Format conversion¶

MATLAB functions in RAVEN/conversion of the RAVEN toolbox. Help text is collected from the source of the tracked branch.

Functions¶

Function	Summary
`addIdentifierPrefix`	Add identifier prefixes required by SBML.
`ravenCobraWrapper`	Convert between RAVEN and COBRA structures.
`removeIdentifierPrefix`	Remove SBML-required identifier prefixes.
`standardizeModelFieldOrder`	Order RAVEN model structure fields.

Reference¶

addIdentifierPrefix¶

Add identifier prefixes required by SBML.

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 arguments:

Name	Type	Description	Default
`model`	`struct`	model whose identifiers should be modified.	required

Name-value arguments:

Name	Type	Description	Default
`fields`	`cell`	cell array with model field names that should be checked if prefixes should be added, possible values: 'rxns', 'mets', 'comps', 'genes', 'id' (default all listed model fields will be checked).

Output arguments:

Name	Type	Description
`model`	`struct`	modified model.
`hasChanged`	`cell`	cell array with fields and prefixes that are added.

Examples:

[model, hasChanged] = addIdentifierPrefix(model, fields);

ravenCobraWrapper¶

Convert between RAVEN and COBRA structures.

This function is a bidirectional tool to convert between RAVEN and COBRA structures. It recognises a COBRA structure by checking the existence of the field 'rules', which is only found in a COBRA Toolbox structure. If the COBRA model also has a grRules field, then this will be used instead of parsing the rules field.

Input arguments:

Name	Type	Description	Default
`model`	`struct`	a RAVEN/COBRA-compatible model structure.	required

Output arguments:

Name	Type	Description
`newModel`	`struct`	a COBRA/RAVEN-compatible model structure.

Examples:

newModel = ravenCobraWrapper(model);

Notes

During the RAVEN -> COBRA -> RAVEN conversion cycle the following fields are lost: annotation, compOutside, compMiriams, rxnComps, geneComps, unconstrained. Boundary metabolites are lost, because the COBRA structure does not involve boundary metabolites, so they are removed using simplifyModel before RAVEN -> COBRA conversion. The field 'rev' is also partially lost, but during COBRA -> RAVEN conversion it is reconstructed based on lower bound reaction values.

During the COBRA -> RAVEN -> COBRA conversion cycle the following fields are lost: geneEntrezID, modelVersion, proteins.

The information about mandatory RAVEN fields was taken from the checkModelStruct function, whereas the corresponding information about COBRA fields was fetched from the verifyModel function.

removeIdentifierPrefix¶

Remove SBML-required identifier prefixes.

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 have 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 arguments:

Name	Type	Description	Default
`model`	`struct`	model whose identifiers should be modified.	required

Name-value arguments:

Name	Type	Description	Default
`fields`	`cell`	cell array with model field names from which the identifiers should be removed, possible values: 'rxns', 'mets', 'comps', 'genes', 'metNames', 'rxnNames', 'id' (default all listed model fields will be checked).
`forceRemove`	`logical`	if prefixes should be removed even if not all entries in a model field have the prefix (default false).

Output arguments:

Name	Type	Description
`model`	`struct`	modified model.
`hasChanged`	`cell`	cell array with fields and prefixes that are removed.

Examples:

model = removeIdentifierPrefix(model, fields, forceRemove);

standardizeModelFieldOrder¶

Order RAVEN model structure fields.

Orders fields of a RAVEN model structure as specified at https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-Structure

The model fields themselves are not changed, only the order is modified. For changing model fields between RAVEN and COBRA format, use ravenCobraWrapper().

Input arguments:

Name	Type	Description	Default
`model`	`struct`	model structure, either RAVEN or COBRA format.	required

Output arguments:

Name	Type	Description
`orderedModel`	`struct`	model structure with ordered fields.

Examples:

orderedModel = standardizeModelFieldOrder(model);