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| function [newModel, modelChanges] = addMetabolicNetwork(model,rxnsToAdd,metsToAdd) | ||
| %addMetabolicNetwork Integrate a new metabolic network into a model | ||
| % | ||
| % NOTE: The function is to incorporate a subnetwork that is provided by two | ||
| % arrays, rxnsToAdd and metsToAdd, which should be in defined | ||
| % structure as below，and with reactions and metabolites that are | ||
| % NOT included in the model | ||
| % | ||
| % Usage: | ||
| % [newModel, modelChanges] = addMetabolicNetwork(model,rxnsToAdd,metsToAdd) | ||
| % | ||
| % | ||
| % Inputs: | ||
| % model A model structure | ||
| % | ||
| % rxnsToAdd the reaction structure can have the following fields: | ||
| % rxns cell array with unique strings that | ||
| % identifies each reaction | ||
| % equations cell array with equation strings. Decimal | ||
| % coefficients are expressed as "1.2". | ||
| % Reversibility is indicated by "<=>" or "=>" | ||
| % The metabolites have to be written as | ||
| % "metNames[comps]". Only compartments in | ||
| % model.comps are allowed. New metabolites to | ||
| % the model should be added to metsToAdd array | ||
| % rxnNames cell array with the names of each reaction | ||
| % (opt, default '') | ||
| % lb vector with the lower bounds (opt, default | ||
| % to model.annotations.defaultLB or -inf for | ||
| % reversible reactions and 0 for irreversible | ||
| % when "equations" is used. When "mets" and | ||
| % "stoichCoeffs" are used it defaults for all | ||
| % reactions to model.annotations.defaultLB or | ||
| % -inf) | ||
| % ub vector with the upper bounds (opt, default | ||
| % to model.annotations.defaultUB or inf) | ||
| % eccodes cell array with the EC-numbers for each | ||
| % reactions. Delimit several EC-numbers with | ||
| % ";" (opt, default '') | ||
| % subSystems cell array with the subsystems for each | ||
| % reaction (opt, default '') | ||
| % grRules cell array with the gene-reaction | ||
| % relationship for each reaction. For example | ||
| % "(A and B) or (C)" means that the reaction | ||
| % could be catalyzed by a complex between | ||
| % A & B or by C on its own. All the genes | ||
| % have to be present in model.genes. Add | ||
| % genes with addGenesRaven before calling | ||
| % this function if needed (opt, default '') | ||
| % rxnReferences cell array with reaction references (opt, | ||
| % default '') | ||
| % rxnConfidenceScores vector with reaction confidence scores | ||
| % (opt, default NaN) | ||
| % | ||
| % metsToAdd the metabolite structure can have the following fields: | ||
| % mets cell array with unique strings that | ||
| % identifies each metabolite (opt, default IDs | ||
| % of new metabolites are numbered with the | ||
| % prefix defined below) | ||
| % metNames cell array with the names of each | ||
| % metabolite | ||
| % compartments cell array with the compartment of each | ||
| % metabolite. Should match model.comps. | ||
| % If this is a string rather than a cell | ||
| % array it is assumed that all mets are in | ||
| % that compartment | ||
| % inchis cell array with InChI strings for each | ||
| % metabolite (opt, default '') | ||
| % metFormulas cell array with the formulas for each of | ||
| % the metabolites (opt, default '') | ||
| % metCharges metabolite charge (opt, default NaN) | ||
| % | ||
| % | ||
| % Outputs: | ||
| % newModel a new model with the added reactons and metabolites | ||
| % | ||
| % modelChanges a cell structure containing the original and new reaction | ||
| % and/or metabolite properties. Reaction-related changes | ||
| % are reported in the modelChanges.rxns field, whereas | ||
| % metabolite-related changes are reported in the | ||
| % modelChanges.mets field | ||
| % | ||
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| if nargin<2 | ||
| error('Missing input!'); | ||
| end | ||
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| if nargin<3 | ||
| metsToAdd = []; | ||
| end | ||
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| %% Add new metabolites | ||
|
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| if isempty(metsToAdd) | ||
| newModel = model; | ||
| else | ||
| % the following metabolite fields are required to be included | ||
| requiredMetFields = {'mets','metNames','metFormulas','metCharges','compartments'}; | ||
| if ~all(ismember(requiredMetFields, fieldnames(metsToAdd))) | ||
| error('There is missing fields in the metabolite structure to be added.'); | ||
| end | ||
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| % verify that none of the metabolites exist in the current model | ||
| if any(ismember(metsToAdd.mets, model.mets)) | ||
| error('One or more metabolite IDs to be added already exist in the model.'); | ||
| end | ||
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| % add metabolites to the model | ||
| newModel = addMets(model,metsToAdd); | ||
| end | ||
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| %% Check new reactions | ||
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| % the following reaction fields are required to be included | ||
| requiredRxnFields = {'rxns','equations','subSystems','grRules'}; | ||
| if ~all(ismember(requiredRxnFields, fieldnames(rxnsToAdd))) | ||
| error('There is missing fields in the metabolite structure to be added.'); | ||
| end | ||
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| % verify that none of the reactions exist in the current model | ||
| if any(ismember(rxnsToAdd.rxns, model.rxns)) | ||
| error('One or more reactions to be added already exist in the model.'); | ||
| end | ||
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| % make sure all equations have metabolites in a format of "metNames[comps]" | ||
| if ~all(contains(rxnsToAdd.equations, '[') & contains(rxnsToAdd.equations, ']')) | ||
| error('The metabolites in equations should be in a format of "metNames[comps]".'); | ||
| end | ||
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| %% Add new genes | ||
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| % extract genes from grRules | ||
| newGenes = getGenesFromGrRules(rxnsToAdd.grRules); | ||
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| % remove genes that are already existed in model | ||
| if any(ismember(newGenes, newModel.genes)) | ||
| fprintf('One or more genes to be added already exist in the model，therefore they will be merged.\n'); | ||
| newGenes = setdiff(newGenes, newModel.genes); | ||
| end | ||
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| % append new genes to list of model genes | ||
| newModel.genes = [newModel.genes; newGenes]; | ||
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| % add new columns to rxnGeneMat will be updated after the new reactions are added below. | ||
| newModel.rxnGeneMat(:, end+1:end+numel(newGenes)) = 0; | ||
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| %% Integrate new subnetwork to the model | ||
| newModel = addRxns(newModel, rxnsToAdd, 3); | ||
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| % update genes and rxnGeneMat with new grRules | ||
| [newModel.genes, newModel.rxnGeneMat] = getGenesFromGrRules(newModel.grRules); | ||
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| %% Document model changes | ||
| modelChanges = docModelChanges(model, newModel); | ||
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