Json

isValidJSON(fileName)

This function checks if a JSON file is valid or not. A JSON file is considered valid if it can be decoded into a structure.

USAGE:

[isValid] = isValidJSON (fileName)

INPUT:

fileName – A string containing the file name of the JSON file

OUTPUT:

isValid – A logical variable: 1 if JSON file is valid 0 if JSON file is invalid

Example

[isValid] = isValidJSON(‘toyModel_output.json’)

model2JSON(model, fileName)

This function writes a JSON file from Matlab structure. JSON files can be validated by isValidJSON function or online tools like https://jsonlint.com/.

USAGE:

model2JSON (model, fileName)

INPUTS:

• model – model structure with fields:

  • .mets - m x 1 cell array of metabolite identifiers

  • .metNames - m x 1 cell array of metabolite names

  • .rxns - n x 1 cell array of reaction identifiers

  • .rxnNames - n x 1 cell array of reaction names

  • .lb - n x 1 vector of reaction lower bounds

  • .ub - n x 1 vector of reaction upper bounds

  • .grRules - n x 1 cell array of gene-reaction rules

  • .subSystems - n x 1 cell array of subsystem assignments for each reaction

  • .genes - g x 1 cell array of gene identifiers

  • .modelID - (optional) short model identifier

  • .modelAnnotation - (optional) cell array of model annotation entries; the second element is written as the model version

  • .metCharges - (optional) m x 1 vector of metabolite charges

  • .metFormulas - (optional) m x 1 cell array of elemental formulas

  • .metBiGGID - (optional) m x 1 cell array of BiGG metabolite identifiers

  • .metBioCycID - (optional) m x 1 cell array of BioCyc metabolite identifiers

  • .metChEBIID - (optional) m x 1 cell array of ChEBI identifiers

  • .metHMDBID - (optional) m x 1 cell array of HMDB identifiers

  • .metInchiKey - (optional) m x 1 cell array of InChI key strings

  • .metKEGGID - (optional) m x 1 cell array of KEGG metabolite identifiers

  • .metMetaNetXID - (optional) m x 1 cell array of MetaNetX metabolite identifiers

  • .metReactomeID - (optional) m x 1 cell array of Reactome metabolite identifiers

  • .metSabiork - (optional) m x 1 cell array of SABIO-RK metabolite identifiers

  • .metSBOTerms - (optional) m x 1 cell array of SBO terms for metabolites

  • .metSEEDID - (optional) m x 1 cell array of SEED metabolite identifiers

  • .rxnMetaNetXID - (optional) n x 1 cell array of MetaNetX reaction identifiers

  • .rxnSBOTerms - (optional) n x 1 cell array of SBO terms for reactions

  • .geneSBOTerms - (optional) g x 1 cell array of SBO terms for genes

• fileName – name of file including extension .json