0388                 % remove the SBO term from compMiriams so the information is
+0389                 % not duplicated in the "annotation" field later on
+0390                 model.geneMiriams{i}.name(sbo_ind) = [];
+0391                 model.geneMiriams{i}.value(sbo_ind) = [];
+0392             end
+0393         end
+0394         if ~isempty(model.geneMiriams{i}) && isfield(modelSBML.fbc_geneProduct(i),'annotation')
+0395             modelSBML.fbc_geneProduct(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.genes{i} '">'];
+0396             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation '<bqbiol:is><rdf:Bag>'];
+0397             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation getMiriam(model.geneMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
 0398         end
-0399         if ~isempty(model.geneMiriams{i}) && isfield(modelSBML.fbc_geneProduct(i),'annotation')
-0400             modelSBML.fbc_geneProduct(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.genes{i} '">'];
-0401             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation '<bqbiol:is><rdf:Bag>'];
-0402             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation getMiriam(model.geneMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0403         end
-0404         if isfield(modelSBML.fbc_geneProduct, 'fbc_id')
-0405             modelSBML.fbc_geneProduct(i).fbc_id=model.genes{i};
-0406         end
-0407         if isfield(modelSBML.fbc_geneProduct, 'fbc_label') && isfield(model,'geneShortNames')
-0408             if isempty(model.geneShortNames{i})
-0409                 modelSBML.fbc_geneProduct(i).fbc_label=model.genes{i};
-0410             else
-0411                 modelSBML.fbc_geneProduct(i).fbc_label=model.geneShortNames{i};
+0399         if isfield(modelSBML.fbc_geneProduct, 'fbc_id')
+0400             modelSBML.fbc_geneProduct(i).fbc_id=model.genes{i};
+0401         end
+0402         if isfield(modelSBML.fbc_geneProduct, 'fbc_label') && isfield(model,'geneShortNames')
+0403             if isempty(model.geneShortNames{i})
+0404                 modelSBML.fbc_geneProduct(i).fbc_label=model.genes{i};
+0405             else
+0406                 modelSBML.fbc_geneProduct(i).fbc_label=model.geneShortNames{i};
+0407             end
+0408         end
+0409         if isfield(modelSBML.fbc_geneProduct, 'fbc_name') && isfield(model,'proteins')
+0410             if ~isempty(model.proteins{i})
+0411                 modelSBML.fbc_geneProduct(i).fbc_name=model.proteins{i};
 0412             end
 0413         end
-0414         if isfield(modelSBML.fbc_geneProduct, 'fbc_name') && isfield(model,'proteins')
-0415             if ~isempty(model.proteins{i})
-0416                 modelSBML.fbc_geneProduct(i).fbc_name=model.proteins{i};
-0417             end
-0418         end
-0419     end
-0420 end
-0421 
-0422 %Generate a list of unique fbc_bound names
-0423 totalValues=[model.lb; model.ub];
-0424 totalNames=cell(size(totalValues,1),1);
-0425 
-0426 listUniqueValues=unique(totalValues);
-0427 
-0428 for i=1:length(listUniqueValues)
-0429     listUniqueNames{i,1}=['FB',num2str(i),'N',num2str(abs(round(listUniqueValues(i))))]; % create unique flux bound IDs.
-0430     ind=find(ismember(totalValues,listUniqueValues(i)));
-0431     totalNames(ind)=listUniqueNames(i,1);
-0432 end
-0433 
-0434 for i=1:length(listUniqueNames)
-0435     %Add the default values, as these will be the same in all entries
-0436     if i==1
-0437         if isfield(modelSBML.parameter, 'constant')
-0438             modelSBML.parameter(i).constant=1;
-0439         end
-0440         if isfield(modelSBML.parameter, 'isSetValue')
-0441             modelSBML.parameter(i).isSetValue=1;
-0442         end
+0414     end
+0415 end
+0416 
+0417 %Generate a list of unique fbc_bound names
+0418 totalValues=[model.lb; model.ub];
+0419 totalNames=cell(size(totalValues,1),1);
+0420 
+0421 listUniqueValues=unique(totalValues);
+0422 
+0423 for i=1:length(listUniqueValues)
+0424     listUniqueNames{i,1}=['FB',num2str(i),'N',num2str(abs(round(listUniqueValues(i))))]; % create unique flux bound IDs.
+0425     ind=find(ismember(totalValues,listUniqueValues(i)));
+0426     totalNames(ind)=listUniqueNames(i,1);
+0427 end
+0428 
+0429 for i=1:length(listUniqueNames)
+0430     %Add the default values, as these will be the same in all entries
+0431     if i==1
+0432         if isfield(modelSBML.parameter, 'constant')
+0433             modelSBML.parameter(i).constant=1;
+0434         end
+0435         if isfield(modelSBML.parameter, 'isSetValue')
+0436             modelSBML.parameter(i).isSetValue=1;
+0437         end
+0438     end
+0439     %Copy the default values to the next index as long as it is not the
+0440     %last one
+0441     if i<numel(listUniqueNames)
+0442         modelSBML.parameter(i+1)=modelSBML.parameter(i);
 0443     end
-0444     %Copy the default values to the next index as long as it is not the
-0445     %last one
-0446     if i<numel(listUniqueNames)
-0447         modelSBML.parameter(i+1)=modelSBML.parameter(i);
-0448     end
-0449     modelSBML.parameter(i).id=listUniqueNames{i};
-0450     modelSBML.parameter(i).value=listUniqueValues(i);
-0451 end
-0452 
-0453 for i=1:numel(model.rxns)
-0454     %Add the default values, as these will be the same in all entries
-0455     if i==1
-0456         if isfield(modelSBML.reaction, 'sboTerm')
-0457             modelSBML.reaction(i).sboTerm=176;
-0458         end
-0459         if isfield(modelSBML.reaction, 'isSetFast')
-0460             modelSBML.reaction(i).isSetFast=1;
-0461         end
+0444     modelSBML.parameter(i).id=listUniqueNames{i};
+0445     modelSBML.parameter(i).value=listUniqueValues(i);
+0446 end
+0447 
+0448 for i=1:numel(model.rxns)
+0449     %Add the default values, as these will be the same in all entries
+0450     if i==1
+0451         if isfield(modelSBML.reaction, 'sboTerm')
+0452             modelSBML.reaction(i).sboTerm=176;
+0453         end
+0454         if isfield(modelSBML.reaction, 'isSetFast')
+0455             modelSBML.reaction(i).isSetFast=1;
+0456         end
+0457     end
+0458     %Copy the default values to the next index as long as it is not the
+0459     %last one
+0460     if i<numel(model.rxns)
+0461         modelSBML.reaction(i+1)=modelSBML.reaction(i);
 0462     end
-0463     %Copy the default values to the next index as long as it is not the
-0464     %last one
-0465     if i<numel(model.rxns)
-0466         modelSBML.reaction(i+1)=modelSBML.reaction(i);
-0467     end
-0468     
-0469     if isfield(modelSBML.reaction,'metaid')
-0470         modelSBML.reaction(i).metaid=model.rxns{i};
-0471     end
-0472     
-0473     %Export notes information
-0474     if (~isnan(model.rxnConfidenceScores(i)) || ~isempty(model.rxnReferences{i}) || ~isempty(model.rxnNotes{i}))
-0475         modelSBML.reaction(i).notes='<notes><body xmlns="http://www.w3.org/1999/xhtml">';
-0476         if ~isnan(model.rxnConfidenceScores(i))
-0477             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>Confidence Level: ' num2str(model.rxnConfidenceScores(i)) '</p>'];
-0478         end
-0479         if ~isempty(model.rxnReferences{i})
-0480             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>AUTHORS: ' model.rxnReferences{i} '</p>'];
-0481         end
-0482         if ~isempty(model.rxnNotes{i})
-0483             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>NOTES: ' model.rxnNotes{i} '</p>'];
-0484         end
-0485         modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '</body></notes>'];
-0486     end
-0487     
-0488     % Export SBO terms from rxnMiriams
-0489     if ~isempty(model.rxnMiriams{i})
-0490         [~,sbo_ind] = ismember('sbo',model.rxnMiriams{i}.name);
-0491         if sbo_ind > 0
-0492             modelSBML.reaction(i).sboTerm=str2double(regexprep(model.rxnMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0493             % remove the SBO term from rxnMiriams so the information is not
-0494             % duplicated in the "annotation" field later on
-0495             model.rxnMiriams{i}.name(sbo_ind) = [];
-0496             model.rxnMiriams{i}.value(sbo_ind) = [];
-0497         end
-0498     end
-0499     
-0500     %Export annotation information from rxnMiriams
-0501     if (~isempty(model.rxnMiriams{i}) && isfield(modelSBML.reaction(i),'annotation')) || ~isempty(model.eccodes{i})
-0502         modelSBML.reaction(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.rxns{i} '">'];
-0503         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation '<bqbiol:is><rdf:Bag>'];
-0504         if ~isempty(model.eccodes{i})
-0505             eccodes=regexp(model.eccodes{i},';','split');
-0506             for j=1:numel(eccodes)
-0507                 modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation  '<rdf:li rdf:resource="https://identifiers.org/ec-code/' regexprep(eccodes{j},'ec-code/|EC','') '"/>'];
-0508             end
-0509         end
-0510         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation getMiriam(model.rxnMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0511     end
-0512     
-0513     if isfield(modelSBML.reaction, 'name')
-0514         modelSBML.reaction(i).name=model.rxnNames{i};
-0515     end
-0516     if isfield(modelSBML.reaction, 'id')
-0517         modelSBML.reaction(i).id=model.rxns{i};
-0518     end
-0519     
-0520     %Add the information about reactants and products
-0521     involvedMets=addReactantsProducts(model,modelSBML,i);
-0522     for j=1:numel(involvedMets.reactant)
-0523         if j<numel(involvedMets.reactant)
-0524             modelSBML.reaction(i).reactant(j+1)=modelSBML.reaction(i).reactant(j);
-0525         end
-0526         modelSBML.reaction(i).reactant(j).species=involvedMets.reactant(j).species;
-0527         modelSBML.reaction(i).reactant(j).stoichiometry=involvedMets.reactant(j).stoichiometry;
-0528         modelSBML.reaction(i).reactant(j).isSetStoichiometry=involvedMets.reactant(j).isSetStoichiometry;
-0529         modelSBML.reaction(i).reactant(j).constant=involvedMets.reactant(j).constant;
-0530     end
-0531     if numel(involvedMets.reactant)==0
-0532         modelSBML.reaction(i).reactant='';
-0533     end
-0534     for j=1:numel(involvedMets.product)
-0535         if j<numel(involvedMets.product)
-0536             modelSBML.reaction(i).product(j+1)=modelSBML.reaction(i).product(j);
-0537         end
-0538         modelSBML.reaction(i).product(j).species=involvedMets.product(j).species;
-0539         modelSBML.reaction(i).product(j).stoichiometry=involvedMets.product(j).stoichiometry;
-0540         modelSBML.reaction(i).product(j).isSetStoichiometry=involvedMets.product(j).isSetStoichiometry;
-0541         modelSBML.reaction(i).product(j).constant=involvedMets.product(j).constant;
-0542     end
-0543     if numel(involvedMets.product)==0
-0544         modelSBML.reaction(i).product='';
+0463     
+0464     if isfield(modelSBML.reaction,'metaid')
+0465         modelSBML.reaction(i).metaid=model.rxns{i};
+0466     end
+0467     
+0468     %Export notes information
+0469     if (~isnan(model.rxnConfidenceScores(i)) || ~isempty(model.rxnReferences{i}) || ~isempty(model.rxnNotes{i}))
+0470         modelSBML.reaction(i).notes='<notes><body xmlns="http://www.w3.org/1999/xhtml">';
+0471         if ~isnan(model.rxnConfidenceScores(i))
+0472             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>Confidence Level: ' num2str(model.rxnConfidenceScores(i)) '</p>'];
+0473         end
+0474         if ~isempty(model.rxnReferences{i})
+0475             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>AUTHORS: ' model.rxnReferences{i} '</p>'];
+0476         end
+0477         if ~isempty(model.rxnNotes{i})
+0478             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>NOTES: ' model.rxnNotes{i} '</p>'];
+0479         end
+0480         modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '</body></notes>'];
+0481     end
+0482     
+0483     % Export SBO terms from rxnMiriams
+0484     if ~isempty(model.rxnMiriams{i})
+0485         [~,sbo_ind] = ismember('sbo',model.rxnMiriams{i}.name);
+0486         if sbo_ind > 0
+0487             modelSBML.reaction(i).sboTerm=str2double(regexprep(model.rxnMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0488             % remove the SBO term from rxnMiriams so the information is not
+0489             % duplicated in the "annotation" field later on
+0490             model.rxnMiriams{i}.name(sbo_ind) = [];
+0491             model.rxnMiriams{i}.value(sbo_ind) = [];
+0492         end
+0493     end
+0494     
+0495     %Export annotation information from rxnMiriams
+0496     if (~isempty(model.rxnMiriams{i}) && isfield(modelSBML.reaction(i),'annotation')) || ~isempty(model.eccodes{i})
+0497         modelSBML.reaction(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.rxns{i} '">'];
+0498         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation '<bqbiol:is><rdf:Bag>'];
+0499         if ~isempty(model.eccodes{i})
+0500             eccodes=regexp(model.eccodes{i},';','split');
+0501             for j=1:numel(eccodes)
+0502                 modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation  '<rdf:li rdf:resource="https://identifiers.org/ec-code/' regexprep(eccodes{j},'ec-code/|EC','') '"/>'];
+0503             end
+0504         end
+0505         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation getMiriam(model.rxnMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0506     end
+0507     
+0508     if isfield(modelSBML.reaction, 'name')
+0509         modelSBML.reaction(i).name=model.rxnNames{i};
+0510     end
+0511     if isfield(modelSBML.reaction, 'id')
+0512         modelSBML.reaction(i).id=model.rxns{i};
+0513     end
+0514     
+0515     %Add the information about reactants and products
+0516     involvedMets=addReactantsProducts(model,modelSBML,i);
+0517     for j=1:numel(involvedMets.reactant)
+0518         if j<numel(involvedMets.reactant)
+0519             modelSBML.reaction(i).reactant(j+1)=modelSBML.reaction(i).reactant(j);
+0520         end
+0521         modelSBML.reaction(i).reactant(j).species=involvedMets.reactant(j).species;
+0522         modelSBML.reaction(i).reactant(j).stoichiometry=involvedMets.reactant(j).stoichiometry;
+0523         modelSBML.reaction(i).reactant(j).isSetStoichiometry=involvedMets.reactant(j).isSetStoichiometry;
+0524         modelSBML.reaction(i).reactant(j).constant=involvedMets.reactant(j).constant;
+0525     end
+0526     if numel(involvedMets.reactant)==0
+0527         modelSBML.reaction(i).reactant='';
+0528     end
+0529     for j=1:numel(involvedMets.product)
+0530         if j<numel(involvedMets.product)
+0531             modelSBML.reaction(i).product(j+1)=modelSBML.reaction(i).product(j);
+0532         end
+0533         modelSBML.reaction(i).product(j).species=involvedMets.product(j).species;
+0534         modelSBML.reaction(i).product(j).stoichiometry=involvedMets.product(j).stoichiometry;
+0535         modelSBML.reaction(i).product(j).isSetStoichiometry=involvedMets.product(j).isSetStoichiometry;
+0536         modelSBML.reaction(i).product(j).constant=involvedMets.product(j).constant;
+0537     end
+0538     if numel(involvedMets.product)==0
+0539         modelSBML.reaction(i).product='';
+0540     end
+0541     %Export reversibility information. Reactions are irreversible by
+0542     %default
+0543     if model.rev(i)==1
+0544         modelSBML.reaction(i).reversible=1;
 0545     end
-0546     %Export reversibility information. Reactions are irreversible by
-0547     %default
-0548     if model.rev(i)==1
-0549         modelSBML.reaction(i).reversible=1;
-0550     end
-0551     if isfield(model, 'rxnComps')
-0552         modelSBML.reaction(i).compartment=model.comps{model.rxnComps(i)};
-0553     end
-0554     if isfield(model, 'grRules')
-0555         modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association.fbc_association=model.grRules{i};
-0556     end
-0557     modelSBML.reaction(i).fbc_lowerFluxBound=totalNames{i};
-0558     modelSBML.reaction(i).fbc_upperFluxBound=totalNames{length(model.lb)+i};
-0559 end
-0560 
-0561 %Prepare subSystems Code taken from COBRA functions getModelSubSystems,
-0562 %writeSBML, findRxnsFromSubSystem under GNU General Public License v3.0,
-0563 %license file in readme/GPL.MD. Code modified for RAVEN
-0564 if modelHasSubsystems
-0565     modelSBML.groups_group.groups_kind = 'partonomy';
-0566     modelSBML.groups_group.sboTerm = 633;
-0567     tmpStruct=modelSBML.groups_group;
-0568 
-0569     rxns=model.rxns;
-0570     if ~any(cellfun(@iscell,model.subSystems))
-0571         if ~any(~cellfun(@isempty,model.subSystems))
-0572             subSystems = {};
-0573         else
-0574             subSystems = setdiff(model.subSystems,'');
-0575         end
-0576     else
-0577         orderedSubs = cellfun(@(x) columnVector(x),model.subSystems,'UniformOUtput',false);
-0578         subSystems = setdiff(vertcat(orderedSubs{:}),'');
-0579     end
-0580     if isempty(subSystems)
-0581         subSystems = {};
-0582     end
-0583     if ~isempty(subSystems)
-0584         %Build the groups for the group package
-0585         groupIDs = strcat('group',cellfun(@num2str, num2cell(1:length(subSystems)),'UniformOutput',false));
-0586         for i = 1:length(subSystems)
-0587             cgroup = tmpStruct;
-0588             if ~any(cellfun(@iscell,model.subSystems))
-0589                 present = ismember(model.subSystems,subSystems{i});
-0590             else
-0591                 present = cellfun(@(x) any(ismember(x,subSystems{i})),model.subSystems);
-0592             end
-0593             groupMembers = rxns(present);
-0594             for j = 1:numel(groupMembers)
-0595                 cMember = tmpStruct.groups_member;
-0596                 cMember.groups_idRef = groupMembers{j};
-0597                 if j == 1
-0598                     cgroup.groups_member = cMember;
-0599                 else
-0600                     cgroup.groups_member(j) = cMember;
-0601                 end
-0602             end
-0603             cgroup.groups_id = groupIDs{i};
-0604             cgroup.groups_name = subSystems{i};
-0605             if i == 1
-0606                 modelSBML.groups_group = cgroup;
-0607             else
-0608                 modelSBML.groups_group(i) = cgroup;
-0609             end
-0610         end
-0611     end
-0612 end
+0546     if isfield(model, 'rxnComps')
+0547         modelSBML.reaction(i).compartment=model.comps{model.rxnComps(i)};
+0548     end
+0549     if isfield(model, 'grRules')
+0550         modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association.fbc_association=model.grRules{i};
+0551     end
+0552     modelSBML.reaction(i).fbc_lowerFluxBound=totalNames{i};
+0553     modelSBML.reaction(i).fbc_upperFluxBound=totalNames{length(model.lb)+i};
+0554 end
+0555 
+0556 %Prepare subSystems Code taken from COBRA functions getModelSubSystems,
+0557 %writeSBML, findRxnsFromSubSystem under GNU General Public License v3.0,
+0558 %license file in readme/GPL.MD. Code modified for RAVEN
+0559 if modelHasSubsystems
+0560     modelSBML.groups_group.groups_kind = 'partonomy';
+0561     modelSBML.groups_group.sboTerm = 633;
+0562     tmpStruct=modelSBML.groups_group;
+0563 
+0564     rxns=model.rxns;
+0565     if ~any(cellfun(@iscell,model.subSystems))
+0566         if ~any(~cellfun(@isempty,model.subSystems))
+0567             subSystems = {};
+0568         else
+0569             subSystems = setdiff(model.subSystems,'');
+0570         end
+0571     else
+0572         orderedSubs = cellfun(@(x) columnVector(x),model.subSystems,'UniformOUtput',false);
+0573         subSystems = setdiff(vertcat(orderedSubs{:}),'');
+0574     end
+0575     if isempty(subSystems)
+0576         subSystems = {};
+0577     end
+0578     if ~isempty(subSystems)
+0579         %Build the groups for the group package
+0580         groupIDs = strcat('group',cellfun(@num2str, num2cell(1:length(subSystems)),'UniformOutput',false));
+0581         for i = 1:length(subSystems)
+0582             cgroup = tmpStruct;
+0583             if ~any(cellfun(@iscell,model.subSystems))
+0584                 present = ismember(model.subSystems,subSystems{i});
+0585             else
+0586                 present = cellfun(@(x) any(ismember(x,subSystems{i})),model.subSystems);
+0587             end
+0588             groupMembers = rxns(present);
+0589             for j = 1:numel(groupMembers)
+0590                 cMember = tmpStruct.groups_member;
+0591                 cMember.groups_idRef = groupMembers{j};
+0592                 if j == 1
+0593                     cgroup.groups_member = cMember;
+0594                 else
+0595                     cgroup.groups_member(j) = cMember;
+0596                 end
+0597             end
+0598             cgroup.groups_id = groupIDs{i};
+0599             cgroup.groups_name = subSystems{i};
+0600             if i == 1
+0601                 modelSBML.groups_group = cgroup;
+0602             else
+0603                 modelSBML.groups_group(i) = cgroup;
+0604             end
+0605         end
+0606     end
+0607 end
+0608 
+0609 %Prepare fbc_objective subfield
+0610 
+0611 modelSBML.fbc_objective.fbc_type='maximize';
+0612 modelSBML.fbc_objective.fbc_id='obj';
 0613 
-0614 %Prepare fbc_objective subfield
+0614 ind=find(model.c);
 0615 
-0616 modelSBML.fbc_objective.fbc_type='maximize';
-0617 modelSBML.fbc_objective.fbc_id='obj';
-0618 
-0619 ind=find(model.c);
-0620 
-0621 if isempty(ind)
-0622     modelSBML.fbc_objective.fbc_fluxObjective.fbc_coefficient=0;
-0623 else
-0624     for i=1:length(ind)
-0625         %Copy the default values to the next index as long as it is not the
-0626         %last one
-0627         if i<numel(ind)
-0628             modelSBML.reaction(i+1)=modelSBML.reaction(i);
-0629         end
-0630         values=model.c(model.c~=0);
-0631         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_reaction=modelSBML.reaction(ind(i)).id;
-0632         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_coefficient=values(i);
-0633         modelSBML.fbc_objective(i).fbc_fluxObjective.isSetfbc_coefficient=1;
-0634     end
-0635 end
-0636 
-0637 modelSBML.fbc_activeObjective=modelSBML.fbc_objective.fbc_id;
-0638 
-0639 fbcStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/fbc/version',num2str(sbmlPackageVersions(1))];
-0640 if modelHasSubsystems
-0641     groupStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/groups/version',num2str(sbmlPackageVersions(2))];
-0642     modelSBML.namespaces=struct('prefix',{'','fbc','groups'},...
-0643     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
-0644     fbcStr,groupStr});
-0645 else
-0646     modelSBML.namespaces=struct('prefix',{'','fbc'},...
-0647     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
-0648     fbcStr});
+0616 if isempty(ind)
+0617     modelSBML.fbc_objective.fbc_fluxObjective.fbc_coefficient=0;
+0618 else
+0619     for i=1:length(ind)
+0620         %Copy the default values to the next index as long as it is not the
+0621         %last one
+0622         if i<numel(ind)
+0623             modelSBML.reaction(i+1)=modelSBML.reaction(i);
+0624         end
+0625         values=model.c(model.c~=0);
+0626         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_reaction=modelSBML.reaction(ind(i)).id;
+0627         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_coefficient=values(i);
+0628         modelSBML.fbc_objective(i).fbc_fluxObjective.isSetfbc_coefficient=1;
+0629     end
+0630 end
+0631 
+0632 modelSBML.fbc_activeObjective=modelSBML.fbc_objective.fbc_id;
+0633 
+0634 fbcStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/fbc/version',num2str(sbmlPackageVersions(1))];
+0635 if modelHasSubsystems
+0636     groupStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/groups/version',num2str(sbmlPackageVersions(2))];
+0637     modelSBML.namespaces=struct('prefix',{'','fbc','groups'},...
+0638     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
+0639     fbcStr,groupStr});
+0640 else
+0641     modelSBML.namespaces=struct('prefix',{'','fbc'},...
+0642     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
+0643     fbcStr});
+0644 end
+0645 
+0646 if sbmlPackageVersions(1) == 2
+0647     modelSBML.fbc_strict=1;
+0648     modelSBML.isSetfbc_strict = 1;
 0649 end
 0650 
-0651 if sbmlPackageVersions(1) == 2
-0652     modelSBML.fbc_strict=1;
-0653     modelSBML.isSetfbc_strict = 1;
-0654 end
-0655 
-0656 modelSBML.rule=[];
-0657 modelSBML.constraint=[];
-0658 
-0659 [ravenDir,prevDir]=findRAVENroot();
-0660 fileName=checkFileExistence(fileName,1,true,false);
-0661 
-0662 OutputSBML_RAVEN(modelSBML,fileName,1,0,[1,0]);
-0663 end
+0651 modelSBML.rule=[];
+0652 modelSBML.constraint=[];
+0653 
+0654 [ravenDir,prevDir]=findRAVENroot();
+0655 fileName=checkFileExistence(fileName,1,true,false);
+0656 
+0657 OutputSBML_RAVEN(modelSBML,fileName,1,0,[1,0]);
+0658 end
+0659 
+0660 
+0661 function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
+0662 %Returns the blank SBML model structure by using appropriate libSBML
+0663 %functions. This creates structure by considering three levels
 0664 
-0665 
-0666 function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
-0667 %Returns the blank SBML model structure by using appropriate libSBML
-0668 %functions. This creates structure by considering three levels
-0669 
-0670 sbmlFieldNames=getStructureFieldnames('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0671 sbmlDefaultValues=getDefaultValues('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0672 
-0673 for i=1:numel(sbmlFieldNames)
-0674     modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
-0675     sbmlSubfieldNames=getStructureFieldnames(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0676     sbmlSubfieldValues=getDefaultValues(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0677     if ~strcmp(sbmlFieldNames{1,i},'event') && ~strcmp(sbmlFieldNames{1,i},'functionDefinition') && ~strcmp(sbmlFieldNames{1,i},'initialAssignment')
-0678         for j=1:numel(sbmlSubfieldNames)
-0679             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j})=sbmlSubfieldValues{1,j};
-0680             sbmlSubsubfieldNames=getStructureFieldnames(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0681             sbmlSubsubfieldValues=getDefaultValues(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0682             if ~strcmp(sbmlSubfieldNames{1,j},'modifier') && ~strcmp(sbmlSubfieldNames{1,j},'kineticLaw')
-0683                 for k=1:numel(sbmlSubsubfieldNames)
-0684                     %'compartment' and 'species' fields are not supposed to
-0685                     %have their standalone structures if they are subfields
-0686                     %or subsubfields
-0687                     if ~strcmp(sbmlSubfieldNames{1,j},'compartment') && ~strcmp(sbmlSubfieldNames{1,j},'species')
-0688                         modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k})=sbmlSubsubfieldValues{1,k};
-0689                     end
-0690                     %If it is fbc_association in the third level, we need
-0691                     %to establish the fourth level, since libSBML requires
-0692                     %it
-0693                     if strcmp(sbmlSubsubfieldNames{1,k},'fbc_association')
-0694                         fbc_associationFieldNames=getStructureFieldnames('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0695                         fbc_associationFieldValues=getDefaultValues('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0696                         for l=1:numel(fbc_associationFieldNames)
-0697                             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k}).(fbc_associationFieldNames{1,l})=fbc_associationFieldValues{1,l};
-0698                         end
-0699                     end
-0700                 end
-0701             end
-0702         end
-0703     end
-0704     if ~isstruct(modelSBML.(sbmlFieldNames{1,i}))
-0705         modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
-0706     end
-0707 end
+0665 sbmlFieldNames=getStructureFieldnames('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0666 sbmlDefaultValues=getDefaultValues('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0667 
+0668 for i=1:numel(sbmlFieldNames)
+0669     modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
+0670     sbmlSubfieldNames=getStructureFieldnames(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0671     sbmlSubfieldValues=getDefaultValues(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0672     if ~strcmp(sbmlFieldNames{1,i},'event') && ~strcmp(sbmlFieldNames{1,i},'functionDefinition') && ~strcmp(sbmlFieldNames{1,i},'initialAssignment')
+0673         for j=1:numel(sbmlSubfieldNames)
+0674             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j})=sbmlSubfieldValues{1,j};
+0675             sbmlSubsubfieldNames=getStructureFieldnames(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0676             sbmlSubsubfieldValues=getDefaultValues(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0677             if ~strcmp(sbmlSubfieldNames{1,j},'modifier') && ~strcmp(sbmlSubfieldNames{1,j},'kineticLaw')
+0678                 for k=1:numel(sbmlSubsubfieldNames)
+0679                     %'compartment' and 'species' fields are not supposed to
+0680                     %have their standalone structures if they are subfields
+0681                     %or subsubfields
+0682                     if ~strcmp(sbmlSubfieldNames{1,j},'compartment') && ~strcmp(sbmlSubfieldNames{1,j},'species')
+0683                         modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k})=sbmlSubsubfieldValues{1,k};
+0684                     end
+0685                     %If it is fbc_association in the third level, we need
+0686                     %to establish the fourth level, since libSBML requires
+0687                     %it
+0688                     if strcmp(sbmlSubsubfieldNames{1,k},'fbc_association')
+0689                         fbc_associationFieldNames=getStructureFieldnames('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0690                         fbc_associationFieldValues=getDefaultValues('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0691                         for l=1:numel(fbc_associationFieldNames)
+0692                             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k}).(fbc_associationFieldNames{1,l})=fbc_associationFieldValues{1,l};
+0693                         end
+0694                     end
+0695                 end
+0696             end
+0697         end
+0698     end
+0699     if ~isstruct(modelSBML.(sbmlFieldNames{1,i}))
+0700         modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
+0701     end
+0702 end
+0703 
+0704 modelSBML.unitDefinition.id='mmol_per_gDW_per_hr';
+0705 
+0706 unitFieldNames=getStructureFieldnames('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0707 unitDefaultValues=getDefaultValues('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
 0708 
-0709 modelSBML.unitDefinition.id='mmol_per_gDW_per_hr';
-0710 
-0711 unitFieldNames=getStructureFieldnames('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0712 unitDefaultValues=getDefaultValues('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0709 kinds={'mole','gram','second'};
+0710 exponents=[1 -1 -1];
+0711 scales=[-3 0 0];
+0712 multipliers=[1 1 1*60*60];
 0713 
-0714 kinds={'mole','gram','second'};
-0715 exponents=[1 -1 -1];
-0716 scales=[-3 0 0];
-0717 multipliers=[1 1 1*60*60];
-0718 
-0719 for i=1:numel(unitFieldNames)
-0720     modelSBML.unitDefinition.unit(1).(unitFieldNames{1,i})=unitDefaultValues{1,i};
-0721     for j=1:3
-0722         modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=unitDefaultValues{1,i};
-0723         if strcmp(unitFieldNames{1,i},'kind')
-0724             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=kinds{j};
-0725         elseif strcmp(unitFieldNames{1,i},'exponent')
-0726             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=exponents(j);
-0727         elseif strcmp(unitFieldNames{1,i},'scale')
-0728             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=scales(j);
-0729         elseif strcmp(unitFieldNames{1,i},'multiplier')
-0730             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=multipliers(j);
-0731         end
-0732     end
-0733 end
-0734 end
-0735 
-0736 function miriamString=getMiriam(miriamStruct)
-0737 %Returns a string with list elements for a miriam structure ('<rdf:li
-0738 %rdf:resource="https://identifiers.org/go/GO:0005739"/>' for example). This
-0739 %is just to speed up things since this is done many times during the
-0740 %exporting
-0741 
-0742 miriamString='';
-0743 if isfield(miriamStruct,'name')
-0744     for i=1:numel(miriamStruct.name)
-0745         miriamString=[miriamString '<rdf:li rdf:resource="https://identifiers.org/' miriamStruct.name{i} '/' miriamStruct.value{i} '"/>'];
-0746     end
-0747 end
-0748 end
-0749 
-0750 function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
-0751 %This function provides reactants and products for particular reaction. The
-0752 %function was 'borrowed' from writeSBML in COBRA toolbox, lines 663-679
-0753 
-0754 met_idx = find(model.S(:, i));
-0755 tmp_Rxn.product=[];
-0756 tmp_Rxn.reactant=[];
-0757 for j_met=1:size(met_idx,1)
-0758     tmp_idx = met_idx(j_met,1);
-0759     sbml_tmp_species_ref.species = sbmlModel.species(tmp_idx).id;
-0760     met_stoich = model.S(tmp_idx, i);
-0761     sbml_tmp_species_ref.stoichiometry = abs(met_stoich);
-0762     sbml_tmp_species_ref.isSetStoichiometry=1;
-0763     sbml_tmp_species_ref.constant=1;
-0764     if (met_stoich > 0)
-0765         tmp_Rxn.product = [ tmp_Rxn.product, sbml_tmp_species_ref ];
-0766     else
-0767         tmp_Rxn.reactant = [ tmp_Rxn.reactant, sbml_tmp_species_ref];
-0768     end
-0769 end
-0770 end
-0771 
-0772 function vecT = columnVector(vec)
-0773 % Code below taken from COBRA Toolbox under GNU General Public License v3.0
-0774 % license file in readme/GPL.MD.
-0775 %
-0776 % Converts a vector to a column vector
-0777 %
-0778 % USAGE:
+0714 for i=1:numel(unitFieldNames)
+0715     modelSBML.unitDefinition.unit(1).(unitFieldNames{1,i})=unitDefaultValues{1,i};
+0716     for j=1:3
+0717         modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=unitDefaultValues{1,i};
+0718         if strcmp(unitFieldNames{1,i},'kind')
+0719             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=kinds{j};
+0720         elseif strcmp(unitFieldNames{1,i},'exponent')
+0721             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=exponents(j);
+0722         elseif strcmp(unitFieldNames{1,i},'scale')
+0723             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=scales(j);
+0724         elseif strcmp(unitFieldNames{1,i},'multiplier')
+0725             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=multipliers(j);
+0726         end
+0727     end
+0728 end
+0729 end
+0730 
+0731 function miriamString=getMiriam(miriamStruct)
+0732 %Returns a string with list elements for a miriam structure ('<rdf:li
+0733 %rdf:resource="https://identifiers.org/go/GO:0005739"/>' for example). This
+0734 %is just to speed up things since this is done many times during the
+0735 %exporting
+0736 
+0737 miriamString='';
+0738 if isfield(miriamStruct,'name')
+0739     for i=1:numel(miriamStruct.name)
+0740         miriamString=[miriamString '<rdf:li rdf:resource="https://identifiers.org/' miriamStruct.name{i} '/' miriamStruct.value{i} '"/>'];
+0741     end
+0742 end
+0743 end
+0744 
+0745 function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
+0746 %This function provides reactants and products for particular reaction. The
+0747 %function was 'borrowed' from writeSBML in COBRA toolbox, lines 663-679
+0748 
+0749 met_idx = find(model.S(:, i));
+0750 tmp_Rxn.product=[];
+0751 tmp_Rxn.reactant=[];
+0752 for j_met=1:size(met_idx,1)
+0753     tmp_idx = met_idx(j_met,1);
+0754     sbml_tmp_species_ref.species = sbmlModel.species(tmp_idx).id;
+0755     met_stoich = model.S(tmp_idx, i);
+0756     sbml_tmp_species_ref.stoichiometry = abs(met_stoich);
+0757     sbml_tmp_species_ref.isSetStoichiometry=1;
+0758     sbml_tmp_species_ref.constant=1;
+0759     if (met_stoich > 0)
+0760         tmp_Rxn.product = [ tmp_Rxn.product, sbml_tmp_species_ref ];
+0761     else
+0762         tmp_Rxn.reactant = [ tmp_Rxn.reactant, sbml_tmp_species_ref];
+0763     end
+0764 end
+0765 end
+0766 
+0767 function vecT = columnVector(vec)
+0768 % Code below taken from COBRA Toolbox under GNU General Public License v3.0
+0769 % license file in readme/GPL.MD.
+0770 %
+0771 % Converts a vector to a column vector
+0772 %
+0773 % USAGE:
+0774 %
+0775 %   vecT = columnVector(vec)
+0776 %
+0777 % INPUT:
+0778 %   vec:     a vector
 0779 %
-0780 %   vecT = columnVector(vec)
-0781 %
-0782 % INPUT:
-0783 %   vec:     a vector
-0784 %
-0785 % OUTPUT:
-0786 %   vecT:    a column vector
-0787 
-0788 [n, m] = size(vec);
-0789 
-0790 if n < m
-0791     vecT = vec';
-0792 else
-0793     vecT = vec;
-0794 end
-0795 end
    
+0780 % OUTPUT:
+0781 %   vecT:    a column vector
+0782 
+0783 [n, m] = size(vec);
+0784 
+0785 if n < m
+0786     vecT = vec';
+0787 else
+0788     vecT = vec;
+0789 end
+0790 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/importModel.html b/doc/io/importModel.html
index e54a025a..d0d442fc 100644
--- a/doc/io/importModel.html
+++ b/doc/io/importModel.html
@@ -24,11 +24,11 @@ 
    PURPOSE ^importModel

    SYNOPSIS ^

    -
    function model=importModel(fileName,removeExcMets,COBRAstyle,supressWarnings)
    +
    function model=importModel(fileName,removeExcMets,removePrefix,supressWarnings)

    DESCRIPTION ^

     importModel
-   Import a constraint-based model from a SBML file
+   Import a constraint-based model from an SBML file.
 
  Input:
    fileName        a SBML file to import. A dialog window will open if
@@ -37,10 +37,11 @@ 
    DESCRIPTION ^DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
@@ -107,9 +108,9 @@ 
    SUBFUNCTIONS ^function matchGenes=getGeneList(grRules)
  • function fieldContent=parseNote(searchString,fieldName)
  • function fieldContent=parseAnnotation(searchString,startString,midString,fieldName)
  • function miriamStruct=parseMiriam(searchString)
  • function miriam = addSBOtoMiriam(miriam,sboTerm)
    • 
 
 
    SOURCE CODE ^
    
-
    0001 function model=importModel(fileName,removeExcMets,COBRAstyle,supressWarnings)
+
    0001 function model=importModel(fileName,removeExcMets,removePrefix,supressWarnings)
 0002 % importModel
-0003 %   Import a constraint-based model from a SBML file
+0003 %   Import a constraint-based model from an SBML file.
 0004 %
 0005 % Input:
 0006 %   fileName        a SBML file to import. A dialog window will open if
@@ -118,1185 +119,1171 @@ 
    SOURCE CODE ^%                   needed to be able to run simulations, but it could also
 0010 %                   be done using simplifyModel at a later stage (optional,
 0011 %                   default true)
-0012 %   COBRAstyle      true if the model uses COBRA style identifier prefixes
-0013 %                   that should be removed when loading the model: G_ for
-0014 %                   genes, R_ for reactions, M_ for metabolites, and C_ for
-0015 %                   compartments. (optional, default false)
-0016 %   supressWarnings true if warnings regarding the model structure should
-0017 %                   be supressed (optional, default false)
-0018 %
-0019 % Output:
-0020 %   model
-0021 %       id               model ID
-0022 %       name             name of model contents
-0023 %       annotation       additional information about model
-0024 %       rxns             reaction ids
-0025 %       mets             metabolite ids
-0026 %       S                stoichiometric matrix
-0027 %       lb               lower bounds
-0028 %       ub               upper bounds
-0029 %       rev              reversibility vector
-0030 %       c                objective coefficients
-0031 %       b                equality constraints for the metabolite equations
-0032 %       comps            compartment ids
-0033 %       compNames        compartment names
-0034 %       compOutside      the id (as in comps) for the compartment
-0035 %                        surrounding each of the compartments
-0036 %       compMiriams      structure with MIRIAM information about the
-0037 %                        compartments
-0038 %       rxnNames         reaction description
-0039 %       rxnComps         compartments for reactions
-0040 %       grRules          reaction to gene rules in text form
-0041 %       rxnGeneMat       reaction-to-gene mapping in sparse matrix form
-0042 %       subSystems       subsystem name for each reaction
-0043 %       eccodes          EC-codes for the reactions
-0044 %       rxnMiriams       structure with MIRIAM information about the reactions
-0045 %       rxnNotes         reaction notes
-0046 %       rxnReferences    reaction references
-0047 %       rxnConfidenceScores reaction confidence scores
-0048 %       genes            list of all genes
-0049 %       geneComps        compartments for genes
-0050 %       geneMiriams      structure with MIRIAM information about the genes
-0051 %       geneShortNames   gene alternative names (e.g. ERG10)
-0052 %       proteins     protein associated to each gene
-0053 %       metNames         metabolite description
-0054 %       metComps         compartments for metabolites
-0055 %       inchis           InChI-codes for metabolites
-0056 %       metFormulas      metabolite chemical formula
-0057 %       metMiriams       structure with MIRIAM information about the metabolites
-0058 %       metCharges       metabolite charge
-0059 %       unconstrained    true if the metabolite is an exchange metabolite
-0060 %
-0061 % A number of consistency checks are performed in order to ensure that the
-0062 % model is valid. Take these warnings seriously and modify the model
-0063 % structure to solve them.
-0064 %
-0065 % Usage: model = importModel(fileName, removeExcMets, COBRAstyle, supressWarnings)
-0066 
-0067 if nargin<1 || isempty(fileName)
-0068     [fileName, pathName] = uigetfile({'*.xml;*.sbml'}, 'Please select the model file');
-0069     if fileName == 0
-0070         error('You should select a model file')
-0071     else
-0072         fileName = fullfile(pathName,fileName);
-0073     end
-0074 end
-0075 fileName=char(fileName);
-0076 if nargin<2 || isempty(removeExcMets)
-0077     removeExcMets=true;
-0078 end
-0079 
-0080 if nargin<3 || isempty(COBRAstyle)
-0081     COBRAstyle=false;
-0082 end
-0083 
-0084 if nargin<4
-0085     supressWarnings=false;
-0086 end
-0087 
-0088 fileName=checkFileExistence(fileName,1);
-0089 % If path contains non-ASCII characters, copy file to tempdir first, as
-0090 % libSBML is known to have problems with this on Windows:
-0091 % https://sbml.org/software/libsbml/libsbml-docs/known-pitfalls/#matlab-on-windows-has-issues-with-unicode-filenames
-0092 if ispc && any(double(fileName)>128)
-0093     [~,originalFile,ext] = fileparts(fileName);
-0094     tempFile = fullfile(tempdir,[originalFile ext]);
-0095     copyfile(fileName,tempFile);
-0096     fileName = tempFile;
-0097 end
-0098 
-0099 %This is to match the order of the fields to those you get from importing
-0100 %from Excel
-0101 model=[];
-0102 model.id=[];
-0103 model.name=[];
-0104 model.annotation=[];
-0105 model.rxns={};
-0106 model.mets={};
-0107 model.S=[];
-0108 model.lb=[];
-0109 model.ub=[];
-0110 model.rev=[];
-0111 model.c=[];
-0112 model.b=[];
-0113 model.comps={};
-0114 model.compNames={};
-0115 model.compOutside={};
-0116 model.compMiriams={};
-0117 model.rxnNames={};
-0118 model.rxnComps=[];
-0119 model.grRules={};
-0120 model.rxnGeneMat=[];
-0121 model.subSystems={};
-0122 model.eccodes={};
-0123 model.rxnMiriams={};
-0124 model.rxnNotes={};
-0125 model.rxnReferences={};
-0126 model.rxnConfidenceScores=[];
-0127 model.genes={};
-0128 model.geneComps=[];
-0129 model.geneMiriams={};
-0130 model.geneShortNames={};
-0131 model.proteins={};
-0132 model.metNames={};
-0133 model.metComps=[];
-0134 model.inchis={};
-0135 model.metFormulas={};
-0136 model.metMiriams={};
-0137 model.metCharges=[];
-0138 model.unconstrained=[];
-0139 
-0140 %Load the model using libSBML
-0141 [modelSBML,errorMsg] = TranslateSBML_RAVEN(fileName,0,0,[1 1]);
-0142 if exist('tempFile','var')
-0143     delete(tempFile)
-0144 end
-0145 
-0146 if isempty(modelSBML)
-0147     EM=['There is a problem with the SBML file. Try using the SBML Validator at http://sbml.org/Facilities/Validator.\nlibSBML reports: ', errorMsg.message];
-0148     dispEM(EM);
-0149 end
-0150 
-0151 %Retrieve compartment names and IDs
-0152 compartmentNames=cell(numel(modelSBML.compartment),1);
-0153 compartmentIDs=cell(numel(modelSBML.compartment),1);
-0154 compartmentOutside=cell(numel(modelSBML.compartment),1);
-0155 compartmentMiriams=cell(numel(modelSBML.compartment),1);
-0156 
-0157 if isfield(modelSBML.compartment,'sboTerm') && numel(unique([modelSBML.compartment.sboTerm])) == 1
-0158     %If all the SBO terms are identical, don't add them to compMiriams
-0159     modelSBML.compartment = rmfield(modelSBML.compartment,'sboTerm');
-0160 end
-0161 
-0162 for i=1:numel(modelSBML.compartment)
-0163     compartmentNames{i}=modelSBML.compartment(i).name;
-0164     compartmentIDs{i}=modelSBML.compartment(i).id;
-0165     if isfield(modelSBML.compartment(i),'outside')
-0166         if ~isempty(modelSBML.compartment(i).outside)
-0167             compartmentOutside{i}=modelSBML.compartment(i).outside;
-0168         else
-0169             compartmentOutside{i}='';
-0170         end
-0171     else
-0172         compartmentOutside{i}=[];
-0173     end
-0174 
-0175     if isfield(modelSBML.compartment(i),'annotation')
-0176         compartmentMiriams{i}=parseMiriam(modelSBML.compartment(i).annotation);
-0177     else
-0178         compartmentMiriams{i}=[];
-0179     end
-0180 
-0181     if isfield(modelSBML.compartment(i),'sboTerm') && ~(modelSBML.compartment(i).sboTerm==-1)
-0182         compartmentMiriams{i} = addSBOtoMiriam(compartmentMiriams{i},modelSBML.compartment(i).sboTerm);
-0183     end
-0184 end
-0185 
-0186 %If there are no compartment names then use compartment id as name
-0187 if all(cellfun(@isempty,compartmentNames))
-0188     compartmentNames=compartmentIDs;
-0189 end
-0190 
-0191 %Retrieve info on metabolites, genes, complexes
-0192 metaboliteNames={};
-0193 metaboliteIDs={};
-0194 metaboliteCompartments={};
-0195 metaboliteUnconstrained=[];
-0196 metaboliteFormula={};
-0197 metaboliteInChI={};
-0198 metaboliteMiriams={};
-0199 metaboliteCharges=[];
-0200 
-0201 geneNames={};
-0202 geneIDs={};
-0203 geneMiriams={};
-0204 geneShortNames={};
-0205 proteins={};
-0206 geneCompartments={};
-0207 complexIDs={};
-0208 complexNames={};
-0209 
-0210 %If the file is not a COBRA Toolbox model. According to the format
-0211 %specified in the yeast consensus model both metabolites and genes are a
-0212 %type of 'species'. The metabolites have names starting with 'M_' and genes
-0213 %with 'E_'
-0214 geneSBOs = [];
-0215 metSBOs = [];
-0216 %Regex of compartment names, later to be used to remove from metabolite
-0217 %names if present as suffix.
-0218 regexCompNames = ['\s?\[((' strjoin({modelSBML.compartment.name},')|(') '))\]$'];
-0219 for i=1:numel(modelSBML.species)
-0220     if length(modelSBML.species(i).id)>=2 && strcmpi(modelSBML.species(i).id(1:2),'E_')
-0221         geneNames{numel(geneNames)+1,1}=modelSBML.species(i).name;
-0222 
-0223         %The "E_" is included in the ID. This is because it's only used
-0224         %internally in this file and it makes the matching a little
-0225         %smoother
-0226         geneIDs{numel(geneIDs)+1,1}=modelSBML.species(i).id;
-0227         geneCompartments{numel(geneCompartments)+1,1}=modelSBML.species(i).compartment;
-0228 
-0229         %Get Miriam structure
-0230         if isfield(modelSBML.species(i),'annotation')
-0231             %Get Miriam info
-0232             geneMiriam=parseMiriam(modelSBML.species(i).annotation);
-0233             geneMiriams{numel(geneMiriams)+1,1}=geneMiriam;
-0234         else
-0235             geneMiriams{numel(geneMiriams)+1,1}=[];
-0236         end
-0237 
-0238         %Protein short names (for example ERG10) are saved as SHORT
-0239         %NAME: NAME in the notes-section of metabolites for SBML Level
-0240         %2 and as PROTEIN_ASSOCIATION for each reaction in SBML Level 2
-0241         %COBRA Toolbox format. For now only the SHORT NAME is loaded
-0242         %and no mapping takes place
-0243         if isfield(modelSBML.species(i),'notes')
-0244             geneShortNames{numel(geneShortNames)+1,1}=parseNote(modelSBML.species(i).notes,'SHORT NAME');
-0245         else
-0246             geneShortNames{numel(geneShortNames)+1,1}='';
-0247         end
-0248 
-0249         %Get SBO term
-0250         if isfield(modelSBML.species(i),'sboTerm') && ~(modelSBML.species(i).sboTerm==-1)
-0251             geneSBOs(end+1,1) = modelSBML.species(i).sboTerm;
-0252         end
-0253     elseif length(modelSBML.species(i).id)>=2 && strcmpi(modelSBML.species(i).id(1:3),'Cx_')
-0254         %If it's a complex keep the ID and name
-0255         complexIDs=[complexIDs;modelSBML.species(i).id];
-0256         complexNames=[complexNames;modelSBML.species(i).name];
-0257     else
-0258         %If it is not gene or complex, then it must be a metabolite
-0259         metaboliteNames{numel(metaboliteNames)+1,1}=modelSBML.species(i).name;
-0260         metaboliteIDs{numel(metaboliteIDs)+1,1}=modelSBML.species(i).id;
-0261         metaboliteCompartments{numel(metaboliteCompartments)+1,1}=modelSBML.species(i).compartment;
-0262         metaboliteUnconstrained(numel(metaboliteUnconstrained)+1,1)=modelSBML.species(i).boundaryCondition;
-0263 
-0264         %For each metabolite retrieve the formula and the InChI code if
-0265         %available First add the InChI code and the formula from the
-0266         %InChI. This allows for overwriting the formula by setting the
-0267         %actual formula field
-0268         if ~isempty(modelSBML.species(i).annotation)
-0269             %Get the formula if available
-0270             startString='>InChI=';
-0271             endString='</in:inchi>';
-0272             formStart=strfind(modelSBML.species(i).annotation,startString);
-0273             if isempty(formStart)
-0274                 startString='InChI=';
-0275                 endString='"/>';
-0276             end
-0277             formStart=strfind(modelSBML.species(i).annotation,startString);
-0278             if ~isempty(formStart)
-0279                 formEnd=strfind(modelSBML.species(i).annotation,endString);
-0280                 formEndIndex=find(formEnd>formStart, 1 );
-0281                 formula=modelSBML.species(i).annotation(formStart+numel(startString):formEnd(formEndIndex)-1);
-0282                 metaboliteInChI{numel(metaboliteInChI)+1,1}=formula;
-0283 
-0284                 %The composition is most often present between the
-0285                 %first and second "/" in the model. In some simple
-0286                 %molecules, such as salts, there is no second "/". The
-0287                 %formula is then assumed to be to the end of the string
-0288                 compositionIndexes=strfind(formula,'/');
-0289                 if numel(compositionIndexes)>1
-0290                     metaboliteFormula{numel(metaboliteFormula)+1,1}=...
-0291                         formula(compositionIndexes(1)+1:compositionIndexes(2)-1);
-0292                 else
-0293                     if numel(compositionIndexes)==1
-0294                         %Probably a simple molecule which can have only
-0295                         %one conformation
-0296                         metaboliteFormula{numel(metaboliteFormula)+1,1}=...
-0297                             formula(compositionIndexes(1)+1:numel(formula));
-0298                     else
-0299                         metaboliteFormula{numel(metaboliteFormula)+1,1}='';
-0300                     end
-0301                 end
-0302             elseif isfield(modelSBML.species(i),'fbc_chemicalFormula')
-0303                 metaboliteInChI{numel(metaboliteInChI)+1,1}='';
-0304                 if ~isempty(modelSBML.species(i).fbc_chemicalFormula)
-0305                     %Cannot extract InChi from formula, so remains
-0306                     %empty
-0307                     metaboliteFormula{numel(metaboliteFormula)+1,1}=modelSBML.species(i).fbc_chemicalFormula;
-0308                 else
-0309                     metaboliteFormula{numel(metaboliteFormula)+1,1}='';
-0310                 end
-0311             else
-0312                 metaboliteInChI{numel(metaboliteInChI)+1,1}='';
-0313                 metaboliteFormula{numel(metaboliteFormula)+1,1}='';
-0314             end
-0315 
-0316             %Get Miriam info
-0317             metMiriam=parseMiriam(modelSBML.species(i).annotation);
-0318             metaboliteMiriams{numel(metaboliteMiriams)+1,1}=metMiriam;
-0319         else
-0320             metaboliteInChI{numel(metaboliteInChI)+1,1}='';
-0321             if isfield(modelSBML.species(i),'notes')
-0322                 metaboliteFormula{numel(metaboliteFormula)+1,1}=parseNote(modelSBML.species(i).notes,'FORMULA');
-0323             else
-0324                 metaboliteFormula{numel(metaboliteFormula)+1,1}='';
-0325             end
-0326             metaboliteMiriams{numel(metaboliteMiriams)+1,1}=[];
-0327         end
-0328         if ~isempty(modelSBML.species(i).notes)
-0329             if ~isfield(modelSBML.species(i),'annotation')
-0330                 metaboliteFormula{numel(metaboliteFormula)+1,1}=parseNote(modelSBML.species(i).notes,'FORMULA');
-0331             end
-0332         elseif ~isfield(modelSBML.species(i),'annotation')
-0333             metaboliteFormula{numel(metaboliteFormula)+1,1}='';
-0334         end
-0335         %Get SBO term
-0336         if isfield(modelSBML.species(i),'sboTerm') && ~(modelSBML.species(i).sboTerm==-1)
-0337             metSBOs(end+1,1) = modelSBML.species(i).sboTerm;
-0338         end
-0339     end
-0340 
-0341     %The following lines are executed regardless isSBML2COBRA setting
-0342     if isempty(modelSBML.species(i).id) || ~strcmpi(modelSBML.species(i).id(1:2),'E_')
-0343         if isempty(modelSBML.species(i).id) || ~strcmpi(modelSBML.species(i).id(1:3),'Cx_')
-0344             %Remove trailing [compartment] from metabolite name if present
-0345             metaboliteNames{end,1}=regexprep(metaboliteNames{end,1},regexCompNames,'');
-0346             metaboliteNames{end,1}=metaboliteNames{end,1};
-0347             if isfield(modelSBML.species(i),'fbc_charge')
-0348                 if ~isempty(modelSBML.species(i).fbc_charge) && modelSBML.species(i).isSetfbc_charge
-0349                     metaboliteCharges(numel(metaboliteCharges)+1,1)=double(modelSBML.species(i).fbc_charge);
-0350                 else
-0351                     if isfield(modelSBML.species(i),'notes')
-0352                         if strfind(modelSBML.species(i).notes,'CHARGE')
-0353                             metaboliteCharges(numel(metaboliteCharges)+1,1)=str2double(parseNote(modelSBML.species(i).notes,'CHARGE'));
-0354                         else
-0355                             metaboliteCharges(numel(metaboliteCharges)+1,1)=NaN;
-0356                         end
-0357                     else
-0358                         metaboliteCharges(numel(metaboliteCharges)+1,1)=NaN;
-0359                     end
-0360                 end
-0361             elseif isfield(modelSBML.species(i),'notes')
-0362                 if strfind(modelSBML.species(i).notes,'CHARGE')
-0363                     metaboliteCharges(numel(metaboliteCharges)+1,1)=str2double(parseNote(modelSBML.species(i).notes,'CHARGE'));
-0364                 else
-0365                     metaboliteCharges(numel(metaboliteCharges)+1,1)=NaN;
-0366                 end
-0367             else
-0368                 metaboliteCharges(numel(metaboliteCharges)+1,1)=NaN;
-0369             end
-0370             %Additional information from FBC format Chemical formula
-0371             if isfield(modelSBML.species(i),'fbc_chemicalFormula')
-0372                 if ~isempty(modelSBML.species(i).fbc_chemicalFormula)
-0373                     metaboliteFormula{numel(metaboliteFormula),1}=modelSBML.species(i).fbc_chemicalFormula;
-0374                 end
-0375             end
-0376         end
-0377     end
-0378 end
-0379 
-0380 %Add SBO terms to gene and metabolite miriam fields
-0381 if numel(unique(geneSBOs)) > 1  % don't add if they're all identical
-0382     for i = 1:numel(geneNames)
-0383         geneMiriams{i} = addSBOtoMiriam(geneMiriams{i},geneSBOs(i));
-0384     end
-0385 end
-0386 if numel(unique(metSBOs)) > 1
-0387     for i = 1:numel(metaboliteNames)
-0388         metaboliteMiriams{i} = addSBOtoMiriam(metaboliteMiriams{i},metSBOs(i));
-0389     end
-0390 end
-0391 
-0392 %Retrieve info on reactions
-0393 reactionNames=cell(numel(modelSBML.reaction),1);
-0394 reactionIDs=cell(numel(modelSBML.reaction),1);
-0395 subsystems=cell(numel(modelSBML.reaction),1);
-0396 eccodes=cell(numel(modelSBML.reaction),1);
-0397 eccodes(:,:)=cellstr('');
-0398 rxnconfidencescores=NaN(numel(modelSBML.reaction),1);
-0399 rxnreferences=cell(numel(modelSBML.reaction),1);
-0400 rxnreferences(:,:)=cellstr('');
-0401 rxnnotes=cell(numel(modelSBML.reaction),1);
-0402 rxnnotes(:,:)=cellstr('');
-0403 grRules=cell(numel(modelSBML.reaction),1);
-0404 grRules(:,:)=cellstr('');
-0405 grRulesFromModifier=grRules;
-0406 rxnComps=zeros(numel(modelSBML.reaction),1);
-0407 rxnMiriams=cell(numel(modelSBML.reaction),1);
-0408 reactionReversibility=zeros(numel(modelSBML.reaction),1);
-0409 reactionUB=zeros(numel(modelSBML.reaction),1);
-0410 reactionLB=zeros(numel(modelSBML.reaction),1);
-0411 reactionObjective=zeros(numel(modelSBML.reaction),1);
-0412 
-0413 %Construct the stoichiometric matrix while the reaction info is read
-0414 S=zeros(numel(metaboliteIDs),numel(modelSBML.reaction));
-0415 
-0416 counter=0;
-0417 %If FBC, then bounds have parameter ids defined for the whole model
-0418 if isfield(modelSBML,'parameter')
-0419     parameter.name=cell(numel(modelSBML.parameter),1);
-0420     parameter.name={modelSBML.parameter(:).id}';
-0421     parameter.value={modelSBML.parameter(:).value}';
-0422 end
-0423 
-0424 if isfield(modelSBML.reaction,'sboTerm') && numel(unique([modelSBML.reaction.sboTerm])) == 1
-0425     %If all the SBO terms are identical, don't add them to rxnMiriams
-0426     modelSBML.reaction = rmfield(modelSBML.reaction,'sboTerm');
-0427 end
-0428 
-0429 for i=1:numel(modelSBML.reaction)
-0430 
-0431     %Check that the reaction doesn't produce a complex and nothing else. If
-0432     %so, then jump to the next reaction. This is because I get the genes
-0433     %for complexes from the names and not from the reactions that create
-0434     %them. This only applies to the non-COBRA format
-0435     if numel(modelSBML.reaction(i).product)==1
-0436         if length(modelSBML.reaction(i).product(1).species)>=3
-0437             if strcmp(modelSBML.reaction(i).product(1).species(1:3),'Cx_')==true
-0438                 continue;
-0439             end
-0440         end
-0441     end
-0442 
-0443     %It didn't look like a gene complex-forming reaction
-0444     counter=counter+1;
-0445 
-0446     reactionNames{counter}=modelSBML.reaction(i).name;
-0447 
-0448     reactionIDs{counter}=modelSBML.reaction(i).id;
-0449     reactionReversibility(counter)=modelSBML.reaction(i).reversible;
-0450 
-0451     %If model is FBC, first get parameter of bound and then replace it with
-0452     %the correct value. Probably faster with replace(), but this was only
-0453     %introduced in Matlab R2016b
-0454     if isfield(modelSBML.reaction(i),'fbc_lowerFluxBound')
-0455         lb=modelSBML.reaction(i).fbc_lowerFluxBound;
-0456         ub=modelSBML.reaction(i).fbc_upperFluxBound;
-0457         for n=1:numel(parameter.value)
-0458             lb=regexprep(lb,parameter.name(n),num2str(parameter.value{n}));
-0459             ub=regexprep(ub,parameter.name(n),num2str(parameter.value{n}));
-0460         end
-0461         if isempty(lb)
-0462             lb='-Inf';
-0463         end
-0464         if isempty(ub)
-0465             ub='Inf';
-0466         end
-0467         reactionLB(counter)=str2num(lb);
-0468         reactionUB(counter)=str2num(ub);
-0469         %The order of these parameters should not be hard coded
-0470     elseif isfield(modelSBML.reaction(i).kineticLaw,'parameter')
-0471         reactionLB(counter)=modelSBML.reaction(i).kineticLaw.parameter(1).value;
-0472         reactionUB(counter)=modelSBML.reaction(i).kineticLaw.parameter(2).value;
-0473         reactionObjective(counter)=modelSBML.reaction(i).kineticLaw.parameter(3).value;
-0474     else
-0475         if reactionReversibility(counter)==true
-0476             reactionLB(counter)=-inf;
-0477         else
-0478             reactionLB(counter)=0;
-0479         end
-0480         reactionUB(counter)=inf;
-0481         reactionObjective(counter)=0;
-0482     end
-0483 
-0484     %Find the associated gene if available
-0485     %If FBC, get gene association data from corresponding fields
-0486     if isfield(modelSBML.reaction(i),'fbc_geneProductAssociation')
-0487         if ~isempty(modelSBML.reaction(i).fbc_geneProductAssociation) && ~isempty(modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association)
-0488             grRules{counter}=modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association.fbc_association;
-0489         end
-0490     elseif isfield(modelSBML.reaction(i),'notes')
-0491         %This section was previously executed only if isSBML2COBRA is true. Now
-0492         %it will be executed, if 'GENE_ASSOCIATION' is found in
-0493         %modelSBML.reaction(i).notes
-0494         if strfind(modelSBML.reaction(i).notes,'GENE_ASSOCIATION')
-0495             geneAssociation=parseNote(modelSBML.reaction(i).notes,'GENE_ASSOCIATION');
-0496         elseif strfind(modelSBML.reaction(i).notes,'GENE ASSOCIATION')
-0497             geneAssociation=parseNote(modelSBML.reaction(i).notes,'GENE ASSOCIATION');
-0498         else
-0499             geneAssociation='';
-0500         end
-0501         if ~isempty(geneAssociation)
-0502             %This adds the grRules. The gene list and rxnGeneMat are created
-0503             %later
-0504             grRules{counter}=geneAssociation;
-0505         end
-0506     end
-0507     if isempty(grRules{counter}) && ~isempty(modelSBML.reaction(i).modifier)
-0508         rules='';
-0509         for j=1:numel(modelSBML.reaction(i).modifier)
-0510             modifier=modelSBML.reaction(i).modifier(j).species;
-0511             if ~isempty(modifier)
-0512                 if strcmpi(modifier(1:2),'E_')
-0513                     index=find(strcmp(modifier,geneIDs));
-0514                     %This should be unique and in the geneIDs list,
-0515                     %otherwise something is wrong
-0516                     if numel(index)~=1
-0517                         EM=['Could not get the gene association data from reaction ' reactionIDs{i}];
-0518                         dispEM(EM);
-0519                     end
-0520                     if ~isempty(rules)
-0521                         rules=[rules ' or (' geneNames{index} ')'];
-0522                     else
-0523                         rules=['(' geneNames{index} ')'];
-0524                     end
-0525                 elseif strcmp(modifier(1:2),'s_')
-0526                     index=find(strcmp(modifier,metaboliteIDs));
-0527                     %This should be unique and in the geneIDs list,
-0528                     %otherwise something is wrong
-0529                     if numel(index)~=1
-0530                         EM=['Could not get the gene association data from reaction ' reactionIDs{i}];
-0531                         dispEM(EM);
-0532                     end
-0533                     if ~isempty(rules)
-0534                         rules=[rules ' or (' metaboliteIDs{index} ')'];
-0535                     else
-0536                         rules=['(' metaboliteIDs{index} ')'];
-0537                     end
-0538                 else
-0539                     %It seems to be a complex. Add the corresponding
-0540                     %genes from the name of the complex (not the
-0541                     %reaction that creates it)
-0542                     index=find(strcmp(modifier,complexIDs));
-0543                     if numel(index)==1
-0544                         if ~isempty(rules)
-0545                             rules=[rules ' or (' strrep(complexNames{index},':',' and ') ')'];
-0546                         else
-0547                             rules=['(' strrep(complexNames{index},':',' and ') ')'];
-0548                         end
-0549                     else
-0550                         %Could not find a complex
-0551                         EM=['Could not get the gene association data from reaction ' reactionIDs{i}];
-0552                         dispEM(EM);
-0553                     end
-0554                 end
-0555             end
-0556         end
-0557         grRules{counter}=rules;
-0558         grRulesFromModifier{counter}=rules;%Backup copy for grRules, useful to parse Yeast 7.6
-0559     end
-0560 
-0561     %Add reaction compartment
-0562     if isfield(modelSBML.reaction(i),'compartment')
-0563         if ~isempty(modelSBML.reaction(i).compartment)
-0564             rxnComp=modelSBML.reaction(i).compartment;
-0565         else
-0566             rxnComp='';
-0567         end
-0568     elseif isfield(modelSBML.reaction(i),'notes')
-0569         rxnComp=parseNote(modelSBML.reaction(i).notes,'COMPARTMENT');
-0570     end
-0571     if ~isempty(rxnComp)
-0572         %Find it in the compartment list
-0573         [~, J]=ismember(rxnComp,compartmentIDs);
-0574         rxnComps(counter)=J;
-0575     end
-0576 
+0012 %   removePrefix    true if identifier prefixes should be removed when
+0013 %                   loading the model: G_ for genes, R_ for reactions,
+0014 %                   M_ for metabolites, and C_ for compartments. These are
+0015 %                   only removed if all identifiers of a certain type
+0016 %                   contain the prefix. (optional, default true)
+0017 %   supressWarnings true if warnings regarding the model structure should
+0018 %                   be supressed (optional, default false)
+0019 %
+0020 % Output:
+0021 %   model
+0022 %       id               model ID
+0023 %       name             name of model contents
+0024 %       annotation       additional information about model
+0025 %       rxns             reaction ids
+0026 %       mets             metabolite ids
+0027 %       S                stoichiometric matrix
+0028 %       lb               lower bounds
+0029 %       ub               upper bounds
+0030 %       rev              reversibility vector
+0031 %       c                objective coefficients
+0032 %       b                equality constraints for the metabolite equations
+0033 %       comps            compartment ids
+0034 %       compNames        compartment names
+0035 %       compOutside      the id (as in comps) for the compartment
+0036 %                        surrounding each of the compartments
+0037 %       compMiriams      structure with MIRIAM information about the
+0038 %                        compartments
+0039 %       rxnNames         reaction description
+0040 %       rxnComps         compartments for reactions
+0041 %       grRules          reaction to gene rules in text form
+0042 %       rxnGeneMat       reaction-to-gene mapping in sparse matrix form
+0043 %       subSystems       subsystem name for each reaction
+0044 %       eccodes          EC-codes for the reactions
+0045 %       rxnMiriams       structure with MIRIAM information about the reactions
+0046 %       rxnNotes         reaction notes
+0047 %       rxnReferences    reaction references
+0048 %       rxnConfidenceScores reaction confidence scores
+0049 %       genes            list of all genes
+0050 %       geneComps        compartments for genes
+0051 %       geneMiriams      structure with MIRIAM information about the genes
+0052 %       geneShortNames   gene alternative names (e.g. ERG10)
+0053 %       proteins         protein associated to each gene
+0054 %       metNames         metabolite description
+0055 %       metComps         compartments for metabolites
+0056 %       inchis           InChI-codes for metabolites
+0057 %       metFormulas      metabolite chemical formula
+0058 %       metMiriams       structure with MIRIAM information about the metabolites
+0059 %       metCharges       metabolite charge
+0060 %       unconstrained    true if the metabolite is an exchange metabolite
+0061 %
+0062 % Note: A number of consistency checks are performed in order to ensure that the
+0063 % model is valid. Take these warnings seriously and modify the model
+0064 % structure to solve them.
+0065 %
+0066 % Usage: model = importModel(fileName, removeExcMets, removePrefix, supressWarnings)
+0067 
+0068 if nargin<1 || isempty(fileName)
+0069     [fileName, pathName] = uigetfile({'*.xml;*.sbml'}, 'Please select the model file');
+0070     if fileName == 0
+0071         error('You should select a model file')
+0072     else
+0073         fileName = fullfile(pathName,fileName);
+0074     end
+0075 end
+0076 fileName=char(fileName);
+0077 if nargin<2 || isempty(removeExcMets)
+0078     removeExcMets=true;
+0079 end
+0080 
+0081 if nargin<3 || isempty(removePrefix)
+0082     removePrefix=true;
+0083 end
+0084 
+0085 if nargin<4
+0086     supressWarnings=false;
+0087 end
+0088 
+0089 fileName=checkFileExistence(fileName,1);
+0090 % If path contains non-ASCII characters, copy file to tempdir first, as
+0091 % libSBML is known to have problems with this on Windows:
+0092 % https://sbml.org/software/libsbml/libsbml-docs/known-pitfalls/#matlab-on-windows-has-issues-with-unicode-filenames
+0093 if ispc && any(double(fileName)>128)
+0094     [~,originalFile,ext] = fileparts(fileName);
+0095     tempFile = fullfile(tempdir,[originalFile ext]);
+0096     copyfile(fileName,tempFile);
+0097     fileName = tempFile;
+0098 end
+0099 
+0100 %This is to match the order of the fields to those you get from importing
+0101 %from Excel
+0102 model=[];
+0103 model.id=[];
+0104 model.name=[];
+0105 model.annotation=[];
+0106 model.rxns={};
+0107 model.mets={};
+0108 model.S=[];
+0109 model.lb=[];
+0110 model.ub=[];
+0111 model.rev=[];
+0112 model.c=[];
+0113 model.b=[];
+0114 model.comps={};
+0115 model.compNames={};
+0116 model.compOutside={};
+0117 model.compMiriams={};
+0118 model.rxnNames={};
+0119 model.rxnComps=[];
+0120 model.grRules={};
+0121 model.rxnGeneMat=[];
+0122 model.subSystems={};
+0123 model.eccodes={};
+0124 model.rxnMiriams={};
+0125 model.rxnNotes={};
+0126 model.rxnReferences={};
+0127 model.rxnConfidenceScores=[];
+0128 model.genes={};
+0129 model.geneComps=[];
+0130 model.geneMiriams={};
+0131 model.geneShortNames={};
+0132 model.proteins={};
+0133 model.metNames={};
+0134 model.metComps=[];
+0135 model.inchis={};
+0136 model.metFormulas={};
+0137 model.metMiriams={};
+0138 model.metCharges=[];
+0139 model.unconstrained=[];
+0140 
+0141 %Load the model using libSBML
+0142 [modelSBML,errorMsg] = TranslateSBML_RAVEN(fileName,0,0,[1 1]);
+0143 if exist('tempFile','var')
+0144     delete(tempFile)
+0145 end
+0146 
+0147 if isempty(modelSBML)
+0148     EM=['There is a problem with the SBML file. Try using the SBML Validator at http://sbml.org/Facilities/Validator.\nlibSBML reports: ', errorMsg.message];
+0149     dispEM(EM);
+0150 end
+0151 
+0152 %Retrieve compartment names and IDs
+0153 compartmentNames=cell(numel(modelSBML.compartment),1);
+0154 compartmentIDs=cell(numel(modelSBML.compartment),1);
+0155 compartmentOutside=cell(numel(modelSBML.compartment),1);
+0156 compartmentMiriams=cell(numel(modelSBML.compartment),1);
+0157 
+0158 if isfield(modelSBML.compartment,'sboTerm') && numel(unique([modelSBML.compartment.sboTerm])) == 1
+0159     %If all the SBO terms are identical, don't add them to compMiriams
+0160     modelSBML.compartment = rmfield(modelSBML.compartment,'sboTerm');
+0161 end
+0162 
+0163 for i=1:numel(modelSBML.compartment)
+0164     compartmentNames{i}=modelSBML.compartment(i).name;
+0165     compartmentIDs{i}=modelSBML.compartment(i).id;
+0166     if isfield(modelSBML.compartment(i),'outside')
+0167         if ~isempty(modelSBML.compartment(i).outside)
+0168             compartmentOutside{i}=modelSBML.compartment(i).outside;
+0169         else
+0170             compartmentOutside{i}='';
+0171         end
+0172     else
+0173         compartmentOutside{i}=[];
+0174     end
+0175 
+0176     if isfield(modelSBML.compartment(i),'annotation')
+0177         compartmentMiriams{i}=parseMiriam(modelSBML.compartment(i).annotation);
+0178     else
+0179         compartmentMiriams{i}=[];
+0180     end
+0181 
+0182     if isfield(modelSBML.compartment(i),'sboTerm') && ~(modelSBML.compartment(i).sboTerm==-1)
+0183         compartmentMiriams{i} = addSBOtoMiriam(compartmentMiriams{i},modelSBML.compartment(i).sboTerm);
+0184     end
+0185 end
+0186 
+0187 %If there are no compartment names then use compartment id as name
+0188 if all(cellfun(@isempty,compartmentNames))
+0189     compartmentNames=compartmentIDs;
+0190 end
+0191 
+0192 %Retrieve info on metabolites, genes, complexes
+0193 metaboliteNames={};
+0194 metaboliteIDs={};
+0195 metaboliteCompartments={};
+0196 metaboliteUnconstrained=[];
+0197 metaboliteFormula={};
+0198 metaboliteInChI={};
+0199 metaboliteMiriams={};
+0200 metaboliteCharges=[];
+0201 
+0202 geneNames={};
+0203 geneIDs={};
+0204 geneMiriams={};
+0205 geneShortNames={};
+0206 proteins={};
+0207 geneCompartments={};
+0208 complexIDs={};
+0209 complexNames={};
+0210 
+0211 %If the file is not a COBRA Toolbox model. According to the format
+0212 %specified in the yeast consensus model both metabolites and genes are a
+0213 %type of 'species'. The metabolites have names starting with 'M_' and genes
+0214 %with 'E_'
+0215 geneSBOs = [];
+0216 metSBOs = [];
+0217 %Regex of compartment names, later to be used to remove from metabolite
+0218 %names if present as suffix.
+0219 regexCompNames = ['\s?\[((' strjoin({modelSBML.compartment.name},')|(') '))\]$'];
+0220 for i=1:numel(modelSBML.species)
+0221     if length(modelSBML.species(i).id)>=2 && strcmpi(modelSBML.species(i).id(1:2),'E_')
+0222         geneNames{numel(geneNames)+1,1}=modelSBML.species(i).name;
+0223 
+0224         %The "E_" is included in the ID. This is because it's only used
+0225         %internally in this file and it makes the matching a little
+0226         %smoother
+0227         geneIDs{numel(geneIDs)+1,1}=modelSBML.species(i).id;
+0228         geneCompartments{numel(geneCompartments)+1,1}=modelSBML.species(i).compartment;
+0229 
+0230         %Get Miriam structure
+0231         if isfield(modelSBML.species(i),'annotation')
+0232             %Get Miriam info
+0233             geneMiriam=parseMiriam(modelSBML.species(i).annotation);
+0234             geneMiriams{numel(geneMiriams)+1,1}=geneMiriam;
+0235         else
+0236             geneMiriams{numel(geneMiriams)+1,1}=[];
+0237         end
+0238 
+0239         %Protein short names (for example ERG10) are saved as SHORT
+0240         %NAME: NAME in the notes-section of metabolites for SBML Level
+0241         %2 and as PROTEIN_ASSOCIATION for each reaction in SBML Level 2
+0242         %COBRA Toolbox format. For now only the SHORT NAME is loaded
+0243         %and no mapping takes place
+0244         if isfield(modelSBML.species(i),'notes')
+0245             geneShortNames{numel(geneShortNames)+1,1}=parseNote(modelSBML.species(i).notes,'SHORT NAME');
+0246         else
+0247             geneShortNames{numel(geneShortNames)+1,1}='';
+0248         end
+0249 
+0250         %Get SBO term
+0251         if isfield(modelSBML.species(i),'sboTerm') && ~(modelSBML.species(i).sboTerm==-1)
+0252             geneSBOs(end+1,1) = modelSBML.species(i).sboTerm;
+0253         end
+0254     elseif length(modelSBML.species(i).id)>=2 && strcmpi(modelSBML.species(i).id(1:3),'Cx_')
+0255         %If it's a complex keep the ID and name
+0256         complexIDs=[complexIDs;modelSBML.species(i).id];
+0257         complexNames=[complexNames;modelSBML.species(i).name];
+0258     else
+0259         %If it is not gene or complex, then it must be a metabolite
+0260         metaboliteNames{numel(metaboliteNames)+1,1}=modelSBML.species(i).name;
+0261         metaboliteIDs{numel(metaboliteIDs)+1,1}=modelSBML.species(i).id;
+0262         metaboliteCompartments{numel(metaboliteCompartments)+1,1}=modelSBML.species(i).compartment;
+0263         metaboliteUnconstrained(numel(metaboliteUnconstrained)+1,1)=modelSBML.species(i).boundaryCondition;
+0264 
+0265         %For each metabolite retrieve the formula and the InChI code if
+0266         %available First add the InChI code and the formula from the
+0267         %InChI. This allows for overwriting the formula by setting the
+0268         %actual formula field
+0269         if ~isempty(modelSBML.species(i).annotation)
+0270             %Get the formula if available
+0271             startString='>InChI=';
+0272             endString='</in:inchi>';
+0273             formStart=strfind(modelSBML.species(i).annotation,startString);
+0274             if isempty(formStart)
+0275                 startString='InChI=';
+0276                 endString='"/>';
+0277             end
+0278             formStart=strfind(modelSBML.species(i).annotation,startString);
+0279             if ~isempty(formStart)
+0280                 formEnd=strfind(modelSBML.species(i).annotation,endString);
+0281                 formEndIndex=find(formEnd>formStart, 1 );
+0282                 formula=modelSBML.species(i).annotation(formStart+numel(startString):formEnd(formEndIndex)-1);
+0283                 metaboliteInChI{numel(metaboliteInChI)+1,1}=formula;
+0284 
+0285                 %The composition is most often present between the
+0286                 %first and second "/" in the model. In some simple
+0287                 %molecules, such as salts, there is no second "/". The
+0288                 %formula is then assumed to be to the end of the string
+0289                 compositionIndexes=strfind(formula,'/');
+0290                 if numel(compositionIndexes)>1
+0291                     metaboliteFormula{numel(metaboliteFormula)+1,1}=...
+0292                         formula(compositionIndexes(1)+1:compositionIndexes(2)-1);
+0293                 else
+0294                     if numel(compositionIndexes)==1
+0295                         %Probably a simple molecule which can have only
+0296                         %one conformation
+0297                         metaboliteFormula{numel(metaboliteFormula)+1,1}=...
+0298                             formula(compositionIndexes(1)+1:numel(formula));
+0299                     else
+0300                         metaboliteFormula{numel(metaboliteFormula)+1,1}='';
+0301                     end
+0302                 end
+0303             elseif isfield(modelSBML.species(i),'fbc_chemicalFormula')
+0304                 metaboliteInChI{numel(metaboliteInChI)+1,1}='';
+0305                 if ~isempty(modelSBML.species(i).fbc_chemicalFormula)
+0306                     %Cannot extract InChi from formula, so remains
+0307                     %empty
+0308                     metaboliteFormula{numel(metaboliteFormula)+1,1}=modelSBML.species(i).fbc_chemicalFormula;
+0309                 else
+0310                     metaboliteFormula{numel(metaboliteFormula)+1,1}='';
+0311                 end
+0312             else
+0313                 metaboliteInChI{numel(metaboliteInChI)+1,1}='';
+0314                 metaboliteFormula{numel(metaboliteFormula)+1,1}='';
+0315             end
+0316 
+0317             %Get Miriam info
+0318             metMiriam=parseMiriam(modelSBML.species(i).annotation);
+0319             metaboliteMiriams{numel(metaboliteMiriams)+1,1}=metMiriam;
+0320         else
+0321             metaboliteInChI{numel(metaboliteInChI)+1,1}='';
+0322             if isfield(modelSBML.species(i),'notes')
+0323                 metaboliteFormula{numel(metaboliteFormula)+1,1}=parseNote(modelSBML.species(i).notes,'FORMULA');
+0324             else
+0325                 metaboliteFormula{numel(metaboliteFormula)+1,1}='';
+0326             end
+0327             metaboliteMiriams{numel(metaboliteMiriams)+1,1}=[];
+0328         end
+0329         if ~isempty(modelSBML.species(i).notes)
+0330             if ~isfield(modelSBML.species(i),'annotation')
+0331                 metaboliteFormula{numel(metaboliteFormula)+1,1}=parseNote(modelSBML.species(i).notes,'FORMULA');
+0332             end
+0333         elseif ~isfield(modelSBML.species(i),'annotation')
+0334             metaboliteFormula{numel(metaboliteFormula)+1,1}='';
+0335         end
+0336         %Get SBO term
+0337         if isfield(modelSBML.species(i),'sboTerm') && ~(modelSBML.species(i).sboTerm==-1)
+0338             metSBOs(end+1,1) = modelSBML.species(i).sboTerm;
+0339         end
+0340     end
+0341 
+0342     %The following lines are executed regardless isSBML2COBRA setting
+0343     if isempty(modelSBML.species(i).id) || ~strcmpi(modelSBML.species(i).id(1:2),'E_')
+0344         if isempty(modelSBML.species(i).id) || ~strcmpi(modelSBML.species(i).id(1:3),'Cx_')
+0345             %Remove trailing [compartment] from metabolite name if present
+0346             metaboliteNames{end,1}=regexprep(metaboliteNames{end,1},regexCompNames,'');
+0347             metaboliteNames{end,1}=metaboliteNames{end,1};
+0348             if isfield(modelSBML.species(i),'fbc_charge')
+0349                 if ~isempty(modelSBML.species(i).fbc_charge) && modelSBML.species(i).isSetfbc_charge
+0350                     metaboliteCharges(numel(metaboliteCharges)+1,1)=double(modelSBML.species(i).fbc_charge);
+0351                 else
+0352                     if isfield(modelSBML.species(i),'notes')
+0353                         if strfind(modelSBML.species(i).notes,'CHARGE')
+0354                             metaboliteCharges(numel(metaboliteCharges)+1,1)=str2double(parseNote(modelSBML.species(i).notes,'CHARGE'));
+0355                         else
+0356                             metaboliteCharges(numel(metaboliteCharges)+1,1)=NaN;
+0357                         end
+0358                     else
+0359                         metaboliteCharges(numel(metaboliteCharges)+1,1)=NaN;
+0360                     end
+0361                 end
+0362             elseif isfield(modelSBML.species(i),'notes')
+0363                 if strfind(modelSBML.species(i).notes,'CHARGE')
+0364                     metaboliteCharges(numel(metaboliteCharges)+1,1)=str2double(parseNote(modelSBML.species(i).notes,'CHARGE'));
+0365                 else
+0366                     metaboliteCharges(numel(metaboliteCharges)+1,1)=NaN;
+0367                 end
+0368             else
+0369                 metaboliteCharges(numel(metaboliteCharges)+1,1)=NaN;
+0370             end
+0371             %Additional information from FBC format Chemical formula
+0372             if isfield(modelSBML.species(i),'fbc_chemicalFormula')
+0373                 if ~isempty(modelSBML.species(i).fbc_chemicalFormula)
+0374                     metaboliteFormula{numel(metaboliteFormula),1}=modelSBML.species(i).fbc_chemicalFormula;
+0375                 end
+0376             end
+0377         end
+0378     end
+0379 end
+0380 
+0381 %Add SBO terms to gene and metabolite miriam fields
+0382 if numel(unique(geneSBOs)) > 1  % don't add if they're all identical
+0383     for i = 1:numel(geneNames)
+0384         geneMiriams{i} = addSBOtoMiriam(geneMiriams{i},geneSBOs(i));
+0385     end
+0386 end
+0387 if numel(unique(metSBOs)) > 1
+0388     for i = 1:numel(metaboliteNames)
+0389         metaboliteMiriams{i} = addSBOtoMiriam(metaboliteMiriams{i},metSBOs(i));
+0390     end
+0391 end
+0392 
+0393 %Retrieve info on reactions
+0394 reactionNames=cell(numel(modelSBML.reaction),1);
+0395 reactionIDs=cell(numel(modelSBML.reaction),1);
+0396 subsystems=cell(numel(modelSBML.reaction),1);
+0397 eccodes=cell(numel(modelSBML.reaction),1);
+0398 eccodes(:,:)=cellstr('');
+0399 rxnconfidencescores=NaN(numel(modelSBML.reaction),1);
+0400 rxnreferences=cell(numel(modelSBML.reaction),1);
+0401 rxnreferences(:,:)=cellstr('');
+0402 rxnnotes=cell(numel(modelSBML.reaction),1);
+0403 rxnnotes(:,:)=cellstr('');
+0404 grRules=cell(numel(modelSBML.reaction),1);
+0405 grRules(:,:)=cellstr('');
+0406 grRulesFromModifier=grRules;
+0407 rxnComps=zeros(numel(modelSBML.reaction),1);
+0408 rxnMiriams=cell(numel(modelSBML.reaction),1);
+0409 reactionReversibility=zeros(numel(modelSBML.reaction),1);
+0410 reactionUB=zeros(numel(modelSBML.reaction),1);
+0411 reactionLB=zeros(numel(modelSBML.reaction),1);
+0412 reactionObjective=zeros(numel(modelSBML.reaction),1);
+0413 
+0414 %Construct the stoichiometric matrix while the reaction info is read
+0415 S=zeros(numel(metaboliteIDs),numel(modelSBML.reaction));
+0416 
+0417 counter=0;
+0418 %If FBC, then bounds have parameter ids defined for the whole model
+0419 if isfield(modelSBML,'parameter')
+0420     parameter.name=cell(numel(modelSBML.parameter),1);
+0421     parameter.name={modelSBML.parameter(:).id}';
+0422     parameter.value={modelSBML.parameter(:).value}';
+0423 end
+0424 
+0425 if isfield(modelSBML.reaction,'sboTerm') && numel(unique([modelSBML.reaction.sboTerm])) == 1
+0426     %If all the SBO terms are identical, don't add them to rxnMiriams
+0427     modelSBML.reaction = rmfield(modelSBML.reaction,'sboTerm');
+0428 end
+0429 
+0430 for i=1:numel(modelSBML.reaction)
+0431 
+0432     %Check that the reaction doesn't produce a complex and nothing else. If
+0433     %so, then jump to the next reaction. This is because I get the genes
+0434     %for complexes from the names and not from the reactions that create
+0435     %them. This only applies to the non-COBRA format
+0436     if numel(modelSBML.reaction(i).product)==1
+0437         if length(modelSBML.reaction(i).product(1).species)>=3
+0438             if strcmp(modelSBML.reaction(i).product(1).species(1:3),'Cx_')==true
+0439                 continue;
+0440             end
+0441         end
+0442     end
+0443 
+0444     %It didn't look like a gene complex-forming reaction
+0445     counter=counter+1;
+0446 
+0447     reactionNames{counter}=modelSBML.reaction(i).name;
+0448 
+0449     reactionIDs{counter}=modelSBML.reaction(i).id;
+0450     reactionReversibility(counter)=modelSBML.reaction(i).reversible;
+0451 
+0452     %If model is FBC, first get parameter of bound and then replace it with
+0453     %the correct value. Probably faster with replace(), but this was only
+0454     %introduced in Matlab R2016b
+0455     if isfield(modelSBML.reaction(i),'fbc_lowerFluxBound')
+0456         lb=modelSBML.reaction(i).fbc_lowerFluxBound;
+0457         ub=modelSBML.reaction(i).fbc_upperFluxBound;
+0458         for n=1:numel(parameter.value)
+0459             lb=regexprep(lb,parameter.name(n),num2str(parameter.value{n}));
+0460             ub=regexprep(ub,parameter.name(n),num2str(parameter.value{n}));
+0461         end
+0462         if isempty(lb)
+0463             lb='-Inf';
+0464         end
+0465         if isempty(ub)
+0466             ub='Inf';
+0467         end
+0468         reactionLB(counter)=str2num(lb);
+0469         reactionUB(counter)=str2num(ub);
+0470         %The order of these parameters should not be hard coded
+0471     elseif isfield(modelSBML.reaction(i).kineticLaw,'parameter')
+0472         reactionLB(counter)=modelSBML.reaction(i).kineticLaw.parameter(1).value;
+0473         reactionUB(counter)=modelSBML.reaction(i).kineticLaw.parameter(2).value;
+0474         reactionObjective(counter)=modelSBML.reaction(i).kineticLaw.parameter(3).value;
+0475     else
+0476         if reactionReversibility(counter)==true
+0477             reactionLB(counter)=-inf;
+0478         else
+0479             reactionLB(counter)=0;
+0480         end
+0481         reactionUB(counter)=inf;
+0482         reactionObjective(counter)=0;
+0483     end
+0484 
+0485     %Find the associated gene if available
+0486     %If FBC, get gene association data from corresponding fields
+0487     if isfield(modelSBML.reaction(i),'fbc_geneProductAssociation')
+0488         if ~isempty(modelSBML.reaction(i).fbc_geneProductAssociation) && ~isempty(modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association)
+0489             grRules{counter}=modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association.fbc_association;
+0490         end
+0491     elseif isfield(modelSBML.reaction(i),'notes')
+0492         %This section was previously executed only if isSBML2COBRA is true. Now
+0493         %it will be executed, if 'GENE_ASSOCIATION' is found in
+0494         %modelSBML.reaction(i).notes
+0495         if strfind(modelSBML.reaction(i).notes,'GENE_ASSOCIATION')
+0496             geneAssociation=parseNote(modelSBML.reaction(i).notes,'GENE_ASSOCIATION');
+0497         elseif strfind(modelSBML.reaction(i).notes,'GENE ASSOCIATION')
+0498             geneAssociation=parseNote(modelSBML.reaction(i).notes,'GENE ASSOCIATION');
+0499         else
+0500             geneAssociation='';
+0501         end
+0502         if ~isempty(geneAssociation)
+0503             %This adds the grRules. The gene list and rxnGeneMat are created
+0504             %later
+0505             grRules{counter}=geneAssociation;
+0506         end
+0507     end
+0508     if isempty(grRules{counter}) && ~isempty(modelSBML.reaction(i).modifier)
+0509         rules='';
+0510         for j=1:numel(modelSBML.reaction(i).modifier)
+0511             modifier=modelSBML.reaction(i).modifier(j).species;
+0512             if ~isempty(modifier)
+0513                 if strcmpi(modifier(1:2),'E_')
+0514                     index=find(strcmp(modifier,geneIDs));
+0515                     %This should be unique and in the geneIDs list,
+0516                     %otherwise something is wrong
+0517                     if numel(index)~=1
+0518                         EM=['Could not get the gene association data from reaction ' reactionIDs{i}];
+0519                         dispEM(EM);
+0520                     end
+0521                     if ~isempty(rules)
+0522                         rules=[rules ' or (' geneNames{index} ')'];
+0523                     else
+0524                         rules=['(' geneNames{index} ')'];
+0525                     end
+0526                 elseif strcmp(modifier(1:2),'s_')
+0527                     index=find(strcmp(modifier,metaboliteIDs));
+0528                     %This should be unique and in the geneIDs list,
+0529                     %otherwise something is wrong
+0530                     if numel(index)~=1
+0531                         EM=['Could not get the gene association data from reaction ' reactionIDs{i}];
+0532                         dispEM(EM);
+0533                     end
+0534                     if ~isempty(rules)
+0535                         rules=[rules ' or (' metaboliteIDs{index} ')'];
+0536                     else
+0537                         rules=['(' metaboliteIDs{index} ')'];
+0538                     end
+0539                 else
+0540                     %It seems to be a complex. Add the corresponding
+0541                     %genes from the name of the complex (not the
+0542                     %reaction that creates it)
+0543                     index=find(strcmp(modifier,complexIDs));
+0544                     if numel(index)==1
+0545                         if ~isempty(rules)
+0546                             rules=[rules ' or (' strrep(complexNames{index},':',' and ') ')'];
+0547                         else
+0548                             rules=['(' strrep(complexNames{index},':',' and ') ')'];
+0549                         end
+0550                     else
+0551                         %Could not find a complex
+0552                         EM=['Could not get the gene association data from reaction ' reactionIDs{i}];
+0553                         dispEM(EM);
+0554                     end
+0555                 end
+0556             end
+0557         end
+0558         grRules{counter}=rules;
+0559         grRulesFromModifier{counter}=rules;%Backup copy for grRules, useful to parse Yeast 7.6
+0560     end
+0561 
+0562     %Add reaction compartment
+0563     if isfield(modelSBML.reaction(i),'compartment')
+0564         if ~isempty(modelSBML.reaction(i).compartment)
+0565             rxnComp=modelSBML.reaction(i).compartment;
+0566         else
+0567             rxnComp='';
+0568         end
+0569     elseif isfield(modelSBML.reaction(i),'notes')
+0570         rxnComp=parseNote(modelSBML.reaction(i).notes,'COMPARTMENT');
+0571     end
+0572     if ~isempty(rxnComp)
+0573         %Find it in the compartment list
+0574         [~, J]=ismember(rxnComp,compartmentIDs);
+0575         rxnComps(counter)=J;
+0576     end
 0577 
-0578     miriamStruct=parseMiriam(modelSBML.reaction(i).annotation);
-0579     rxnMiriams{counter}=miriamStruct;
-0580     if isfield(modelSBML.reaction(i),'notes')
-0581         subsystems{counter,1}=cellstr(parseNote(modelSBML.reaction(i).notes,'SUBSYSTEM'));
-0582         subsystems{counter,1}(cellfun('isempty',subsystems{counter,1})) = [];
-0583         if strfind(modelSBML.reaction(i).notes,'Confidence Level')
-0584             confScore = parseNote(modelSBML.reaction(i).notes,'Confidence Level');
-0585             if isempty(confScore)
-0586                 confScore = 0;
-0587             end
-0588             rxnconfidencescores(counter)=str2double(confScore);
-0589         end
-0590         rxnreferences{counter,1}=parseNote(modelSBML.reaction(i).notes,'AUTHORS');
-0591         rxnnotes{counter,1}=parseNote(modelSBML.reaction(i).notes,'NOTES');
-0592     end
-0593 
-0594     %Get SBO terms
-0595     if isfield(modelSBML.reaction(i),'sboTerm') && ~(modelSBML.reaction(i).sboTerm==-1)
-0596         rxnMiriams{counter} = addSBOtoMiriam(rxnMiriams{counter}, modelSBML.reaction(i).sboTerm);
-0597     end
-0598 
-0599     %Get ec-codes
-0600     eccode='';
-0601     if ~isempty(modelSBML.reaction(i).annotation)
-0602         if strfind(modelSBML.reaction(i).annotation,'urn:miriam:ec-code')
-0603             eccode=parseAnnotation(modelSBML.reaction(i).annotation,'urn:miriam:',':','ec-code');
-0604         elseif strfind(modelSBML.reaction(i).annotation,'http://identifiers.org/ec-code')
-0605             eccode=parseAnnotation(modelSBML.reaction(i).annotation,'http://identifiers.org/','/','ec-code');
-0606         elseif strfind(modelSBML.reaction(i).annotation,'https://identifiers.org/ec-code')
-0607             eccode=parseAnnotation(modelSBML.reaction(i).annotation,'https://identifiers.org/','/','ec-code');
-0608         end
-0609     elseif isfield(modelSBML.reaction(i),'notes')
-0610         if strfind(modelSBML.reaction(i).notes,'EC Number')
-0611             eccode=[eccode parseNote(modelSBML.reaction(i).notes,'EC Number')];
-0612         elseif strfind(modelSBML.reaction(i).notes,'PROTEIN_CLASS')
-0613             eccode=[eccode parseNote(modelSBML.reaction(i).notes,'PROTEIN_CLASS')];
-0614         end
-0615     end
-0616     eccodes{counter}=eccode;
-0617 
-0618     %Add all reactants
-0619     for j=1:numel(modelSBML.reaction(i).reactant)
-0620         %Get the index of the metabolite in metaboliteIDs. External
-0621         %metabolites will be removed at a later stage
-0622         metIndex=find(strcmp(modelSBML.reaction(i).reactant(j).species,metaboliteIDs),1);
-0623         if isempty(metIndex)
-0624             EM=['Could not find metabolite ' modelSBML.reaction(i).reactant(j).species ' in reaction ' reactionIDs{counter}];
-0625             dispEM(EM);
-0626         end
-0627         S(metIndex,counter)=S(metIndex,counter)+modelSBML.reaction(i).reactant(j).stoichiometry*-1;
-0628     end
-0629 
-0630     %Add all products
-0631     for j=1:numel(modelSBML.reaction(i).product)
-0632         %Get the index of the metabolite in metaboliteIDs.
-0633         metIndex=find(strcmp(modelSBML.reaction(i).product(j).species,metaboliteIDs),1);
-0634         if isempty(metIndex)
-0635             EM=['Could not find metabolite ' modelSBML.reaction(i).product(j).species ' in reaction ' reactionIDs{counter}];
-0636             dispEM(EM);
-0637         end
-0638         S(metIndex,counter)=S(metIndex,counter)+modelSBML.reaction(i).product(j).stoichiometry;
-0639     end
-0640 end
-0641 
-0642 %if FBC, objective function is separately defined. Multiple objective
-0643 %functions can be defined, one is set as active
-0644 if isfield(modelSBML, 'fbc_activeObjective')
-0645     obj=modelSBML.fbc_activeObjective;
-0646     for i=1:numel(modelSBML.fbc_objective)
-0647         if strcmp(obj,modelSBML.fbc_objective(i).fbc_id)
-0648             if ~isempty(modelSBML.fbc_objective(i).fbc_fluxObjective)
-0649                 rxn=modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_reaction;
-0650                 idx=find(ismember(reactionIDs,rxn));
-0651                 reactionObjective(idx)=modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_coefficient;
-0652             end
-0653         end
-0654     end
-0655 end
-0656 
-0657 %subSystems can be stored as groups instead of in annotations
-0658 if isfield(modelSBML,'groups_group')
-0659     for i=1:numel(modelSBML.groups_group)
-0660         groupreactions={modelSBML.groups_group(i).groups_member(:).groups_idRef};
-0661         [~, idx] = ismember(groupreactions, reactionIDs);
-0662         if any(idx)
-0663             for j=1:numel(idx)
-0664                 if isempty(subsystems{idx(j)}) % First subsystem
-0665                     subsystems{idx(j)} = {modelSBML.groups_group(i).groups_name};
-0666                 else % Consecutive subsystems: concatenate
-0667                     subsystems{idx(j)} = horzcat(subsystems{idx(j)}, modelSBML.groups_group(i).groups_name);
-0668                 end
-0669             end
-0670         end
-0671     end
-0672 end
-0673 
-0674 %Shrink the structures if complex-forming reactions had to be skipped
-0675 reactionNames=reactionNames(1:counter);
-0676 reactionIDs=reactionIDs(1:counter);
-0677 subsystems=subsystems(1:counter);
-0678 eccodes=eccodes(1:counter);
-0679 rxnconfidencescores=rxnconfidencescores(1:counter);
-0680 rxnreferences=rxnreferences(1:counter);
-0681 rxnnotes=rxnnotes(1:counter);
-0682 grRules=grRules(1:counter);
-0683 rxnMiriams=rxnMiriams(1:counter);
-0684 reactionReversibility=reactionReversibility(1:counter);
-0685 reactionUB=reactionUB(1:counter);
-0686 reactionLB=reactionLB(1:counter);
-0687 reactionObjective=reactionObjective(1:counter);
-0688 S=S(:,1:counter);
-0689 
-0690 model.name=modelSBML.name;
-0691 model.id=modelSBML.id;
-0692 model.rxns=reactionIDs;
-0693 model.mets=metaboliteIDs;
-0694 model.S=sparse(S);
-0695 model.lb=reactionLB;
-0696 model.ub=reactionUB;
-0697 model.rev=reactionReversibility;
-0698 model.c=reactionObjective;
-0699 model.b=zeros(numel(metaboliteIDs),1);
-0700 model.comps=compartmentIDs;
-0701 model.compNames=compartmentNames;
-0702 model.rxnConfidenceScores=rxnconfidencescores;
-0703 model.rxnReferences=rxnreferences;
-0704 model.rxnNotes=rxnnotes;
-0705 
-0706 %Load annotation if available. If there are several authors, only the first
-0707 %author credentials are imported
-0708 if isfield(modelSBML,'annotation')
-0709     endString='</';
-0710     I=strfind(modelSBML.annotation,endString);
-0711     J=strfind(modelSBML.annotation,'<vCard:Family>');
-0712     if any(J)
-0713         model.annotation.familyName=modelSBML.annotation(J(1)+14:I(find(I>J(1),1))-1);
-0714     end
-0715     J=strfind(modelSBML.annotation,'<vCard:Given>');
-0716     if any(J)
-0717         model.annotation.givenName=modelSBML.annotation(J(1)+13:I(find(I>J(1),1))-1);
-0718     end
-0719     J=strfind(modelSBML.annotation,'<vCard:EMAIL>');
-0720     if any(J)
-0721         model.annotation.email=modelSBML.annotation(J(1)+13:I(find(I>J(1),1))-1);
-0722     end
-0723     J=strfind(modelSBML.annotation,'<vCard:Orgname>');
-0724     if any(J)
-0725         model.annotation.organization=modelSBML.annotation(J(1)+15:I(find(I>J(1),1))-1);
-0726     end
-0727     endString='"/>';
-0728     I=strfind(modelSBML.annotation,endString);
-0729     if strfind(modelSBML.annotation,'"urn:miriam:')
-0730         J=strfind(modelSBML.annotation,'"urn:miriam:');
-0731         if any(J)
-0732             model.annotation.taxonomy=modelSBML.annotation(J+12:I(find(I>J,1))-1);
-0733         end
-0734     else
-0735         J=strfind(modelSBML.annotation,'"http://identifiers.org/');
-0736         if any(J)
-0737             model.annotation.taxonomy=modelSBML.annotation(J+24:I(find(I>J,1))-1);
-0738         else
-0739             J=strfind(modelSBML.annotation,'"https://identifiers.org/');
-0740             if any(J)
-0741                 model.annotation.taxonomy=modelSBML.annotation(J+25:I(find(I>J,1))-1);
-0742             end
-0743         end
-0744     end
-0745 end
-0746 if isfield(modelSBML,'notes')
-0747     startString=strfind(modelSBML.notes,'xhtml">');
-0748     endString=strfind(modelSBML.notes,'</body>');
-0749     if any(startString) && any(endString)
-0750         model.annotation.note=modelSBML.notes(startString+7:endString-1);
-0751         model.annotation.note=regexprep(model.annotation.note,'<p>|</p>','');
-0752         model.annotation.note=strtrim(model.annotation.note);
-0753         if regexp(model.annotation.note,'This file was generated using the exportModel function in RAVEN Toolbox \d\.\d and OutputSBML in libSBML')
-0754             model.annotation=rmfield(model.annotation,'note'); % Default note added when running exportModel
-0755         end
-0756     end
-0757 end
-0758 
-0759 if any(~cellfun(@isempty,compartmentOutside))
-0760     model.compOutside=compartmentOutside;
-0761 end
-0762 
-0763 model.rxnNames=reactionNames;
-0764 model.metNames=metaboliteNames;
-0765 
-0766 %Match the compartments for metabolites
-0767 [~, J]=ismember(metaboliteCompartments,model.comps);
-0768 model.metComps=J;
-0769 
-0770 %If any genes have been loaded (only for the new format)
-0771 if ~isempty(geneNames)
-0772     %In some rare cases geneNames may not necessarily be used in grRules.
-0773     %That is true for Yeast 7.6. It's therefore important to change gene
-0774     %systematic names to geneIDs in sophisticated way. Gene systematic
-0775     %names are not unique, since exactly the same name may be in different
-0776     %compartments
-0777     if all(cellfun(@isempty,strfind(grRules,geneNames{1})))
-0778         geneShortNames=geneNames;
-0779         %geneShortNames contain compartments as well, so these are removed
-0780         geneShortNames=regexprep(geneShortNames,' \[.+$','');
-0781         %grRules obtained from modifier fields contain geneNames. These are
-0782         %changed into geneIDs. grRulesFromModifier is a good way to have
-0783         %geneIDs and rxns association when it's important to resolve
-0784         %systematic name ambiguities
-0785         grRulesFromModifier=regexprep(regexprep(grRulesFromModifier,'\[|\]','_'),regexprep(geneNames,'\[|\]','_'),geneIDs);
-0786         grRules=regexprep(regexprep(grRules,'\[|\]','_'),regexprep(geneNames,'\[|\]','_'),geneIDs);
-0787 
-0788         %Yeast 7.6 contains several metabolites, which were used in gene
-0789         %associations. For that reason, the list of species ID is created
-0790         %and we then check whether any of them have kegg.genes annotation
-0791         %thereby obtaining systematic gene names
-0792         geneShortNames=vertcat(geneShortNames,metaboliteNames);
-0793         geneIDs=vertcat(geneIDs,metaboliteIDs);
-0794         geneSystNames=extractMiriam(vertcat(geneMiriams,metaboliteMiriams),'kegg.genes');
-0795         geneCompartments=vertcat(geneCompartments,metaboliteCompartments);
-0796         geneMiriams=vertcat(geneMiriams,metaboliteMiriams);
-0797 
-0798         %Now we retain information for only these entries, which have
-0799         %kegg.genes annotation
-0800         geneShortNames=geneShortNames(~cellfun('isempty',geneSystNames));
-0801         geneIDs=geneIDs(~cellfun('isempty',geneSystNames));
-0802         geneSystNames=geneSystNames(~cellfun('isempty',geneSystNames));
-0803         geneCompartments=geneCompartments(~cellfun('isempty',geneSystNames));
-0804         geneMiriams=geneMiriams(~cellfun('isempty',geneSystNames));
-0805         %Now we reorder geneIDs and geneSystNames by geneSystNames string
-0806         %length
-0807         geneNames=geneIDs;%Backuping geneIDs, since we need unsorted order for later
-0808         [~, Indx] = sort(cellfun('size', geneSystNames, 2), 'descend');
-0809         geneIDs = geneIDs(Indx);
-0810         geneSystNames = geneSystNames(Indx);
-0811         for i=1:numel(geneSystNames)
-0812             for j=1:numel(grRules)
-0813                 if strfind(grRules{j},geneSystNames{i})
-0814                     if ~isempty(grRules{j})
-0815                         if sum(ismember(geneSystNames,geneSystNames{i}))==1
-0816                             grRules{j}=regexprep(grRules{j},geneSystNames{i},geneIDs{i});
-0817                         elseif sum(ismember(geneSystNames,geneSystNames{i}))>1
-0818                             counter=0;
-0819                             ovrlpIDs=geneIDs(ismember(geneSystNames,geneSystNames{i}));
-0820                             for k=1:numel(ovrlpIDs)
-0821                                 if strfind(grRulesFromModifier{j},ovrlpIDs{k})
-0822                                     counter=counter+1;
-0823                                     grRules{j}=regexprep(grRules{j},geneSystNames{i},ovrlpIDs{k});
-0824                                 end
-0825                                 if counter>1
-0826                                     EM=['Gene association is ambiguous for reaction ' modelSBML.reaction(j).id];
-0827                                     dispEM(EM);
-0828                                 end
-0829                             end
-0830                         end
-0831                     end
-0832                 end
-0833             end
-0834         end
-0835     end
-0836     model.genes=geneNames;
-0837     model.grRules=grRules;
-0838     [grRules,rxnGeneMat] = standardizeGrRules(model,true);
-0839     model.grRules = grRules;
-0840     model.rxnGeneMat = rxnGeneMat;
-0841 
-0842     %Match the compartments for genes
-0843     [~, J]=ismember(geneCompartments,model.comps);
-0844     model.geneComps=J;
-0845 else
-0846     if ~all(cellfun(@isempty,grRules))
-0847         %If fbc_geneProduct exists, follow the specified gene order, such
-0848         %that matching geneShortNames in function below will work
-0849         if isfield(modelSBML,'fbc_geneProduct')
-0850             genes={modelSBML.fbc_geneProduct.fbc_id};
-0851 
-0852             %Get gene Miriams if they were not retrieved above (this occurs
-0853             %when genes are stored as fbc_geneProduct instead of species)
-0854             if isempty(geneMiriams)
-0855                 geneMiriams = cell(numel(genes),1);
-0856                 if isfield(modelSBML.fbc_geneProduct,'sboTerm') && numel(unique([modelSBML.fbc_geneProduct.sboTerm])) == 1
-0857                     %If all the SBO terms are identical, don't add them to geneMiriams
-0858                     modelSBML.fbc_geneProduct = rmfield(modelSBML.fbc_geneProduct,'sboTerm');
-0859                 end
-0860                 for i = 1:numel(genes)
-0861                     geneMiriams{i}=parseMiriam(modelSBML.fbc_geneProduct(i).annotation);
-0862                     if isfield(modelSBML.fbc_geneProduct(i),'sboTerm') && ~(modelSBML.fbc_geneProduct(i).sboTerm==-1)
-0863                         geneMiriams{i} = addSBOtoMiriam(geneMiriams{i},modelSBML.fbc_geneProduct(i).sboTerm);
-0864                     end
-0865                 end
-0866             end
-0867             proteins={modelSBML.fbc_geneProduct.fbc_name};
-0868         else
-0869             genes=getGeneList(grRules);
-0870         end
-0871         model.genes=genes;
-0872         model.grRules=grRules;
-0873         [grRules,rxnGeneMat] = standardizeGrRules(model,true);
-0874         model.grRules = grRules;
-0875         model.rxnGeneMat = rxnGeneMat;
-0876     end
-0877 end
-0878 
-0879 if all(cellfun(@isempty,geneShortNames))
-0880     if isfield(modelSBML,'fbc_geneProduct')
-0881         for i=1:numel(genes)
-0882             if ~isempty(modelSBML.fbc_geneProduct(i).fbc_label)
-0883                 geneShortNames{i,1}=modelSBML.fbc_geneProduct(i).fbc_label;
-0884             elseif ~isempty(modelSBML.fbc_geneProduct(i).fbc_name)
-0885                 geneShortNames{i,1}=modelSBML.fbc_geneProduct(i).fbc_name;
-0886             else
-0887                 geneShortNames{i,1}='';
-0888             end
-0889         end
-0890     end
-0891 end
-0892 
-0893 %If any InChIs have been loaded
-0894 if any(~cellfun(@isempty,metaboliteInChI))
-0895     model.inchis=metaboliteInChI;
-0896 end
-0897 
-0898 %If any formulas have been loaded
-0899 if any(~cellfun(@isempty,metaboliteFormula))
-0900     model.metFormulas=metaboliteFormula;
-0901 end
-0902 
-0903 %If any charges have been loaded
-0904 if ~isempty(metaboliteCharges)
-0905     model.metCharges=metaboliteCharges;
-0906 end
-0907 
-0908 %If any gene short names have been loaded
-0909 if any(~cellfun(@isempty,geneShortNames))
-0910     model.geneShortNames=geneShortNames;
-0911 end
-0912 
-0913 %If any Miriam strings for compartments have been loaded
-0914 if any(~cellfun(@isempty,compartmentMiriams))
-0915     model.compMiriams=compartmentMiriams;
-0916 end
-0917 
-0918 %If any Miriam strings for metabolites have been loaded
-0919 if any(~cellfun(@isempty,metaboliteMiriams))
-0920     model.metMiriams=metaboliteMiriams;
-0921 end
-0922 
-0923 %If any subsystems have been loaded
-0924 if any(~cellfun(@isempty,subsystems))
-0925     model.subSystems=subsystems;
-0926 end
-0927 if any(rxnComps)
-0928     if all(rxnComps)
-0929         model.rxnComps=rxnComps;
-0930     else
-0931         if supressWarnings==false
-0932             EM='The compartments for the following reactions could not be matched. Ignoring reaction compartment information';
-0933             dispEM(EM,false,model.rxns(rxnComps==0));
-0934         end
-0935     end
-0936 end
-0937 
-0938 %If any ec-codes have been loaded
-0939 if any(~cellfun(@isempty,eccodes))
-0940     model.eccodes=eccodes;
-0941 end
-0942 
-0943 %If any Miriam strings for reactions have been loaded
-0944 if any(~cellfun(@isempty,rxnMiriams))
-0945     model.rxnMiriams=rxnMiriams;
-0946 end
-0947 
-0948 %If any Miriam strings for genes have been loaded
-0949 if any(~cellfun(@isempty,geneMiriams))
-0950     model.geneMiriams=geneMiriams;
-0951 end
-0952 
-0953 %If any protein strings have been loaded
-0954 if any(~cellfun(@isempty,proteins))
-0955     proteins = reshape(proteins,[],1);
-0956     model.proteins=proteins;
-0957 end
-0958 
-0959 model.unconstrained=metaboliteUnconstrained;
-0960 
-0961 %Convert SBML IDs back into their original strings. Here we are using part
-0962 %from convertSBMLID, originating from the COBRA Toolbox
-0963 model.rxns=regexprep(model.rxns,'__([0-9]+)__','${char(str2num($1))}');
-0964 model.mets=regexprep(model.mets,'__([0-9]+)__','${char(str2num($1))}');
-0965 model.comps=regexprep(model.comps,'__([0-9]+)__','${char(str2num($1))}');
-0966 model.grRules=regexprep(model.grRules,'__([0-9]+)__','${char(str2num($1))}');
-0967 model.genes=regexprep(model.genes,'__([0-9]+)__','${char(str2num($1))}');
-0968 model.id=regexprep(model.id,'__([0-9]+)__','${char(str2num($1))}');
-0969 
-0970 if COBRAstyle
-0971     model=removeCOBRAstylePrefixes(model);
-0972 else
-0973     hasCOBRAids(1) = all(startsWith(model.rxns,'R_'));
-0974     hasCOBRAids(2) = all(startsWith(model.mets,'M_'));
-0975     hasCOBRAids(3) = all(startsWith(model.comps,'C_'));
-0976     hasCOBRAids(4) = all(startsWith(model.genes,'G_'));
-0977     if any(hasCOBRAids)
-0978         hasCOBRAidsMsg = {'model.rxns (R_ prefix)',...
-0979             'model.mets (M_ prefix)',...
-0980             'model.comps (C_ prefix)',...
-0981             'model.genes (G_ prefix)'};
-0982         hasCOBRAidsMsg(~hasCOBRAids) = [];
-0983         printOrange(['COBRA style identifier prefixes are found in: "' ...
-0984             strjoin(hasCOBRAidsMsg,'"; "') '". Since RAVEN 2.10.0, identifiers ' ...
-0985             'are by default imported "as-is". If you do prefer to remove these ' ...
-0986             'identifier prefixes, run "removeCOBRAstylePrefixes" on the ' ...
-0987             'imported model, or directly run importModel with COBRAstyle as true ' ...
-0988             'Example:   importModel(''filename.xml'', [], true);\n']);
-0989     end
+0578 
+0579     miriamStruct=parseMiriam(modelSBML.reaction(i).annotation);
+0580     rxnMiriams{counter}=miriamStruct;
+0581     if isfield(modelSBML.reaction(i),'notes')
+0582         subsystems{counter,1}=cellstr(parseNote(modelSBML.reaction(i).notes,'SUBSYSTEM'));
+0583         subsystems{counter,1}(cellfun('isempty',subsystems{counter,1})) = [];
+0584         if strfind(modelSBML.reaction(i).notes,'Confidence Level')
+0585             confScore = parseNote(modelSBML.reaction(i).notes,'Confidence Level');
+0586             if isempty(confScore)
+0587                 confScore = 0;
+0588             end
+0589             rxnconfidencescores(counter)=str2double(confScore);
+0590         end
+0591         rxnreferences{counter,1}=parseNote(modelSBML.reaction(i).notes,'AUTHORS');
+0592         rxnnotes{counter,1}=parseNote(modelSBML.reaction(i).notes,'NOTES');
+0593     end
+0594 
+0595     %Get SBO terms
+0596     if isfield(modelSBML.reaction(i),'sboTerm') && ~(modelSBML.reaction(i).sboTerm==-1)
+0597         rxnMiriams{counter} = addSBOtoMiriam(rxnMiriams{counter}, modelSBML.reaction(i).sboTerm);
+0598     end
+0599 
+0600     %Get ec-codes
+0601     eccode='';
+0602     if ~isempty(modelSBML.reaction(i).annotation)
+0603         if strfind(modelSBML.reaction(i).annotation,'urn:miriam:ec-code')
+0604             eccode=parseAnnotation(modelSBML.reaction(i).annotation,'urn:miriam:',':','ec-code');
+0605         elseif strfind(modelSBML.reaction(i).annotation,'http://identifiers.org/ec-code')
+0606             eccode=parseAnnotation(modelSBML.reaction(i).annotation,'http://identifiers.org/','/','ec-code');
+0607         elseif strfind(modelSBML.reaction(i).annotation,'https://identifiers.org/ec-code')
+0608             eccode=parseAnnotation(modelSBML.reaction(i).annotation,'https://identifiers.org/','/','ec-code');
+0609         end
+0610     elseif isfield(modelSBML.reaction(i),'notes')
+0611         if strfind(modelSBML.reaction(i).notes,'EC Number')
+0612             eccode=[eccode parseNote(modelSBML.reaction(i).notes,'EC Number')];
+0613         elseif strfind(modelSBML.reaction(i).notes,'PROTEIN_CLASS')
+0614             eccode=[eccode parseNote(modelSBML.reaction(i).notes,'PROTEIN_CLASS')];
+0615         end
+0616     end
+0617     eccodes{counter}=eccode;
+0618 
+0619     %Add all reactants
+0620     for j=1:numel(modelSBML.reaction(i).reactant)
+0621         %Get the index of the metabolite in metaboliteIDs. External
+0622         %metabolites will be removed at a later stage
+0623         metIndex=find(strcmp(modelSBML.reaction(i).reactant(j).species,metaboliteIDs),1);
+0624         if isempty(metIndex)
+0625             EM=['Could not find metabolite ' modelSBML.reaction(i).reactant(j).species ' in reaction ' reactionIDs{counter}];
+0626             dispEM(EM);
+0627         end
+0628         S(metIndex,counter)=S(metIndex,counter)+modelSBML.reaction(i).reactant(j).stoichiometry*-1;
+0629     end
+0630 
+0631     %Add all products
+0632     for j=1:numel(modelSBML.reaction(i).product)
+0633         %Get the index of the metabolite in metaboliteIDs.
+0634         metIndex=find(strcmp(modelSBML.reaction(i).product(j).species,metaboliteIDs),1);
+0635         if isempty(metIndex)
+0636             EM=['Could not find metabolite ' modelSBML.reaction(i).product(j).species ' in reaction ' reactionIDs{counter}];
+0637             dispEM(EM);
+0638         end
+0639         S(metIndex,counter)=S(metIndex,counter)+modelSBML.reaction(i).product(j).stoichiometry;
+0640     end
+0641 end
+0642 
+0643 %if FBC, objective function is separately defined. Multiple objective
+0644 %functions can be defined, one is set as active
+0645 if isfield(modelSBML, 'fbc_activeObjective')
+0646     obj=modelSBML.fbc_activeObjective;
+0647     for i=1:numel(modelSBML.fbc_objective)
+0648         if strcmp(obj,modelSBML.fbc_objective(i).fbc_id)
+0649             if ~isempty(modelSBML.fbc_objective(i).fbc_fluxObjective)
+0650                 rxn=modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_reaction;
+0651                 idx=find(ismember(reactionIDs,rxn));
+0652                 reactionObjective(idx)=modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_coefficient;
+0653             end
+0654         end
+0655     end
+0656 end
+0657 
+0658 %subSystems can be stored as groups instead of in annotations
+0659 if isfield(modelSBML,'groups_group')
+0660     for i=1:numel(modelSBML.groups_group)
+0661         groupreactions={modelSBML.groups_group(i).groups_member(:).groups_idRef};
+0662         [~, idx] = ismember(groupreactions, reactionIDs);
+0663         if any(idx)
+0664             for j=1:numel(idx)
+0665                 if isempty(subsystems{idx(j)}) % First subsystem
+0666                     subsystems{idx(j)} = {modelSBML.groups_group(i).groups_name};
+0667                 else % Consecutive subsystems: concatenate
+0668                     subsystems{idx(j)} = horzcat(subsystems{idx(j)}, modelSBML.groups_group(i).groups_name);
+0669                 end
+0670             end
+0671         end
+0672     end
+0673 end
+0674 
+0675 %Shrink the structures if complex-forming reactions had to be skipped
+0676 reactionNames=reactionNames(1:counter);
+0677 reactionIDs=reactionIDs(1:counter);
+0678 subsystems=subsystems(1:counter);
+0679 eccodes=eccodes(1:counter);
+0680 rxnconfidencescores=rxnconfidencescores(1:counter);
+0681 rxnreferences=rxnreferences(1:counter);
+0682 rxnnotes=rxnnotes(1:counter);
+0683 grRules=grRules(1:counter);
+0684 rxnMiriams=rxnMiriams(1:counter);
+0685 reactionReversibility=reactionReversibility(1:counter);
+0686 reactionUB=reactionUB(1:counter);
+0687 reactionLB=reactionLB(1:counter);
+0688 reactionObjective=reactionObjective(1:counter);
+0689 S=S(:,1:counter);
+0690 
+0691 model.name=modelSBML.name;
+0692 model.id=modelSBML.id;
+0693 model.rxns=reactionIDs;
+0694 model.mets=metaboliteIDs;
+0695 model.S=sparse(S);
+0696 model.lb=reactionLB;
+0697 model.ub=reactionUB;
+0698 model.rev=reactionReversibility;
+0699 model.c=reactionObjective;
+0700 model.b=zeros(numel(metaboliteIDs),1);
+0701 model.comps=compartmentIDs;
+0702 model.compNames=compartmentNames;
+0703 model.rxnConfidenceScores=rxnconfidencescores;
+0704 model.rxnReferences=rxnreferences;
+0705 model.rxnNotes=rxnnotes;
+0706 
+0707 %Load annotation if available. If there are several authors, only the first
+0708 %author credentials are imported
+0709 if isfield(modelSBML,'annotation')
+0710     endString='</';
+0711     I=strfind(modelSBML.annotation,endString);
+0712     J=strfind(modelSBML.annotation,'<vCard:Family>');
+0713     if any(J)
+0714         model.annotation.familyName=modelSBML.annotation(J(1)+14:I(find(I>J(1),1))-1);
+0715     end
+0716     J=strfind(modelSBML.annotation,'<vCard:Given>');
+0717     if any(J)
+0718         model.annotation.givenName=modelSBML.annotation(J(1)+13:I(find(I>J(1),1))-1);
+0719     end
+0720     J=strfind(modelSBML.annotation,'<vCard:EMAIL>');
+0721     if any(J)
+0722         model.annotation.email=modelSBML.annotation(J(1)+13:I(find(I>J(1),1))-1);
+0723     end
+0724     J=strfind(modelSBML.annotation,'<vCard:Orgname>');
+0725     if any(J)
+0726         model.annotation.organization=modelSBML.annotation(J(1)+15:I(find(I>J(1),1))-1);
+0727     end
+0728     endString='"/>';
+0729     I=strfind(modelSBML.annotation,endString);
+0730     if strfind(modelSBML.annotation,'"urn:miriam:')
+0731         J=strfind(modelSBML.annotation,'"urn:miriam:');
+0732         if any(J)
+0733             model.annotation.taxonomy=modelSBML.annotation(J+12:I(find(I>J,1))-1);
+0734         end
+0735     else
+0736         J=strfind(modelSBML.annotation,'"http://identifiers.org/');
+0737         if any(J)
+0738             model.annotation.taxonomy=modelSBML.annotation(J+24:I(find(I>J,1))-1);
+0739         else
+0740             J=strfind(modelSBML.annotation,'"https://identifiers.org/');
+0741             if any(J)
+0742                 model.annotation.taxonomy=modelSBML.annotation(J+25:I(find(I>J,1))-1);
+0743             end
+0744         end
+0745     end
+0746 end
+0747 if isfield(modelSBML,'notes')
+0748     startString=strfind(modelSBML.notes,'xhtml">');
+0749     endString=strfind(modelSBML.notes,'</body>');
+0750     if any(startString) && any(endString)
+0751         model.annotation.note=modelSBML.notes(startString+7:endString-1);
+0752         model.annotation.note=regexprep(model.annotation.note,'<p>|</p>','');
+0753         model.annotation.note=strtrim(model.annotation.note);
+0754         if regexp(model.annotation.note,'This file was generated using the exportModel function in RAVEN Toolbox \d\.\d and OutputSBML in libSBML')
+0755             model.annotation=rmfield(model.annotation,'note'); % Default note added when running exportModel
+0756         end
+0757     end
+0758 end
+0759 
+0760 if any(~cellfun(@isempty,compartmentOutside))
+0761     model.compOutside=compartmentOutside;
+0762 end
+0763 
+0764 model.rxnNames=reactionNames;
+0765 model.metNames=metaboliteNames;
+0766 
+0767 %Match the compartments for metabolites
+0768 [~, J]=ismember(metaboliteCompartments,model.comps);
+0769 model.metComps=J;
+0770 
+0771 %If any genes have been loaded (only for the new format)
+0772 if ~isempty(geneNames)
+0773     %In some rare cases geneNames may not necessarily be used in grRules.
+0774     %That is true for Yeast 7.6. It's therefore important to change gene
+0775     %systematic names to geneIDs in sophisticated way. Gene systematic
+0776     %names are not unique, since exactly the same name may be in different
+0777     %compartments
+0778     if all(cellfun(@isempty,strfind(grRules,geneNames{1})))
+0779         geneShortNames=geneNames;
+0780         %geneShortNames contain compartments as well, so these are removed
+0781         geneShortNames=regexprep(geneShortNames,' \[.+$','');
+0782         %grRules obtained from modifier fields contain geneNames. These are
+0783         %changed into geneIDs. grRulesFromModifier is a good way to have
+0784         %geneIDs and rxns association when it's important to resolve
+0785         %systematic name ambiguities
+0786         grRulesFromModifier=regexprep(regexprep(grRulesFromModifier,'\[|\]','_'),regexprep(geneNames,'\[|\]','_'),geneIDs);
+0787         grRules=regexprep(regexprep(grRules,'\[|\]','_'),regexprep(geneNames,'\[|\]','_'),geneIDs);
+0788 
+0789         %Yeast 7.6 contains several metabolites, which were used in gene
+0790         %associations. For that reason, the list of species ID is created
+0791         %and we then check whether any of them have kegg.genes annotation
+0792         %thereby obtaining systematic gene names
+0793         geneShortNames=vertcat(geneShortNames,metaboliteNames);
+0794         geneIDs=vertcat(geneIDs,metaboliteIDs);
+0795         geneSystNames=extractMiriam(vertcat(geneMiriams,metaboliteMiriams),'kegg.genes');
+0796         geneCompartments=vertcat(geneCompartments,metaboliteCompartments);
+0797         geneMiriams=vertcat(geneMiriams,metaboliteMiriams);
+0798 
+0799         %Now we retain information for only these entries, which have
+0800         %kegg.genes annotation
+0801         geneShortNames=geneShortNames(~cellfun('isempty',geneSystNames));
+0802         geneIDs=geneIDs(~cellfun('isempty',geneSystNames));
+0803         geneSystNames=geneSystNames(~cellfun('isempty',geneSystNames));
+0804         geneCompartments=geneCompartments(~cellfun('isempty',geneSystNames));
+0805         geneMiriams=geneMiriams(~cellfun('isempty',geneSystNames));
+0806         %Now we reorder geneIDs and geneSystNames by geneSystNames string
+0807         %length
+0808         geneNames=geneIDs;%Backuping geneIDs, since we need unsorted order for later
+0809         [~, Indx] = sort(cellfun('size', geneSystNames, 2), 'descend');
+0810         geneIDs = geneIDs(Indx);
+0811         geneSystNames = geneSystNames(Indx);
+0812         for i=1:numel(geneSystNames)
+0813             for j=1:numel(grRules)
+0814                 if strfind(grRules{j},geneSystNames{i})
+0815                     if ~isempty(grRules{j})
+0816                         if sum(ismember(geneSystNames,geneSystNames{i}))==1
+0817                             grRules{j}=regexprep(grRules{j},geneSystNames{i},geneIDs{i});
+0818                         elseif sum(ismember(geneSystNames,geneSystNames{i}))>1
+0819                             counter=0;
+0820                             ovrlpIDs=geneIDs(ismember(geneSystNames,geneSystNames{i}));
+0821                             for k=1:numel(ovrlpIDs)
+0822                                 if strfind(grRulesFromModifier{j},ovrlpIDs{k})
+0823                                     counter=counter+1;
+0824                                     grRules{j}=regexprep(grRules{j},geneSystNames{i},ovrlpIDs{k});
+0825                                 end
+0826                                 if counter>1
+0827                                     EM=['Gene association is ambiguous for reaction ' modelSBML.reaction(j).id];
+0828                                     dispEM(EM);
+0829                                 end
+0830                             end
+0831                         end
+0832                     end
+0833                 end
+0834             end
+0835         end
+0836     end
+0837     model.genes=geneNames;
+0838     model.grRules=grRules;
+0839     [grRules,rxnGeneMat] = standardizeGrRules(model,true);
+0840     model.grRules = grRules;
+0841     model.rxnGeneMat = rxnGeneMat;
+0842 
+0843     %Match the compartments for genes
+0844     [~, J]=ismember(geneCompartments,model.comps);
+0845     model.geneComps=J;
+0846 else
+0847     if ~all(cellfun(@isempty,grRules))
+0848         %If fbc_geneProduct exists, follow the specified gene order, such
+0849         %that matching geneShortNames in function below will work
+0850         if isfield(modelSBML,'fbc_geneProduct')
+0851             genes={modelSBML.fbc_geneProduct.fbc_id};
+0852 
+0853             %Get gene Miriams if they were not retrieved above (this occurs
+0854             %when genes are stored as fbc_geneProduct instead of species)
+0855             if isempty(geneMiriams)
+0856                 geneMiriams = cell(numel(genes),1);
+0857                 if isfield(modelSBML.fbc_geneProduct,'sboTerm') && numel(unique([modelSBML.fbc_geneProduct.sboTerm])) == 1
+0858                     %If all the SBO terms are identical, don't add them to geneMiriams
+0859                     modelSBML.fbc_geneProduct = rmfield(modelSBML.fbc_geneProduct,'sboTerm');
+0860                 end
+0861                 for i = 1:numel(genes)
+0862                     geneMiriams{i}=parseMiriam(modelSBML.fbc_geneProduct(i).annotation);
+0863                     if isfield(modelSBML.fbc_geneProduct(i),'sboTerm') && ~(modelSBML.fbc_geneProduct(i).sboTerm==-1)
+0864                         geneMiriams{i} = addSBOtoMiriam(geneMiriams{i},modelSBML.fbc_geneProduct(i).sboTerm);
+0865                     end
+0866                 end
+0867             end
+0868             proteins={modelSBML.fbc_geneProduct.fbc_name};
+0869         else
+0870             genes=getGeneList(grRules);
+0871         end
+0872         model.genes=genes;
+0873         model.grRules=grRules;
+0874         [grRules,rxnGeneMat] = standardizeGrRules(model,true);
+0875         model.grRules = grRules;
+0876         model.rxnGeneMat = rxnGeneMat;
+0877     end
+0878 end
+0879 
+0880 if all(cellfun(@isempty,geneShortNames))
+0881     if isfield(modelSBML,'fbc_geneProduct')
+0882         for i=1:numel(genes)
+0883             if ~isempty(modelSBML.fbc_geneProduct(i).fbc_label)
+0884                 geneShortNames{i,1}=modelSBML.fbc_geneProduct(i).fbc_label;
+0885             elseif ~isempty(modelSBML.fbc_geneProduct(i).fbc_name)
+0886                 geneShortNames{i,1}=modelSBML.fbc_geneProduct(i).fbc_name;
+0887             else
+0888                 geneShortNames{i,1}='';
+0889             end
+0890         end
+0891     end
+0892 end
+0893 
+0894 %If any InChIs have been loaded
+0895 if any(~cellfun(@isempty,metaboliteInChI))
+0896     model.inchis=metaboliteInChI;
+0897 end
+0898 
+0899 %If any formulas have been loaded
+0900 if any(~cellfun(@isempty,metaboliteFormula))
+0901     model.metFormulas=metaboliteFormula;
+0902 end
+0903 
+0904 %If any charges have been loaded
+0905 if ~isempty(metaboliteCharges)
+0906     model.metCharges=metaboliteCharges;
+0907 end
+0908 
+0909 %If any gene short names have been loaded
+0910 if any(~cellfun(@isempty,geneShortNames))
+0911     model.geneShortNames=geneShortNames;
+0912 end
+0913 
+0914 %If any Miriam strings for compartments have been loaded
+0915 if any(~cellfun(@isempty,compartmentMiriams))
+0916     model.compMiriams=compartmentMiriams;
+0917 end
+0918 
+0919 %If any Miriam strings for metabolites have been loaded
+0920 if any(~cellfun(@isempty,metaboliteMiriams))
+0921     model.metMiriams=metaboliteMiriams;
+0922 end
+0923 
+0924 %If any subsystems have been loaded
+0925 if any(~cellfun(@isempty,subsystems))
+0926     model.subSystems=subsystems;
+0927 end
+0928 if any(rxnComps)
+0929     if all(rxnComps)
+0930         model.rxnComps=rxnComps;
+0931     else
+0932         if supressWarnings==false
+0933             EM='The compartments for the following reactions could not be matched. Ignoring reaction compartment information';
+0934             dispEM(EM,false,model.rxns(rxnComps==0));
+0935         end
+0936     end
+0937 end
+0938 
+0939 %If any ec-codes have been loaded
+0940 if any(~cellfun(@isempty,eccodes))
+0941     model.eccodes=eccodes;
+0942 end
+0943 
+0944 %If any Miriam strings for reactions have been loaded
+0945 if any(~cellfun(@isempty,rxnMiriams))
+0946     model.rxnMiriams=rxnMiriams;
+0947 end
+0948 
+0949 %If any Miriam strings for genes have been loaded
+0950 if any(~cellfun(@isempty,geneMiriams))
+0951     model.geneMiriams=geneMiriams;
+0952 end
+0953 
+0954 %If any protein strings have been loaded
+0955 if any(~cellfun(@isempty,proteins))
+0956     proteins = reshape(proteins,[],1);
+0957     model.proteins=proteins;
+0958 end
+0959 
+0960 model.unconstrained=metaboliteUnconstrained;
+0961 
+0962 %Convert SBML IDs back into their original strings. Here we are using part
+0963 %from convertSBMLID, originating from the COBRA Toolbox
+0964 model.rxns=regexprep(model.rxns,'__([0-9]+)__','${char(str2num($1))}');
+0965 model.mets=regexprep(model.mets,'__([0-9]+)__','${char(str2num($1))}');
+0966 model.comps=regexprep(model.comps,'__([0-9]+)__','${char(str2num($1))}');
+0967 model.grRules=regexprep(model.grRules,'__([0-9]+)__','${char(str2num($1))}');
+0968 model.genes=regexprep(model.genes,'__([0-9]+)__','${char(str2num($1))}');
+0969 model.id=regexprep(model.id,'__([0-9]+)__','${char(str2num($1))}');
+0970 
+0971 if removePrefix
+0972     [model, hasChanged]=removeIdentifierPrefix(model);
+0973     dispEM(['The following fields have prefixes removed from all entries. '...
+0974     'If this is undesired, run importModel with removePrefix as false. Example: '...
+0975     'importModel(''filename.xml'',[],false);'],false,hasChanged)
+0976 end
+0977 
+0978 %Remove unused fields
+0979 if isempty(model.annotation)
+0980     model=rmfield(model,'annotation');
+0981 end
+0982 if isempty(model.compOutside)
+0983     model=rmfield(model,'compOutside');
+0984 end
+0985 if isempty(model.compMiriams)
+0986     model=rmfield(model,'compMiriams');
+0987 end
+0988 if isempty(model.rxnComps)
+0989     model=rmfield(model,'rxnComps');
 0990 end
-0991 
-0992 %Remove unused fields
-0993 if isempty(model.annotation)
-0994     model=rmfield(model,'annotation');
-0995 end
-0996 if isempty(model.compOutside)
-0997     model=rmfield(model,'compOutside');
-0998 end
-0999 if isempty(model.compMiriams)
-1000     model=rmfield(model,'compMiriams');
+0991 if isempty(model.grRules)
+0992     model=rmfield(model,'grRules');
+0993 end
+0994 if isempty(model.rxnGeneMat)
+0995     model=rmfield(model,'rxnGeneMat');
+0996 end
+0997 if isempty(model.subSystems)
+0998     model=rmfield(model,'subSystems');
+0999 else
+1000     model.subSystems(cellfun(@isempty,subsystems))={{''}};
 1001 end
-1002 if isempty(model.rxnComps)
-1003     model=rmfield(model,'rxnComps');
+1002 if isempty(model.eccodes)
+1003     model=rmfield(model,'eccodes');
 1004 end
-1005 if isempty(model.grRules)
-1006     model=rmfield(model,'grRules');
+1005 if isempty(model.rxnMiriams)
+1006     model=rmfield(model,'rxnMiriams');
 1007 end
-1008 if isempty(model.rxnGeneMat)
-1009     model=rmfield(model,'rxnGeneMat');
+1008 if cellfun(@isempty,model.rxnNotes)
+1009     model=rmfield(model,'rxnNotes');
 1010 end
-1011 if isempty(model.subSystems)
-1012     model=rmfield(model,'subSystems');
-1013 else
-1014     model.subSystems(cellfun(@isempty,subsystems))={{''}};
-1015 end
-1016 if isempty(model.eccodes)
-1017     model=rmfield(model,'eccodes');
-1018 end
-1019 if isempty(model.rxnMiriams)
-1020     model=rmfield(model,'rxnMiriams');
+1011 if cellfun(@isempty,model.rxnReferences)
+1012     model=rmfield(model,'rxnReferences');
+1013 end
+1014 if isempty(model.rxnConfidenceScores) || all(isnan(model.rxnConfidenceScores))
+1015     model=rmfield(model,'rxnConfidenceScores');
+1016 end
+1017 if isempty(model.genes)
+1018     model=rmfield(model,'genes');
+1019 elseif isrow(model.genes)
+1020     model.genes=transpose(model.genes);
 1021 end
-1022 if cellfun(@isempty,model.rxnNotes)
-1023     model=rmfield(model,'rxnNotes');
+1022 if isempty(model.geneComps)
+1023     model=rmfield(model,'geneComps');
 1024 end
-1025 if cellfun(@isempty,model.rxnReferences)
-1026     model=rmfield(model,'rxnReferences');
+1025 if isempty(model.geneMiriams)
+1026     model=rmfield(model,'geneMiriams');
 1027 end
-1028 if isempty(model.rxnConfidenceScores) || all(isnan(model.rxnConfidenceScores))
-1029     model=rmfield(model,'rxnConfidenceScores');
+1028 if isempty(model.geneShortNames)
+1029     model=rmfield(model,'geneShortNames');
 1030 end
-1031 if isempty(model.genes)
-1032     model=rmfield(model,'genes');
-1033 elseif isrow(model.genes)
-1034     model.genes=transpose(model.genes);
-1035 end
-1036 if isempty(model.geneComps)
-1037     model=rmfield(model,'geneComps');
-1038 end
-1039 if isempty(model.geneMiriams)
-1040     model=rmfield(model,'geneMiriams');
-1041 end
-1042 if isempty(model.geneShortNames)
-1043     model=rmfield(model,'geneShortNames');
-1044 end
-1045 if isempty(model.proteins)
-1046     model=rmfield(model,'proteins');
-1047 end
-1048 if isempty(model.inchis)
-1049     model=rmfield(model,'inchis');
+1031 if isempty(model.proteins)
+1032     model=rmfield(model,'proteins');
+1033 end
+1034 if isempty(model.inchis)
+1035     model=rmfield(model,'inchis');
+1036 end
+1037 if isempty(model.metFormulas)
+1038     model=rmfield(model,'metFormulas');
+1039 end
+1040 if isempty(model.metMiriams)
+1041     model=rmfield(model,'metMiriams');
+1042 end
+1043 if ~any(model.metCharges)
+1044     model=rmfield(model,'metCharges');
+1045 end
+1046 
+1047 %This just removes the grRules if no genes have been loaded
+1048 if ~isfield(model,'genes') && isfield(model,'grRules')
+1049     model=rmfield(model,'grRules');
 1050 end
-1051 if isempty(model.metFormulas)
-1052     model=rmfield(model,'metFormulas');
-1053 end
-1054 if isempty(model.metMiriams)
-1055     model=rmfield(model,'metMiriams');
-1056 end
-1057 if ~any(model.metCharges)
-1058     model=rmfield(model,'metCharges');
+1051 
+1052 %Print warnings about bad structure
+1053 if supressWarnings==false
+1054     checkModelStruct(model,false);
+1055 end
+1056 
+1057 if removeExcMets==true
+1058     model=simplifyModel(model);
 1059 end
-1060 
-1061 %This just removes the grRules if no genes have been loaded
-1062 if ~isfield(model,'genes') && isfield(model,'grRules')
-1063     model=rmfield(model,'grRules');
-1064 end
-1065 
-1066 %Print warnings about bad structure
-1067 if supressWarnings==false
-1068     checkModelStruct(model,false);
-1069 end
-1070 
-1071 if removeExcMets==true
-1072     model=simplifyModel(model);
-1073 end
-1074 end
-1075 
-1076 function matchGenes=getGeneList(grRules)
-1077 %Constructs the list of unique genes from grRules
-1078 
-1079 %Assumes that everything that isn't a paranthesis, " AND " or " or " is a
-1080 %gene name
-1081 genes=strrep(grRules,'(','');
-1082 genes=strrep(genes,')','');
-1083 genes=strrep(genes,' or ',' ');
-1084 genes=strrep(genes,' and ',' ');
-1085 genes=strrep(genes,' OR ',' ');
-1086 genes=strrep(genes,' AND ',' ');
-1087 genes=regexp(genes,' ','split');
-1088 
-1089 allNames={};
-1090 for i=1:numel(genes)
-1091     allNames=[allNames genes{i}];
-1092 end
-1093 matchGenes=unique(allNames)';
-1094 
-1095 %Remove the empty element if present
-1096 if isempty(matchGenes{1})
-1097     matchGenes(1)=[];
-1098 end
-1099 end
-1100 
-1101 function fieldContent=parseNote(searchString,fieldName)
-1102 %The function obtains the particular information from 'notes' field, using
-1103 %fieldName as the dummy string
-1104 
-1105 fieldContent='';
-1106 
-1107 if strfind(searchString,fieldName)
-1108     [~,targetString] = regexp(searchString,['<p>' fieldName '.*?</p>'],'tokens','match');
-1109     targetString=regexprep(targetString,'<p>|</p>','');
-1110     targetString=regexprep(targetString,[fieldName, ':'],'');
-1111     for i=1:numel(targetString)
-1112         fieldContent=[fieldContent ';' strtrim(targetString{1,i})];
-1113     end
-1114     fieldContent=regexprep(fieldContent,'^;|;$','');
-1115 else
-1116     fieldContent='';
-1117 end
-1118 end
-1119 
-1120 function fieldContent=parseAnnotation(searchString,startString,midString,fieldName)
+1060 end
+1061 
+1062 function matchGenes=getGeneList(grRules)
+1063 %Constructs the list of unique genes from grRules
+1064 
+1065 %Assumes that everything that isn't a paranthesis, " AND " or " or " is a
+1066 %gene name
+1067 genes=strrep(grRules,'(','');
+1068 genes=strrep(genes,')','');
+1069 genes=strrep(genes,' or ',' ');
+1070 genes=strrep(genes,' and ',' ');
+1071 genes=strrep(genes,' OR ',' ');
+1072 genes=strrep(genes,' AND ',' ');
+1073 genes=regexp(genes,' ','split');
+1074 
+1075 allNames={};
+1076 for i=1:numel(genes)
+1077     allNames=[allNames genes{i}];
+1078 end
+1079 matchGenes=unique(allNames)';
+1080 
+1081 %Remove the empty element if present
+1082 if isempty(matchGenes{1})
+1083     matchGenes(1)=[];
+1084 end
+1085 end
+1086 
+1087 function fieldContent=parseNote(searchString,fieldName)
+1088 %The function obtains the particular information from 'notes' field, using
+1089 %fieldName as the dummy string
+1090 
+1091 fieldContent='';
+1092 
+1093 if strfind(searchString,fieldName)
+1094     [~,targetString] = regexp(searchString,['<p>' fieldName '.*?</p>'],'tokens','match');
+1095     targetString=regexprep(targetString,'<p>|</p>','');
+1096     targetString=regexprep(targetString,[fieldName, ':'],'');
+1097     for i=1:numel(targetString)
+1098         fieldContent=[fieldContent ';' strtrim(targetString{1,i})];
+1099     end
+1100     fieldContent=regexprep(fieldContent,'^;|;$','');
+1101 else
+1102     fieldContent='';
+1103 end
+1104 end
+1105 
+1106 function fieldContent=parseAnnotation(searchString,startString,midString,fieldName)
+1107 
+1108 fieldContent='';
+1109 
+1110 %Removing whitespace characters from the ending strings, which may occur in
+1111 %several cases
+1112 searchString=regexprep(searchString,'" />','"/>');
+1113 [~,targetString] = regexp(searchString,['<rdf:li rdf:resource="' startString fieldName midString '.*?"/>'],'tokens','match');
+1114 targetString=regexprep(targetString,'<rdf:li rdf:resource="|"/>','');
+1115 targetString=regexprep(targetString,startString,'');
+1116 targetString=regexprep(targetString,[fieldName midString],'');
+1117 
+1118 for i=1:numel(targetString)
+1119     fieldContent=[fieldContent ';' strtrim(targetString{1,i})];
+1120 end
 1121 
-1122 fieldContent='';
-1123 
-1124 %Removing whitespace characters from the ending strings, which may occur in
-1125 %several cases
-1126 searchString=regexprep(searchString,'" />','"/>');
-1127 [~,targetString] = regexp(searchString,['<rdf:li rdf:resource="' startString fieldName midString '.*?"/>'],'tokens','match');
-1128 targetString=regexprep(targetString,'<rdf:li rdf:resource="|"/>','');
-1129 targetString=regexprep(targetString,startString,'');
-1130 targetString=regexprep(targetString,[fieldName midString],'');
-1131 
-1132 for i=1:numel(targetString)
-1133     fieldContent=[fieldContent ';' strtrim(targetString{1,i})];
-1134 end
-1135 
-1136 fieldContent=regexprep(fieldContent,'^;|;$','');
-1137 end
-1138 
-1139 function miriamStruct=parseMiriam(searchString)
-1140 %Generates miriam structure from annotation field
-1141 
-1142 %Finding whether miriams are written in the old or the new way
-1143 if strfind(searchString,'urn:miriam:')
-1144     startString='urn:miriam:';
-1145     midString=':';
-1146 elseif strfind(searchString,'http://identifiers.org/')
-1147     startString='http://identifiers.org/';
-1148     midString='/';
-1149 elseif strfind(searchString,'https://identifiers.org/')
-1150     startString='https://identifiers.org/';
-1151     midString='/';
-1152 else
-1153     miriamStruct=[];
-1154     return;
-1155 end
-1156 
-1157 miriamStruct=[];
-1158 
-1159 searchString=regexprep(searchString,'" />','"/>');
-1160 [~,targetString] = regexp(searchString,'<rdf:li rdf:resource=".*?"/>','tokens','match');
-1161 targetString=regexprep(targetString,'<rdf:li rdf:resource="|"/>','');
-1162 targetString=regexprep(targetString,startString,'');
-1163 targetString=regexprep(targetString,midString,'/','once');
+1122 fieldContent=regexprep(fieldContent,'^;|;$','');
+1123 end
+1124 
+1125 function miriamStruct=parseMiriam(searchString)
+1126 %Generates miriam structure from annotation field
+1127 
+1128 %Finding whether miriams are written in the old or the new way
+1129 if strfind(searchString,'urn:miriam:')
+1130     startString='urn:miriam:';
+1131     midString=':';
+1132 elseif strfind(searchString,'http://identifiers.org/')
+1133     startString='http://identifiers.org/';
+1134     midString='/';
+1135 elseif strfind(searchString,'https://identifiers.org/')
+1136     startString='https://identifiers.org/';
+1137     midString='/';
+1138 else
+1139     miriamStruct=[];
+1140     return;
+1141 end
+1142 
+1143 miriamStruct=[];
+1144 
+1145 searchString=regexprep(searchString,'" />','"/>');
+1146 [~,targetString] = regexp(searchString,'<rdf:li rdf:resource=".*?"/>','tokens','match');
+1147 targetString=regexprep(targetString,'<rdf:li rdf:resource="|"/>','');
+1148 targetString=regexprep(targetString,startString,'');
+1149 targetString=regexprep(targetString,midString,'/','once');
+1150 
+1151 counter=0;
+1152 for i=1:numel(targetString)
+1153     if isempty(regexp(targetString{1,i},'inchi|ec-code', 'once'))
+1154         counter=counter+1;
+1155         miriamStruct.name{counter,1} = regexprep(targetString{1,i},'/.+','','once');
+1156         miriamStruct.value{counter,1} = regexprep(targetString{1,i},[miriamStruct.name{counter,1} '/'],'','once');
+1157         miriamStruct.name{counter,1} = regexprep(miriamStruct.name{counter,1},'^obo\.','');
+1158     end
+1159 end
+1160 end
+1161 
+1162 function miriam = addSBOtoMiriam(miriam,sboTerm)
+1163 %Appends SBO term to miriam structure
 1164 
-1165 counter=0;
-1166 for i=1:numel(targetString)
-1167     if isempty(regexp(targetString{1,i},'inchi|ec-code', 'once'))
-1168         counter=counter+1;
-1169         miriamStruct.name{counter,1} = regexprep(targetString{1,i},'/.+','','once');
-1170         miriamStruct.value{counter,1} = regexprep(targetString{1,i},[miriamStruct.name{counter,1} '/'],'','once');
-1171         miriamStruct.name{counter,1} = regexprep(miriamStruct.name{counter,1},'^obo\.','');
-1172     end
-1173 end
-1174 end
-1175 
-1176 function miriam = addSBOtoMiriam(miriam,sboTerm)
-1177 %Appends SBO term to miriam structure
-1178 
-1179 sboTerm = {['SBO:' sprintf('%07u',sboTerm)]};  % convert to proper format
-1180 if isempty(miriam)
-1181     miriam.name = {'sbo'};
-1182     miriam.value = sboTerm;
-1183 elseif any(strcmp('sbo',miriam.name))
-1184     currSbo = strcmp('sbo',miriam.name);
-1185     miriam.value(currSbo) = sboTerm;
-1186 else
-1187     miriam.name(end+1) = {'sbo'};
-1188     miriam.value(end+1) = sboTerm;
-1189 end
-1190 end
    
+1165 sboTerm = {['SBO:' sprintf('%07u',sboTerm)]};  % convert to proper format
+1166 if isempty(miriam)
+1167     miriam.name = {'sbo'};
+1168     miriam.value = sboTerm;
+1169 elseif any(strcmp('sbo',miriam.name))
+1170     currSbo = strcmp('sbo',miriam.name);
+1171     miriam.value(currSbo) = sboTerm;
+1172 else
+1173     miriam.name(end+1) = {'sbo'};
+1174     miriam.value(end+1) = sboTerm;
+1175 end
+1176 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/sortIdentifiers.html b/doc/io/sortIdentifiers.html
index ee3d8aaa..71563563 100644
--- a/doc/io/sortIdentifiers.html
+++ b/doc/io/sortIdentifiers.html
@@ -47,7 +47,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • exportForGit	exportForGit
  • exportModel	exportModel
  • exportToExcelFormat	exportToExcelFormat
  • exportToTabDelimited	exportToTabDelimited
  • writeYAMLmodel	writeYAMLmodel
    • 
+
  • exportForGit	exportForGit
  • exportModel	exportModel
  • exportToExcelFormat	exportToExcelFormat
  • exportToTabDelimited	exportToTabDelimited
  • writeYAMLmodel	writeYAMLmodel
    • 
 
 
 
diff --git a/doc/struct_conversion/addCOBRAstylePrefixes.html b/doc/struct_conversion/addCOBRAstylePrefixes.html
deleted file mode 100644
index a5b0b928..00000000
--- a/doc/struct_conversion/addCOBRAstylePrefixes.html
+++ /dev/null
@@ -1,125 +0,0 @@
-
-
-
-  Description of addCOBRAstylePrefixes
-  
-  
-  
-  
-  
-  
-
-
-
-
    Home >  struct_conversion > addCOBRAstylePrefixes.m
    
-
-
-
-
    addCOBRAstylePrefixes
-
    
-
-
    PURPOSE ^
    
-
    addCOBRAstylePrefixes
    
-
-
    SYNOPSIS ^
    
-
    function model=addCOBRAstylePrefixes(model,fields,printWarnings) 
    
-
-
    DESCRIPTION ^
    
-
     addCOBRAstylePrefixes
-   This function adds COBRA style identifier prefixes, which are:
-       "R_" for model.rxns,
-       "M_" for model.mets,
-       "C_" for model.comps;
-       "G_" for model.genes (and also represented in model.grRules).
-   If all entries in a field already have the prefix, then no additional
-   prefix will be added.
-
- Input:
-   model           model whose identifiers should be modified
-   fields          cell array with model field names to which the prefix
-                   should be added, possible values: {'rxns', 'mets', 
-                   'comps', 'genes'} (optional, by default prefixes are
-                   added to all listed model fields will be checked).
-   printWarnings   if warnings should be shown (optional, default true).
-
- Output:
-   model           modified model
-
- Usage: model=addCOBRAstylePrefixes(model,fields,printWarnings)
    
-
-
-
    CROSS-REFERENCE INFORMATION ^
    
-This function calls:
-
      
-
    
-This function is called by:
-
      
-
    
-
-
-
-
-
    SOURCE CODE ^
    
-
    0001 function model=addCOBRAstylePrefixes(model,fields,printWarnings)
-0002 % addCOBRAstylePrefixes
-0003 %   This function adds COBRA style identifier prefixes, which are:
-0004 %       "R_" for model.rxns,
-0005 %       "M_" for model.mets,
-0006 %       "C_" for model.comps;
-0007 %       "G_" for model.genes (and also represented in model.grRules).
-0008 %   If all entries in a field already have the prefix, then no additional
-0009 %   prefix will be added.
-0010 %
-0011 % Input:
-0012 %   model           model whose identifiers should be modified
-0013 %   fields          cell array with model field names to which the prefix
-0014 %                   should be added, possible values: {'rxns', 'mets',
-0015 %                   'comps', 'genes'} (optional, by default prefixes are
-0016 %                   added to all listed model fields will be checked).
-0017 %   printWarnings   if warnings should be shown (optional, default true).
-0018 %
-0019 % Output:
-0020 %   model           modified model
-0021 %
-0022 % Usage: model=addCOBRAstylePrefixes(model,fields,printWarnings)
-0023 
-0024 if nargin<2 || isempty(fields)
-0025     fields = {'rxns','mets','comps','genes'};
-0026 end
-0027 if nargin<3 || isempty(printWarnings)
-0028     printWarnings = true;
-0029 end
-0030 
-0031 modelFields = {'rxns','R_';
-0032                'mets','M_';
-0033                'comps','C_';
-0034                'genes','G_'};
-0035 
-0036 toChangeIdx = find(ismember(modelFields(:,1),fields));
-0037 for i=1:numel(toChangeIdx)
-0038     currName    = modelFields{toChangeIdx(i),1};
-0039     currPrefix  = modelFields{toChangeIdx(i),2};
-0040     if isfield(model,currName)
-0041         currField   = model.(currName);
-0042     else
-0043         continue;
-0044     end
-0045     if ~all(startsWith(currField,currPrefix))
-0046         currField = strcat(currPrefix, currField);
-0047         if strcmp(currName,'genes')
-0048                 model.grRules = regexprep(model.grRules, '(\<[0-9_a-zA-Z])', 'G_$1');
-0049                 model.grRules = regexprep(model.grRules, ' G_or ', ' or ');
-0050                 model.grRules = regexprep(model.grRules, ' G_and ', ' and ');
-0051         end
-0052         model.(currName) = currField;
-0053     elseif printWarnings
-0054         warning(['All identifiers in "model.' currName '" already start ' ...
-0055             'with "' currPrefix '", no additional prefix added.'])
-0056     end
-0057 end
-0058 end
    
-
    Generated by m2html © 2005
    
-
-
\ No newline at end of file
diff --git a/doc/struct_conversion/addIdentifierPrefix.html b/doc/struct_conversion/addIdentifierPrefix.html
new file mode 100644
index 00000000..de10d34d
--- /dev/null
+++ b/doc/struct_conversion/addIdentifierPrefix.html
@@ -0,0 +1,128 @@
+
+
+
+  Description of addIdentifierPrefix
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  struct_conversion > addIdentifierPrefix.m
    
+
+
+
+
    addIdentifierPrefix
+
    
+
+
    PURPOSE ^
    
+
    addIdentifierPrefix
    
+
+
    SYNOPSIS ^
    
+
    function [model, hasChanged]=addIdentifierPrefix(model,fields) 
    
+
+
    DESCRIPTION ^
    
+
     addIdentifierPrefix
+   If reaction, metabolite, compartment, gene or model identifiers do not
+   start with a letter or _, which conflicts with SBML specifications,
+   prefixes are added for all identifiers in the respective model field.
+   The prefixes are:
+       "R_" for model.rxns,
+       "M_" for model.mets,
+       "C_" for model.comps;
+       "G_" for model.genes (and also represented in model.grRules)
+
+ Input:
+   model           model whose identifiers should be modified
+   fields          cell array with model field names that should be
+                   checked if prefixes should be added, possible values: 
+                   'rxns', 'mets', 'comps', 'genes', 'id'. (optional, by
+                   default all listed model fields will be checked).
+
+ Output:
+   model           modified model
+   hasChanged      cell array with fields and prefixes that are added
+
+ Usage: [model, hasChanged]=addIdentifierPrefix(model,fields)
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
      
+
    
+This function is called by:
+
      
+
    
+
+
+
+
+
    SOURCE CODE ^
    
+
    0001 function [model, hasChanged]=addIdentifierPrefix(model,fields)
+0002 % addIdentifierPrefix
+0003 %   If reaction, metabolite, compartment, gene or model identifiers do not
+0004 %   start with a letter or _, which conflicts with SBML specifications,
+0005 %   prefixes are added for all identifiers in the respective model field.
+0006 %   The prefixes are:
+0007 %       "R_" for model.rxns,
+0008 %       "M_" for model.mets,
+0009 %       "C_" for model.comps;
+0010 %       "G_" for model.genes (and also represented in model.grRules)
+0011 %
+0012 % Input:
+0013 %   model           model whose identifiers should be modified
+0014 %   fields          cell array with model field names that should be
+0015 %                   checked if prefixes should be added, possible values:
+0016 %                   'rxns', 'mets', 'comps', 'genes', 'id'. (optional, by
+0017 %                   default all listed model fields will be checked).
+0018 %
+0019 % Output:
+0020 %   model           modified model
+0021 %   hasChanged      cell array with fields and prefixes that are added
+0022 %
+0023 % Usage: [model, hasChanged]=addIdentifierPrefix(model,fields)
+0024 
+0025 if nargin<2 || isempty(fields)
+0026     fields = {'rxns','mets','comps','genes','id'};
+0027 end
+0028 
+0029 modelFields = {'rxns','R_';
+0030                'mets','M_';
+0031                'comps','C_';
+0032                'genes','G_';
+0033                'id','M_'};
+0034 
+0035 toChangeIdx = find(ismember(modelFields(:,1),fields));
+0036 hasChanged  = false(numel(modelFields(:,1)),1);
+0037 for i=1:numel(toChangeIdx)
+0038     currName    = modelFields{toChangeIdx(i),1};
+0039     currPrefix  = modelFields{toChangeIdx(i),2};
+0040     if isfield(model,currName)
+0041         currField   = model.(currName);
+0042     else
+0043         continue;
+0044     end
+0045     if ~all(startsWith(currField,regexpPattern('^[a-zA-Z_]')))
+0046         currField = strcat(currPrefix, currField);
+0047         hasChanged(toChangeIdx(i)) = true;
+0048 
+0049         if strcmp(currName,'genes')
+0050                 model.grRules = regexprep(model.grRules, '(\<[0-9_a-zA-Z])', 'G_$1');
+0051                 model.grRules = regexprep(model.grRules, ' G_or ', ' or ');
+0052                 model.grRules = regexprep(model.grRules, ' G_and ', ' and ');
+0053         end
+0054         model.(currName) = currField;
+0055     end
+0056 end
+0057 
+0058 hasChanged = modelFields(hasChanged,:);
+0059 hasChanged = append('model.', hasChanged(:,1), ' (', hasChanged(:,2), ' prefix)');
+0060 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/struct_conversion/index.html b/doc/struct_conversion/index.html
index 879c8df1..aa35ccd6 100644
--- a/doc/struct_conversion/index.html
+++ b/doc/struct_conversion/index.html
@@ -19,7 +19,7 @@ 
    Index for struct_conversion
    
 
 
    Matlab files in this directory:
    
 
-
     addCOBRAstylePrefixesaddCOBRAstylePrefixes 
     editMiriameditMiriam 
     extractMiriamextractMiriam 
     ravenCobraWrapperravenCobraWrapper 
     removeCOBRAstylePrefixesremoveCOBRAstylePrefixes 
     standardizeModelFieldOrderstandardizeModelFieldOrder 
    
+ addIdentifierPrefixaddIdentifierPrefix  editMiriameditMiriam  extractMiriamextractMiriam  ravenCobraWrapperravenCobraWrapper  removeIdentifierPrefixremoveIdentifierPrefix  standardizeModelFieldOrderstandardizeModelFieldOrder 
 
 
 
diff --git a/doc/struct_conversion/removeCOBRAstylePrefixes.html b/doc/struct_conversion/removeCOBRAstylePrefixes.html
deleted file mode 100644
index 6bf13d2a..00000000
--- a/doc/struct_conversion/removeCOBRAstylePrefixes.html
+++ /dev/null
@@ -1,133 +0,0 @@
-
-
-
-  Description of removeCOBRAstylePrefixes
-  
-  
-  
-  
-  
-  
-
-
-
-
    Home >  struct_conversion > removeCOBRAstylePrefixes.m
    
-
-
-
-
    removeCOBRAstylePrefixes
-
    
-
-
    PURPOSE ^
    
-
    removeCOBRAstylePrefixes
    
-
-
    SYNOPSIS ^
    
-
    function model=removeCOBRAstylePrefixes(model,fields,forceRemove) 
    
-
-
    DESCRIPTION ^
    
-
     removeCOBRAstylePrefixes
-   This function removes COBRA style identifier prefixes, which are:
-       "R_" for model.rxns, model.rxnNames and model.id,
-       "M_" for model.mets and model.metNames,
-       "C_" for model.comps;
-       "G_" for model.genes (and also represented in model.grRules).
-   By default, the prefixes are only removed if all entries in a
-   particular field has the prefix.
-
- Input:
-   model           model whose identifiers should be modified
-   fields          cell array with model field names from which the
-                   identifiers should be removed, possible values: 
-                   'rxns', 'mets', 'comps', 'genes', 'metNames', 
-                   'rxnNames', 'id'. (optional, by default all listed
-                   model fields will be checked).
-   forceRemove     if prefixes should be removed even if not all entries
-                   in a model field have the prefix (optional, default
-                   false)
-
- Output:
-   model           modified model
-
- Usage: model=removeCOBRAstylePrefixes(model,fields,forceRemove)
    
-
-
-
    CROSS-REFERENCE INFORMATION ^
    
-This function calls:
-
      
-
    
-This function is called by:
-
      
-
    
-
-
-
-
-
    SOURCE CODE ^
    
-
    0001 function model=removeCOBRAstylePrefixes(model,fields,forceRemove)
-0002 % removeCOBRAstylePrefixes
-0003 %   This function removes COBRA style identifier prefixes, which are:
-0004 %       "R_" for model.rxns, model.rxnNames and model.id,
-0005 %       "M_" for model.mets and model.metNames,
-0006 %       "C_" for model.comps;
-0007 %       "G_" for model.genes (and also represented in model.grRules).
-0008 %   By default, the prefixes are only removed if all entries in a
-0009 %   particular field has the prefix.
-0010 %
-0011 % Input:
-0012 %   model           model whose identifiers should be modified
-0013 %   fields          cell array with model field names from which the
-0014 %                   identifiers should be removed, possible values:
-0015 %                   'rxns', 'mets', 'comps', 'genes', 'metNames',
-0016 %                   'rxnNames', 'id'. (optional, by default all listed
-0017 %                   model fields will be checked).
-0018 %   forceRemove     if prefixes should be removed even if not all entries
-0019 %                   in a model field have the prefix (optional, default
-0020 %                   false)
-0021 %
-0022 % Output:
-0023 %   model           modified model
-0024 %
-0025 % Usage: model=removeCOBRAstylePrefixes(model,fields,forceRemove)
-0026 
-0027 if nargin<2 || isempty(fields)
-0028     fields = {'rxns','mets','comps','genes','metNames','rxnNames','id'};
-0029 end
-0030 if nargin<3 || isempty(forceRemove)
-0031     forceRemove = true;
-0032 end
-0033 
-0034 modelFields = {'rxns',      'R_';
-0035     'mets',      'M_';
-0036     'comps',     'C_';
-0037     'genes',     'G_';
-0038     'metNames',  'M_';
-0039     'rxnNames',  'R_';
-0040     'id',        'M_'};
-0041 
-0042 toChangeIdx = find(ismember(modelFields(:,1),fields));
-0043 for i=1:numel(toChangeIdx)
-0044     currName    = modelFields{toChangeIdx(i),1};
-0045     currPrefix  = modelFields{toChangeIdx(i),2};
-0046     currField   = model.(currName);
-0047 
-0048     if forceRemove
-0049         hasPrefix = true;
-0050     else
-0051         hasPrefix = all(startsWith(currField,currPrefix));
-0052     end
-0053     if hasPrefix
-0054         currField = regexprep(currField,['^' currPrefix],'');
-0055         if strcmp(currName,'genes')
-0056             model.grRules=regexprep(model.grRules,'^G_','');
-0057             model.grRules=regexprep(model.grRules,'\(G_','(');
-0058             model.grRules=regexprep(model.grRules,' G_',' ');
-0059         end
-0060     end
-0061     model.(currName) = currField;
-0062 end
-0063 end
    
-
    Generated by m2html © 2005
    
-
-
\ No newline at end of file
diff --git a/doc/struct_conversion/removeIdentifierPrefix.html b/doc/struct_conversion/removeIdentifierPrefix.html
new file mode 100644
index 00000000..3fae6a6c
--- /dev/null
+++ b/doc/struct_conversion/removeIdentifierPrefix.html
@@ -0,0 +1,143 @@
+
+
+
+  Description of removeIdentifierPrefix
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  struct_conversion > removeIdentifierPrefix.m
    
+
+
+
+
    removeIdentifierPrefix
+
    
+
+
    PURPOSE ^
    
+
    removeIdentifierPrefix
    
+
+
    SYNOPSIS ^
    
+
    function [model, hasChanged]=removeIdentifierPrefix(model,fields,forceRemove) 
    
+
+
    DESCRIPTION ^
    
+
     removeIdentifierPrefix
+   This function removes identifier prefixes:
+       "R_" for model.rxns, model.rxnNames and model.id,
+       "M_" for model.mets and model.metNames,
+       "C_" for model.comps;
+       "G_" for model.genes (and also represented in model.grRules).
+   By default, the prefixes are only removed if all entries in a
+   particular field has the prefix. The prefixes might have been present
+   because one or more identifiers do not start with a letter or _, which
+   conflicts with SBML specifications.
+
+ Input:
+   model           model whose identifiers should be modified
+   fields          cell array with model field names from which the
+                   identifiers should be removed, possible values: 
+                   'rxns', 'mets', 'comps', 'genes', 'metNames', 
+                   'rxnNames', 'id'. (optional, by default all listed
+                   model fields will be checked).
+   forceRemove     if prefixes should be removed even if not all entries
+                   in a model field have the prefix (optional, default
+                   false)
+
+ Output:
+   model           modified model
+   hasChanged      cell array with fields and prefixes that are removed
+
+ Usage: model=removeIdentifierPrefix(model,fields,forceRemove)
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
      
+
    
+This function is called by:
+
      
+
    
+
+
+
+
+
    SOURCE CODE ^
    
+
    0001 function [model, hasChanged]=removeIdentifierPrefix(model,fields,forceRemove)
+0002 % removeIdentifierPrefix
+0003 %   This function removes identifier prefixes:
+0004 %       "R_" for model.rxns, model.rxnNames and model.id,
+0005 %       "M_" for model.mets and model.metNames,
+0006 %       "C_" for model.comps;
+0007 %       "G_" for model.genes (and also represented in model.grRules).
+0008 %   By default, the prefixes are only removed if all entries in a
+0009 %   particular field has the prefix. The prefixes might have been present
+0010 %   because one or more identifiers do not start with a letter or _, which
+0011 %   conflicts with SBML specifications.
+0012 %
+0013 % Input:
+0014 %   model           model whose identifiers should be modified
+0015 %   fields          cell array with model field names from which the
+0016 %                   identifiers should be removed, possible values:
+0017 %                   'rxns', 'mets', 'comps', 'genes', 'metNames',
+0018 %                   'rxnNames', 'id'. (optional, by default all listed
+0019 %                   model fields will be checked).
+0020 %   forceRemove     if prefixes should be removed even if not all entries
+0021 %                   in a model field have the prefix (optional, default
+0022 %                   false)
+0023 %
+0024 % Output:
+0025 %   model           modified model
+0026 %   hasChanged      cell array with fields and prefixes that are removed
+0027 %
+0028 % Usage: model=removeIdentifierPrefix(model,fields,forceRemove)
+0029 
+0030 if nargin<2 || isempty(fields)
+0031     fields = {'rxns','mets','comps','genes','metNames','rxnNames','id'};
+0032 end
+0033 if nargin<3 || isempty(forceRemove)
+0034     forceRemove = false;
+0035 end
+0036 
+0037 modelFields = {'rxns',      'R_';
+0038     'mets',      'M_';
+0039     'comps',     'C_';
+0040     'genes',     'G_';
+0041     'metNames',  'M_';
+0042     'rxnNames',  'R_';
+0043     'id',        'M_'};
+0044 
+0045 toChangeIdx = find(ismember(modelFields(:,1),fields));
+0046 hasChanged  = false(numel(modelFields(:,1)),1);
+0047 for i=1:numel(toChangeIdx)
+0048     currName    = modelFields{toChangeIdx(i),1};
+0049     currPrefix  = modelFields{toChangeIdx(i),2};
+0050     currField   = model.(currName);
+0051 
+0052     if forceRemove && any(startsWith(currField,currPrefix))
+0053         hasPrefix = true;
+0054     else
+0055         hasPrefix = all(startsWith(currField,currPrefix));
+0056     end
+0057     if hasPrefix
+0058         currField = regexprep(currField,['^' currPrefix],'');
+0059         hasChanged(toChangeIdx(i)) = true;
+0060         if strcmp(currName,'genes')
+0061             model.grRules=regexprep(model.grRules,'^G_','');
+0062             model.grRules=regexprep(model.grRules,'\(G_','(');
+0063             model.grRules=regexprep(model.grRules,' G_',' ');
+0064         end
+0065     end
+0066     model.(currName) = currField;
+0067 end
+0068 hasChanged = modelFields(hasChanged,:);
+0069 hasChanged = append('model.', hasChanged(:,1), ' (', hasChanged(:,2), ' prefix)');
+0070 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/io/exportModel.m b/io/exportModel.m
index 1d60eef1..8beef3b2 100755
--- a/io/exportModel.m
+++ b/io/exportModel.m
@@ -1,4 +1,4 @@
-function exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
+function exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)
 % exportModel
 %   Exports a constraint-based model to an SBML file (L3V1 FBCv2)
 %
@@ -6,12 +6,9 @@ function exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
 %   model               a model structure
 %   fileName            filename to export the model to. A dialog window
 %                       will open if no file name is specified.
-%   COBRAstyle          true if COBRA-style prefixes should be added to all
-%                       identifiers: R_ for reactions, M_ for metabolites,
-%                       G_ for genes and C_ for compartments. If all
-%                       identifiers of a particular field already have the
-%                       prefix, then no additional prefixes are added.
-%                       (optional, default false)
+%   neverPrefix         true if prefixes are never added to identifiers,
+%                       even if start with e.g. digits. This might result
+%                       in invalid SBML files (optional, default false)
 %   supressWarnings     true if warnings should be supressed. This might
 %                       results in invalid SBML files, as no checks are
 %                       performed (optional, default false)
@@ -19,7 +16,7 @@ function exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
 %                       should be sorted alphabetically by their
 %                       identifiers (optional, default false)
 %
-% Usage: exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
+% Usage: exportModel(model,fileName,neverPrefix,supressWarnings,sortIds)
 
 if nargin<2 || isempty(fileName)
     [fileName, pathName] = uiputfile({'*.xml;*.sbml'}, 'Select file for model export',[model.id '.xml']);
@@ -30,15 +27,13 @@ function exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
     end
 end
 fileName=char(fileName);
-if nargin<3
-    COBRAstyle=false;
-elseif ~islogical(COBRAstyle)
-    error("COBRAstyle should be either true or false")
+if nargin<3 || isempty(neverPrefix)
+    neverPrefix=false;
 end
-if nargin<4
+if nargin<4 || isempty(supressWarnings)
     supressWarnings=false;
 end
-if nargin<5
+if nargin<5 || isempty(sortIds)
     sortIds=false;
 end
 if sortIds==true
@@ -85,17 +80,17 @@ function exportModel(model,fileName,COBRAstyle,supressWarnings,sortIds)
     model.name='blankName';
 end
 
-% Add prefixes if desired
-if COBRAstyle
-    if isfield(model,'ec')
-        error('ecModels cannot be exported with COBRAstyle flag, manually correct any non-compliant identifiers if needed.')
-    end
-    model = addCOBRAstylePrefixes(model,[],false);
+% Add prefixes if required
+if ~neverPrefix
+    [model,hasChanged] = addIdentifierPrefix(model);
+    dispEM(['The following fields have one or more entries that do not start '...
+        'with a letter or _ (conflicting with SBML specifications). Prefixes '...
+        'are added to all entries in those fields:'],false,hasChanged)
 end
 
 %Check the model structure
 if supressWarnings==false
-    checkModelStruct(model,false);
+    checkModelStruct(model);
 end
 
 %Add several blank fields, if they do not exist already. This is to reduce
diff --git a/io/importModel.m b/io/importModel.m
index 56bd19dd..b36a4ad9 100755
--- a/io/importModel.m
+++ b/io/importModel.m
@@ -1,6 +1,6 @@
-function model=importModel(fileName,removeExcMets,COBRAstyle,supressWarnings)
+function model=importModel(fileName,removeExcMets,removePrefix,supressWarnings)
 % importModel
-%   Import a constraint-based model from a SBML file
+%   Import a constraint-based model from an SBML file.
 %
 % Input:
 %   fileName        a SBML file to import. A dialog window will open if
@@ -9,10 +9,11 @@
 %                   needed to be able to run simulations, but it could also
 %                   be done using simplifyModel at a later stage (optional,
 %                   default true)
-%   COBRAstyle      true if the model uses COBRA style identifier prefixes
-%                   that should be removed when loading the model: G_ for
-%                   genes, R_ for reactions, M_ for metabolites, and C_ for
-%                   compartments. (optional, default false)
+%   removePrefix    true if identifier prefixes should be removed when
+%                   loading the model: G_ for genes, R_ for reactions,
+%                   M_ for metabolites, and C_ for compartments. These are
+%                   only removed if all identifiers of a certain type
+%                   contain the prefix. (optional, default true)
 %   supressWarnings true if warnings regarding the model structure should
 %                   be supressed (optional, default false)
 %
@@ -49,7 +50,7 @@
 %       geneComps        compartments for genes
 %       geneMiriams      structure with MIRIAM information about the genes
 %       geneShortNames   gene alternative names (e.g. ERG10)
-%       proteins     protein associated to each gene
+%       proteins         protein associated to each gene
 %       metNames         metabolite description
 %       metComps         compartments for metabolites
 %       inchis           InChI-codes for metabolites
@@ -58,11 +59,11 @@
 %       metCharges       metabolite charge
 %       unconstrained    true if the metabolite is an exchange metabolite
 %
-% A number of consistency checks are performed in order to ensure that the
+% Note: A number of consistency checks are performed in order to ensure that the
 % model is valid. Take these warnings seriously and modify the model
 % structure to solve them.
 %
-% Usage: model = importModel(fileName, removeExcMets, COBRAstyle, supressWarnings)
+% Usage: model = importModel(fileName, removeExcMets, removePrefix, supressWarnings)
 
 if nargin<1 || isempty(fileName)
     [fileName, pathName] = uigetfile({'*.xml;*.sbml'}, 'Please select the model file');
@@ -77,8 +78,8 @@
     removeExcMets=true;
 end
 
-if nargin<3 || isempty(COBRAstyle)
-    COBRAstyle=false;
+if nargin<3 || isempty(removePrefix)
+    removePrefix=true;
 end
 
 if nargin<4
@@ -967,26 +968,11 @@
 model.genes=regexprep(model.genes,'__([0-9]+)__','${char(str2num($1))}');
 model.id=regexprep(model.id,'__([0-9]+)__','${char(str2num($1))}');
 
-if COBRAstyle
-    model=removeCOBRAstylePrefixes(model);
-else
-    hasCOBRAids(1) = all(startsWith(model.rxns,'R_'));
-    hasCOBRAids(2) = all(startsWith(model.mets,'M_'));
-    hasCOBRAids(3) = all(startsWith(model.comps,'C_'));
-    hasCOBRAids(4) = all(startsWith(model.genes,'G_'));
-    if any(hasCOBRAids)
-        hasCOBRAidsMsg = {'model.rxns (R_ prefix)',...
-            'model.mets (M_ prefix)',...
-            'model.comps (C_ prefix)',...
-            'model.genes (G_ prefix)'};
-        hasCOBRAidsMsg(~hasCOBRAids) = [];
-        printOrange(['COBRA style identifier prefixes are found in: "' ...
-            strjoin(hasCOBRAidsMsg,'"; "') '". Since RAVEN 2.10.0, identifiers ' ...
-            'are by default imported "as-is". If you do prefer to remove these ' ...
-            'identifier prefixes, run "removeCOBRAstylePrefixes" on the ' ...
-            'imported model, or directly run importModel with COBRAstyle as true ' ...
-            'Example:   importModel(''filename.xml'', [], true);\n']);
-    end
+if removePrefix
+    [model, hasChanged]=removeIdentifierPrefix(model);
+    dispEM(['The following fields have prefixes removed from all entries. '...
+    'If this is undesired, run importModel with removePrefix as false. Example: '...
+    'importModel(''filename.xml'',[],false);'],false,hasChanged)
 end
 
 %Remove unused fields
diff --git a/struct_conversion/addCOBRAstylePrefixes.m b/struct_conversion/addCOBRAstylePrefixes.m
deleted file mode 100644
index a84a6954..00000000
--- a/struct_conversion/addCOBRAstylePrefixes.m
+++ /dev/null
@@ -1,58 +0,0 @@
-function model=addCOBRAstylePrefixes(model,fields,printWarnings)
-% addCOBRAstylePrefixes
-%   This function adds COBRA style identifier prefixes, which are:
-%       "R_" for model.rxns,
-%       "M_" for model.mets,
-%       "C_" for model.comps;
-%       "G_" for model.genes (and also represented in model.grRules).
-%   If all entries in a field already have the prefix, then no additional
-%   prefix will be added.
-%
-% Input:
-%   model           model whose identifiers should be modified
-%   fields          cell array with model field names to which the prefix
-%                   should be added, possible values: {'rxns', 'mets', 
-%                   'comps', 'genes'} (optional, by default prefixes are
-%                   added to all listed model fields will be checked).
-%   printWarnings   if warnings should be shown (optional, default true).
-%
-% Output:
-%   model           modified model
-%
-% Usage: model=addCOBRAstylePrefixes(model,fields,printWarnings)
-
-if nargin<2 || isempty(fields)
-    fields = {'rxns','mets','comps','genes'};
-end
-if nargin<3 || isempty(printWarnings)
-    printWarnings = true;
-end
-
-modelFields = {'rxns','R_';
-               'mets','M_';
-               'comps','C_';
-               'genes','G_'};
-
-toChangeIdx = find(ismember(modelFields(:,1),fields));
-for i=1:numel(toChangeIdx)
-    currName    = modelFields{toChangeIdx(i),1};
-    currPrefix  = modelFields{toChangeIdx(i),2};
-    if isfield(model,currName)
-        currField   = model.(currName);
-    else
-        continue;
-    end
-    if ~all(startsWith(currField,currPrefix))
-        currField = strcat(currPrefix, currField);
-        if strcmp(currName,'genes')
-                model.grRules = regexprep(model.grRules, '(\<[0-9_a-zA-Z])', 'G_$1');
-                model.grRules = regexprep(model.grRules, ' G_or ', ' or ');
-                model.grRules = regexprep(model.grRules, ' G_and ', ' and ');
-        end
-        model.(currName) = currField;
-    elseif printWarnings
-        warning(['All identifiers in "model.' currName '" already start ' ...
-            'with "' currPrefix '", no additional prefix added.'])
-    end
-end
-end
diff --git a/struct_conversion/addIdentifierPrefix.m b/struct_conversion/addIdentifierPrefix.m
new file mode 100644
index 00000000..74672ff6
--- /dev/null
+++ b/struct_conversion/addIdentifierPrefix.m
@@ -0,0 +1,60 @@
+function [model, hasChanged]=addIdentifierPrefix(model,fields)
+% addIdentifierPrefix
+%   If reaction, metabolite, compartment, gene or model identifiers do not
+%   start with a letter or _, which conflicts with SBML specifications,
+%   prefixes are added for all identifiers in the respective model field.
+%   The prefixes are:
+%       "R_" for model.rxns,
+%       "M_" for model.mets,
+%       "C_" for model.comps;
+%       "G_" for model.genes (and also represented in model.grRules)
+%
+% Input:
+%   model           model whose identifiers should be modified
+%   fields          cell array with model field names that should be
+%                   checked if prefixes should be added, possible values: 
+%                   'rxns', 'mets', 'comps', 'genes', 'id'. (optional, by
+%                   default all listed model fields will be checked).
+%
+% Output:
+%   model           modified model
+%   hasChanged      cell array with fields and prefixes that are added
+%
+% Usage: [model, hasChanged]=addIdentifierPrefix(model,fields)
+
+if nargin<2 || isempty(fields)
+    fields = {'rxns','mets','comps','genes','id'};
+end
+
+modelFields = {'rxns','R_';
+               'mets','M_';
+               'comps','C_';
+               'genes','G_';
+               'id','M_'};
+
+toChangeIdx = find(ismember(modelFields(:,1),fields));
+hasChanged  = false(numel(modelFields(:,1)),1);
+for i=1:numel(toChangeIdx)
+    currName    = modelFields{toChangeIdx(i),1};
+    currPrefix  = modelFields{toChangeIdx(i),2};
+    if isfield(model,currName)
+        currField   = model.(currName);
+    else
+        continue;
+    end
+    if ~all(startsWith(currField,regexpPattern('^[a-zA-Z_]')))
+        currField = strcat(currPrefix, currField);
+        hasChanged(toChangeIdx(i)) = true;
+
+        if strcmp(currName,'genes')
+                model.grRules = regexprep(model.grRules, '(\<[0-9_a-zA-Z])', 'G_$1');
+                model.grRules = regexprep(model.grRules, ' G_or ', ' or ');
+                model.grRules = regexprep(model.grRules, ' G_and ', ' and ');
+        end
+        model.(currName) = currField;
+    end
+end
+
+hasChanged = modelFields(hasChanged,:);
+hasChanged = append('model.', hasChanged(:,1), ' (', hasChanged(:,2), ' prefix)');
+end
diff --git a/struct_conversion/removeCOBRAstylePrefixes.m b/struct_conversion/removeIdentifierPrefix.m
similarity index 71%
rename from struct_conversion/removeCOBRAstylePrefixes.m
rename to struct_conversion/removeIdentifierPrefix.m
index 9f0dfbf4..0a960108 100644
--- a/struct_conversion/removeCOBRAstylePrefixes.m
+++ b/struct_conversion/removeIdentifierPrefix.m
@@ -1,12 +1,14 @@
-function model=removeCOBRAstylePrefixes(model,fields,forceRemove)
-% removeCOBRAstylePrefixes
-%   This function removes COBRA style identifier prefixes, which are:
+function [model, hasChanged]=removeIdentifierPrefix(model,fields,forceRemove)
+% removeIdentifierPrefix
+%   This function removes identifier prefixes:
 %       "R_" for model.rxns, model.rxnNames and model.id,
 %       "M_" for model.mets and model.metNames,
 %       "C_" for model.comps;
 %       "G_" for model.genes (and also represented in model.grRules).
 %   By default, the prefixes are only removed if all entries in a
-%   particular field has the prefix.
+%   particular field has the prefix. The prefixes might have been present
+%   because one or more identifiers do not start with a letter or _, which
+%   conflicts with SBML specifications.
 %
 % Input:
 %   model           model whose identifiers should be modified
@@ -21,14 +23,15 @@
 %
 % Output:
 %   model           modified model
+%   hasChanged      cell array with fields and prefixes that are removed
 %
-% Usage: model=removeCOBRAstylePrefixes(model,fields,forceRemove)
+% Usage: model=removeIdentifierPrefix(model,fields,forceRemove)
 
 if nargin<2 || isempty(fields)
     fields = {'rxns','mets','comps','genes','metNames','rxnNames','id'};
 end
 if nargin<3 || isempty(forceRemove)
-    forceRemove = true;
+    forceRemove = false;
 end
 
 modelFields = {'rxns',      'R_';
@@ -40,18 +43,20 @@
     'id',        'M_'};
 
 toChangeIdx = find(ismember(modelFields(:,1),fields));
+hasChanged  = false(numel(modelFields(:,1)),1);
 for i=1:numel(toChangeIdx)
     currName    = modelFields{toChangeIdx(i),1};
     currPrefix  = modelFields{toChangeIdx(i),2};
     currField   = model.(currName);
 
-    if forceRemove
+    if forceRemove && any(startsWith(currField,currPrefix))
         hasPrefix = true;
     else
         hasPrefix = all(startsWith(currField,currPrefix));
     end
     if hasPrefix
         currField = regexprep(currField,['^' currPrefix],'');
+        hasChanged(toChangeIdx(i)) = true;
         if strcmp(currName,'genes')
             model.grRules=regexprep(model.grRules,'^G_','');
             model.grRules=regexprep(model.grRules,'\(G_','(');
@@ -60,4 +65,6 @@
     end
     model.(currName) = currField;
 end
+hasChanged = modelFields(hasChanged,:);
+hasChanged = append('model.', hasChanged(:,1), ' (', hasChanged(:,2), ' prefix)');
 end
diff --git a/testing/unit_tests/test_data/importExportResults.mat b/testing/unit_tests/test_data/importExportResults.mat
index bc7210f5ec123bb24c2c891d038597b768a6310c..0a5df5ef1977e6c2d780509b52c8d408c8d71bf9 100644
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