MATLAB vs Python

RAVEN ships as a MATLAB toolbox and as the Python package raven-toolbox. This page is generated from the source of both toolboxes at build time. Pairs are found automatically where the names match, completed from a curated list where they do not, and marked with a cobrapy badge where cobrapy covers the function instead of raven-toolbox. Every name is verified to exist.

Paired functions

130 RAVEN functions listed: 53 matched automatically, 49 from a curated list, 28 covered by cobrapy instead of raven-toolbox.

RAVEN (MATLAB)	raven-toolbox (Python)	Summary
addExchangeRxns	cobra.Model.add_boundary cobrapy	Add exchange reactions for some metabolites.
addGenesRaven	cobra.Reaction.gene_reaction_rule cobrapy	Add genes to a model.
addIdentifierPrefix	cobra.io.read_sbml_model cobrapy	Add identifier prefixes required by SBML.
addMets	cobra.Metabolite cobrapy	Add metabolites to a model.
addRxns	add_reactions_from_equations	Add reactions to a model.
addRxnsGenesMets	add_reactions_from_model	Copy reactions from a source model into another model.
addTransport	add_transport_reactions	Add transport reactions between compartments.
analyzeSampling	analyze_sampling	Compare flux change significance with expression change.
applyCondition	apply_condition	Apply a deterministic condition to a model.
assignCompartments	assign_compartments	Assign reactions to compartments by a functionality-constrained MILP.
assignSBOterms	add_sbo_terms	Assign SBO terms to metabolites and reactions.
canExchange	analyse_topology	Check which metabolites a model can produce or consume.
changeGrRules	change_gene_reaction_rules	Change multiple grRules at the same time.
changeRxns	change_reaction_equations	Modify the equations of reactions in a model.
checkModelStruct	check_model	Perform a number of checks to ensure a model structure is ok.
checkProduction	analyse_topology	Check which metabolites can be produced from a model.
checkTasks	check_tasks	Perform a set of simulations as defined in a task file.
closeModel	close_model	Add boundary metabolites and their exchange reactions.
compareFluxes	compare_fluxes	Find the most significant flux changes between two conditions.
compareMultipleModels	compare_models	Compare two or more condition-specific models.
constructEquations	cobra.Reaction.build_reaction_string cobrapy	Construct equation strings for reactions.
contractModel	remove_duplicate_reactions	Contract a model by grouping all identical reactions.
convertToIrrev	convert_to_irreversible	Convert a model to irreversible form.
copyToComps	copy_to_compartment	Copy reactions to new compartment(s).
curateModelFromTables	batch_curate_from_tsv	Curate or add mets, rxns and genes from tables.
deleteUnusedGenes	remove_genes	Delete all genes not associated to any reaction.
diffModels	diff_models	Report the semantic differences between two models.
downloadGenomeData	download_genome_data	Download genome annotation files from NCBI.
expandModel	expand_model	Expand reactions that use several gene associations.
exportForGit	export_for_git	Export a model for a Git-maintained model repository.
exportModel	cobra.io.write_sbml_model cobrapy	Export a constraint-based model to an SBML file (L3V1 FBCv2).
exportToExcelFormat	export_to_excel	Export a model to the Microsoft Excel model format.
fillGaps	connect_blocked_reactions	Use template model(s) to fill gaps in a model.
findDuplicateRxns	find_duplicate_reactions	Find reactions that share identical stoichiometry.
findGeneDeletions	cobra.flux_analysis.single_gene_deletion cobrapy	Delete genes and track the resulting fluxes.
findLeakMetabolite	find_leak_metabolite	Find a metabolite that can be freely made or consumed.
fitParameters	fit_parameters	Fit stoichiometric parameters such as maintenance ATP to measured data.
fitTasks	fill_tasks	Fill gaps in a model so it can perform a list of tasks.
FSEOF	fseof	Flux Scanning based on Enforced Objective Flux.
ftINIT	ftinit	Generate a model using the ftINIT algorithm.
ftINITFillGaps	fill_tasks	Variant of fillGaps specially adapted to speed up generation of ftINIT models.
ftINITInternalAlg	run_ftinit	This function runs the MILP for a step in ftINIT.
gapFillFastCore	fill_gaps_fast_lp	L1-norm LP subroutine for fastGapFill.
gapFillFastLP	fill_gaps_fast_lp	LP-based gap-filling (fastGapFill / swiftGapFill).
gapFillMILP	fill_gaps_milp	Objective-based gap-filling via a global growth-floor MILP.
gapFillSwiftCore	fill_gaps_fast_lp	SWIFTCORE LP subroutine for swiftGapFill.
gapFillTopological	analyse_topology	BFS metabolite-producibility pre-screening.
gapReport	gap_report	Perform a gap analysis and summarize the results.
generateNewIds	generate_new_ids	Generate a list of new metabolite or reaction ids.
getAllowedBounds	cobra.flux_analysis.flux_variability_analysis cobrapy	Return the minimal and maximal fluxes through reactions.
getAllRxnsFromGenes	cobra.Gene.reactions cobrapy	Find all reactions annotated by the genes of a set.
getAllSubGraphs	analyse_topology	Get all metabolic subgraphs in a model.
getBiomassFractions	sum_biomass	Compute mass fraction per biomass component.
getBlast	run_blast	Bidirectional BLAST between an organism and template organisms.
getDiamond	run_diamond	Bidirectional BLAST with DIAMOND against template organisms.
getElementalBalance	get_elemental_balance	Check whether the reactions of a model are balanced.
getEssentialRxns	find_task_essential_reactions	Calculate the essential reactions for a solvable model.
getExchangeRxns	cobra.Model.exchanges cobrapy	Retrieve the exchange reactions from a model.
getFluxZ	get_flux_z	Calculate Z scores between two sets of random flux distributions.
getGeneData	get_gene_data	Build a gene-mapping table from NCBI genome annotation files.
getGenesFromGrRules	cobra.core.gene.GPR cobrapy	Extract gene list and rxnGeneMat from grRules array.
getIndexes	cobra.DictList.get_by_id cobrapy	Retrieve the indexes for a list of reactions or metabolites.
getINITSteps	get_init_steps	Define the steps used as input to ftINIT.
getKEGGModelForOrganism	get_kegg_model_for_organism	Reconstruct a model from KEGG protein homology.
getMinimalMedium	cobra.medium.minimal_medium cobrapy	Find the minimal set of uptake reactions for growth.
getMinNrFluxes	get_min_nr_fluxes	Find the minimal set of fluxes that satisfy the model.
getModelFromHomology	get_model_from_homology	Construct a new model from existing models and homology.
getModelFromKEGG	build_reference_model	Load the global KEGG model.
getPhylDist	phyl_dist	Load the pre-built KEGG phylogenetic distance matrix.
getRxnsInComp	cobra.Reaction.compartments cobrapy	Get the reactions in a specified compartment.
getUniProtScores	load_uniprot	Fetch curated subcellular locations from UniProt -> gene scoring structure.
groupRxnScores	group_rxn_scores	This function sums up the reaction scores for all reactions that were merged
grRuleToDNF	gpr_to_dnf	Convert a grRule to disjunctive normal form.
grRuleToString	cobra.core.gene.GPR cobrapy	Render a grRule syntax tree back to a string.
guessComposition	guess_composition	Guess the composition of metabolites without one.
haveFlux	analyse_topology	Check which reactions can carry a flux.
hitsFromSuppOrth	hits_from_supporth	Read SuppOrth consensus orthologs into a blastStructure.
importModel	cobra.io.read_sbml_model cobrapy	Import a constraint-based model from an SBML file.
isDnfGrRule	is_dnf	Test whether a grRule is in disjunctive normal form.
loadDeltaGCSV	load_delta_g_csv	Load metDeltaG and rxnDeltaG from CSV files.
makeFakeBlastStructure	make_ortholog_hits	Make a fake blastStructure from an ortholog list.
mergeCompartments	merge_compartments	Merge all compartments in a model.
mergeLinear	merge_linear	Simplifies a model by merging rxns with linear dependencies. There are two
mergeModels	merge_models	Merge models into one model structure.
modelSummary	cobra.Model.summary cobrapy	Print a concise overview of a RAVEN model and its flux state.
optimizeProb	cobra.Model.solver cobrapy	Optimize an LP or MILP formulated in COBRA terms.
parseGrRule	cobra.core.gene.GPR cobrapy	Parse a grRule into a syntax tree.
parseHPA	parse_hpa	Parse a database dump of the Human Protein Atlas (HPA).
parseHPArna	parse_hpa_rna	Parse a dump of Human Protein Atlas (HPA) RNA-Seq data.
parseScores	combine_scores	Parse predictor / database output into a gene scoring structure (GSS).
parseTaskList	parse_task_list	Parse a task list file.
predictLocalization	predict_localization	Assign reactions to compartments using localization predictors.
prepINITModel	prep_init_model	Precompute omics-independent data for ftINIT.
printModelStats	cobra.Model cobrapy	Print some statistics about a model to the screen.
processProteinFastaFile	process_protein_fasta_file	Rename protein FASTA headers using a gene mapping table.
randomSampling	random_sampling	Sample the flux solution space (entry point for all samplers).
readKEGGTable	read_kegg_table	Read a gzipped KEGG relational table into a table with
readYAMLmodel	read_yaml_model	Read a model structure from a YAML file.
removeGenes	remove_genes	Delete a set of genes from a model.
removeIdentifierPrefix	cobra.io.write_sbml_model cobrapy	Remove SBML-required identifier prefixes.
removeLowScoreGenes	remove_low_score_genes	Remove low-scoring genes from model.
removeMets	remove_metabolites	Delete a set of metabolites from a model.
removeReactions	cobra.Model.remove_reactions cobrapy	Delete a set of reactions from a model.
renameModelGenes	rename_model_genes	Replace gene identifiers in a RAVEN model.
replaceMets	replace_metabolite	Replace a metabolite with another already in the model.
reporterMetabolites	reporter_metabolites	Identify metabolites around which transcriptional changes occur.
rescaleModelForINIT	rescale_for_init	Rescale a model to avoid large stoichiometric differences.
runPhenotypePhasePlane	cobra.flux_analysis.production_envelope cobrapy	Run phenotype phase plane analysis and plot the results.
runProductionEnvelope	cobra.flux_analysis.production_envelope cobrapy	Calculate the byproduct secretion envelope.
runSuppOrth	run_supporth	Run SuppOrth on an organism and template proteomes.
sampleACHR	random_sampling	Artificially Centered Hit-and-Run flux sampling.
sampleCHRR	random_sampling	Coordinate Hit-and-Run with Rounding flux sampling.
saveDeltaGCSV	save_delta_g_csv	Save metDeltaG and rxnDeltaG to CSV files.
scaleBiomassFraction	scale_biomass	Rescale a biomass component to a target value.
scaleBiomassPseudoreaction	rescale_pseudoreaction	Rescale a biomass component pseudoreaction.
scoreModel	score_reactions_from_genes	Score reactions and genes in a model with complex gene rules.
setExchangeBounds	set_exchange_bounds	Define exchange flux bounds for a set of metabolites.
setExchangeBounds	cobra.Model.medium cobrapy	Define exchange flux bounds for a set of metabolites.
setGAM	set_gam	Set the growth-associated maintenance (GAM) coefficient.
setParam	cobra.Reaction.bounds cobrapy	Set parameters for reactions.
setRavenSolver	cobra.Configuration cobrapy	Set the solver for RAVEN.
simplifyModel	simplify_model	Simplify a model by deleting reactions and metabolites.
solveLP	cobra.Model.optimize cobrapy	Solve a linear programming problem.
sortIdentifiers	sort_identifiers	Sort model identifiers alphabetically.
sortModel	sort_identifiers	Standardize a model's internal ordering: by default orients
standardizeGrRules	gpr_to_dnf	Standardize gene-reaction rules in a model.
traceFluxPath	trace_flux_path	Find the highest-flux-fraction path between two reactions.
walkFluxes	walk_fluxes	Interactively navigate a flux distribution reaction by reaction.
writeFasta	write_fasta	Write sequences to a FASTA file.
writeYAMLmodel	write_yaml_model	Write a model to a yaml file in the standard cobra-format

Deliberately not ported

RAVEN (MATLAB)	Why not
buildEquation	Internal helper for building an equation string from raw metabolites and coefficients; the equivalent is inside add_reactions_from_equations and cobra.Reaction.build_reaction_string, both already mapped.
buildGlobalGPR	Internal to assembling the global KEGG reference model; the equivalent is inside build_reference_model, already mapped from getModelFromKEGG.
buildGlobalKEGGModel	Internal to assembling the global KEGG reference model; the equivalent is inside build_reference_model, already mapped from getModelFromKEGG.
checkFileExistence	A generic file-existence check; Python's own pathlib/os.path cover this directly.
checkSolution	Checks whether a Mosek solution is feasible and optimal; Mosek is not a solver either toolbox supports through this site's documented setup.
cleanSheet	Internal to the old Excel-import pipeline (importExcelModel), which RAVEN 3 removed; raven-toolbox never had an Excel reader either.
constructS	Internal helper for building a stoichiometric matrix from equation strings; the equivalent is inside add_reactions_from_equations, already mapped from addRxns.
convertCharArray	MATLAB char-array/string-array normalisation; Python has one string type.
defaultCompartmentMap	raven-toolbox exposes the same table as a module-level constant, localization.DEFAULT_COMPARTMENT_MAP, not a function.
deprecationWarning	Emits RAVEN's own one-time deprecated-function notice; Python's warnings.warn covers this directly.
editMiriam	cobra's .annotation is already a {namespace: id} dictionary -- read and write it directly.
extractMiriam	cobra's .annotation is already a {namespace: id} dictionary -- read and write it directly.
findPotentialErrors	Detects grRules that are not in disjunctive normal form. cobrapy's own GPR class represents a parsed rule directly, so raven-toolbox has no equivalent "detect an invalid legacy string" step.
getINITModel	The original tINIT implementation. RAVEN keeps it for models already built with it; raven-toolbox, a new implementation with no such installed base, carries ftINIT alone.
getTransportRxns	Classifies which reactions move a metabolite between compartments. raven-toolbox has no equivalent classifier yet.
keggDataVersion	Internal to assembling the global KEGG reference model; the equivalent is inside build_reference_model, already mapped from getModelFromKEGG.
legacyMethodNotice	Emits RAVEN's own one-time legacy-method notice; Python's warnings.warn covers this directly.
parallelWorkersRAVEN	Returns a parfor worker count for the Parallel Computing Toolbox; raven-toolbox's parallelism is configured directly through cobra.Configuration().processes.
parseFormulas	Internal formula-to-elemental-composition parser; the equivalent is inside get_elemental_balance, not exposed separately.
parseRAVENargs	Resolves RAVEN's positional-or-named optional arguments; Python functions take native keyword arguments directly.
parseRxnEqu	Internal helper for extracting metabolite names from equation strings; the equivalent is inside add_reactions_from_equations, already mapped from addRxns.
parseYAML	A generic YAML parser for condition files; Python's standard YAML libraries (PyYAML) cover this directly, with no toolbox wrapper needed.
permuteModel	Reorders the parallel arrays of a RAVEN MATLAB struct; a cobra.Model has no comparable field-order concept to reorder.
printFluxes	No equivalent yet. Use cobra's model.summary(), or the solution's fluxes Series directly.
printOrange	Prints coloured text to the MATLAB Command Window; not applicable outside the MATLAB GUI.
ravenCobraWrapper	Not needed: a raven-toolbox model is a cobra.Model already, so there is nothing to convert.
ravenList	Formats a header and item list for a MATLAB warning()/error() call; Python's own string formatting covers this directly.
ravenModelFields	A registry of RAVEN's own MATLAB struct fields, used internally by permuteModel and removeReactions; a cobra.Model has no comparable struct-field concept.
readFasta	raven-toolbox has no public FASTA reader; the closest relative is write_fasta (already auto-matched from writeFasta), the read side stays internal to the functions that need it.
removeBadRxns	Iteratively removes reactions that let the model make or consume something from nothing. raven-toolbox has no equivalent yet; see find_leak_metabolite (mapped from makeSomething/consumeSomething) for finding the same kind of issue.
reverseRxns	Negates a reaction's stoichiometry and bounds to reverse its direction. Simple enough to do directly against a cobra.Reaction's own API; no dedicated function exists.
runDynamicFBA	Dynamic FBA is covered by maintained Python packages (dfba, reframed, mewpy).
runINIT	The original tINIT implementation. RAVEN keeps it for models already built with it; raven-toolbox, a new implementation with no such installed base, carries ftINIT alone.
runRAVENtests	Runs RAVEN's own MATLAB unit test suite. raven-toolbox's tests run through pytest, the standard Python testing workflow, not a toolbox function.
runRobustnessAnalysis	Robustness analysis for one reaction against an objective. raven-toolbox has no equivalent yet.
runSimpleOptKnock	A simple, brute-force OptKnock implementation. raven-toolbox has no equivalent; strain-design algorithms like OptKnock are explicitly out of scope for both toolboxes, see RAVEN 3 and raven-toolbox.
sampleChebyshevCenter	Internal rounding-step subroutine of RAVEN's own sampleCHRR; raven-toolbox's random_sampling (already mapped from sampleACHR/sampleCHRR) handles rounding and warmup internally without exposing separate functions.
sampleMaxVolEllipse	Internal rounding-step subroutine of RAVEN's own sampleCHRR; raven-toolbox's random_sampling (already mapped from sampleACHR/sampleCHRR) handles rounding and warmup internally without exposing separate functions.
sampleWarmupPoints	Internal warmup-point generator for RAVEN's own sampleACHR; raven-toolbox's random_sampling (already mapped from sampleACHR/sampleCHRR) handles warmup internally.
setRavenProgress	Sets a preference for how RAVEN reports progress in the MATLAB GUI or console; no equivalent concept in Python.
splitProbForConditioning	Improves LP numerical conditioning by splitting wide-ratio columns before solving; cobrapy and the solvers it wraps (through optlang) handle numerical scaling internally, with no equivalent public option.
standardizeModelFieldOrder	Orders the fields of a RAVEN MATLAB struct to a canonical layout; a cobra.Model has no comparable field-order concept.
writeExcel	Internal low-level .xlsx writer; the equivalent is inside export_to_excel, already mapped from exportToExcelFormat.