Modelproperties¶
- checkModelProperties(model, printLevel)[source]¶
- calculates various generic properties of a model, not specific to any
biochemistry
- INPUT
model printLevel
- OUTPUT
model.SIntMetBool m x 1 boolean of metabolites heuristically though to be involved in mass balanced reactions model.SIntRxnBool n x 1 boolean of reactions heuristically though to be mass balanced model.SConsistentMetBool m x 1 boolean vector indicating consistent mets model.SConsistentRxnBool n x 1 boolean vector indicating consistent rxns model.SInConsistentMetBool m x 1 boolean vector indicating inconsistent mets model.SInConsistentRxnBool n x 1 boolean vector indicating inconsistent rxns model.metUnknownInconsistentRemoveBool m x 1 boolean vector indicating removed mets model.rxnUnknownInconsistentRemoveBool n x 1 boolean vector indicating removed rxns model.unknownSConsistencyMetBool m x 1 boolean vector indicating unknown consistent mets (all zeros when algorithm converged perfectly!) model.unknownSConsistencyRxnBool n x 1 boolean vector indicating unknown consistent rxns (all zeros when algorithm converged perfectly!) model.leakMetBool m x 1 boolean of metabolites in a positive leakage mode model.leakRxnBool n x 1 boolean of reactions exclusively involved in a positive leakage mode model.siphonMetBool m x 1 boolean of metabolites in a negative leakage mode model.siphonRxnBool n x 1 boolean of reactions exclusively involved in a negative leakage mode model.fluxConsistentMetBool: m x 1 boolean vector indicating flux consistent mets model.fluxConsistentRxnBool: n x 1 boolean vector indicating flux consistent rxns model.fluxInConsistentMetBool: m x 1 boolean vector indicating flux inconsistent mets model.fluxInConsistentRxnBool: n x 1 boolean vector indicating flux inconsistent rxns model.thermoFluxConsistentMetBool m x 1 boolean vector indicating thermodynamically flux consistent mets model.thermoFluxConsistentRxnBool n x 1 boolean vector indicating thermodynamically flux consistent rxns model.thermoFwdFluxConsistentRxnBool n x 1 boolean vector indicating forward thermodynamically flux consistent rxns model.thermoRevFluxConsistentRxnBool n x 1 boolean vector indicating reverse thermodynamically flux consistent rxns
model.rankFR rank of [F R], when using only FRrows model.rankFRV rank of [F;R], when using only FRVcols model.rankFRvanilla rank of [F R], when using all rows model.rankFRVvanilla rank of [F;R], when using all cols model.FRrows m x 1 boolean of rows of [F R] that are nonzero,
unique upto positive scaling and part of the maximal conservation vector
- model.FRVcols n x 1 boolean of cols of [F;R] that are nonzero,
unique upto positive scaling and part of the maximal conservation vector
model.FRirows m x 1 boolean of rows of [F R] that are independent model.FRdrows m x 1 boolean of rows of [F R] that are dependent model.FRwrows m x 1 boolean of independent rows of [F R] that
have dependent rows amongst model.FRdrows
model.FRVdcols n x 1 boolean of cols of [F;R]that are dependent model.FRnonZeroBool m x 1 boolean vector indicating metabolites involved
in at least one internal reaction
- model.FRuniqueBool m x 1 boolean vector indicating metabolites with
reaction stoichiometry unique upto scalar multiplication
- model.SIntRxnBool n x 1 boolean vector indicating the non exchange
reactions
- model.FRVnonZeroBool n x 1 boolean vector indicating non exchange reactions
with at least one metabolite involved
- model.FRVuniqueBool n x 1 boolean vector indicating non exchange reactions
with stoichiometry unique upto scalar multiplication
model.connectedRowsFRBool m x 1 boolean vector indicating metabolites in connected rows of [F,R] model.connectedRowsFRVBool n x 1 boolean vector indicating complexes in connected columns of [F;R] model.V S*V=0, 1’*|V|>1 for all flux consistent reactions
- makeModelPropertiesTable(modelResults, modelMetaData, resultsDirectory, resultsFileName, tableFilename)[source]¶
makes a table of model property results
- INPUT
modelResults output of checkModelProperties
- OPTIONAL INPUT
- modelMetaData Cell array, where each row is metadata for one model
with five columns: species, modelID, fileName, PMID, doi. See function modelMetaData=modelCitations() for example. Table columns ordered by order of rows in modelMetaData.
resultsDirectory directory where output of checkModelProperties has been saved filename filename where output of checkModelProperties has been saved
- plotModelConsistency(modelResults, modelMetaData, schematicFlag, nRows, nCols, resultsDirectory, figureFileName, resultsFileName)[source]¶
plots stoichoiometric and flux consistency figures, given a modelResults structure or by loading the modelResults structure from a specified location
- INPUT
modelResults output of checkModelProperties.m modelMetaData Cell array, where each row is metadata for one model
with five columns: species, modelID, fileName, PMID, doi.
schematicFlag top corner plot illustrating the different colours nRows number of rows in the subplot nCols number of rows in the subplot (nRows*nCols >= length(modelResults)
- OPTIONAL INPUT
- resultsDirectory directory where output of checkModelProperties.m has been saved
same directory where the figure will be saved
figureFileName filename of the figure (without the directory) resultsFileName filename where output of checkModelProperties.m has been saved