API reference#

RAVEN ships in two implementations that build the same genome-scale metabolic models with the same algorithms:

  • RAVEN: the original MATLAB toolbox, built on the COBRA Toolbox and libSBML. Functions use camelCase names.

  • raven-toolbox: the Python port, built on cobrapy. Functions use snake_case names.

The function help on these pages is extracted directly from the source of each toolbox on the branch tracked by this site, so it stays in sync with the code.

How these pages are organised#

The reference is split into two parallel trees, one per language, each organised by the toolbox's own module layout and each function shown with its signature, parameters and returns:

  • MATLAB API (RAVEN): one page per category (Reconstruction, Manipulation, Input / output, …).

  • Python API (raven-toolbox): one page per package, mirroring the same categories.

  • MATLAB vs Python: a third page pairing every function that exists in both, generated at build time from both toolboxes' sources.

Every page opens with a Functions table you can scan, followed by the full help for each function.

To move between the two implementations, use the MATLAB vs Python table, which pairs every function that exists in both (camelCase ↔ snake_case) and links to both references.

How the two compare#

The implementations are deliberately kept aligned. The main differences are in calling convention, not in what the functions compute:

RAVEN (MATLAB)

raven-toolbox (Python)

Naming

camelCase (getModelFromHomology)

snake_case (get_model_from_homology)

Returns

multiple outputs [a,b] = f(...)

one return value; objects often mutated in place

Indexing

1-based

0-based

Model object

RAVEN model struct

cobra.Model with RAVEN extensions

Note

A note on the two docstring styles raven-toolbox's docstrings are NumPy-style, so they render as structured parameter/return tables. RAVEN's MATLAB help blocks use the toolbox's own indented convention, so they render as faithful help text rather than typed tables. The content is the same; only the formatting differs.

Use the navigation to browse either tree, or start from the MATLAB vs Python table.