nVmaxBuilder documentation
========================

**VmaxBuilder** is a modular Python toolbox for converting expression and model inputs
into condition-specific reaction capacity estimates.

Pipeline overview
-----------------

The pipeline is structured as modular stages:

1. Expression preprocessing.
2. Model preprocessing.
3. Protein abundance estimation.
4. Kcat estimation and resolution.
5. Allocation and Vmax calculation.

Start here
----------

- New users: :doc:`getting_started`
- Installation options: :doc:`installation`
- Worked examples: :doc:`examples`
- Practical scenarios: :doc:`use_cases`
- API details: :doc:`VmaxBuilder (API)`

.. note::

   This project is under active development.

.. toctree::
   :maxdepth: 2
   :caption: Contents

   getting_started
   installation
   examples
   use_cases
   usage
   VmaxBuilder (API)