rplibs

rpLibs, contains:

• rpSBML
• inchikeyMIRIAM
• rpPathway, rpReaction, rpCompound (inheritance from chemlite)

rpSBML

Defines an enriched SBML structure with additional fields relative to RetroPath2 objects.

Merging

rpSBML class allows the merging between two rpSBML objects. This method is using to integrate an heterologu pathway within a model.

Compartments

The compartment of the pathway to each compartment of the model. The comparison is done by ID, name or MIRIAM annotations. If a model compartment matches, then we rename the compartment of each species of the pathway to the name of the model matched compartment. Otherwise, the pathway compartment is added to the model.

inchikeyMIRIAM

Uses the rrCache to parse an SBML file to find all the chemical species, and try to recover the inchikey and add it to the MIRIAM annotation.

Statisticis

To print statistics on pathways, type:

python -m rplibs.stats --pathways <Pathway_1> <Pathway_2>


# Installation Guide

## Overview

`rplibs` depends on `cobra`, which requires `python-libsbml`.  
On Apple Silicon (`arm64`) macOS, `python-libsbml` is not available as a native Conda package.

Therefore, installation must be done using an **Intel (`osx-64`) Conda environment under Rosetta**.

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## General case
```bash
conda install -c conda-forge rplibs

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Apple Silicon macOS (M1/M2/M3)

1. Install Rosetta 2

softwareupdate --install-rosetta --agree-to-license

2. Install rpLibs

CONDA_SUBDIR=osx-64 conda install -c conda-forge rplibs

Or with mamba:

CONDA_SUBDIR=osx-64 mamba install -c conda-forge rplibs

3. Persist platform setting

conda config --env --set subdir osx-64

5. Verify installation

python -c "import rplibs; print('rplibs installed successfully')"
python -c "import cobra; print(cobra.__version__)"

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Troubleshooting

Solver fails on Apple Silicon

Make sure you are using:

CONDA_SUBDIR=osx-64

Wrong architecture environment

Check:

conda config --show subdir

Expected output:

subdir: osx-64

Test

python -m pytest tests

## Authors

* **Joan Hérisson**
* **Melchior du Lac**

## Acknowledgments

* Thomas Duigou


## Licence
rplibs is released under the MIT licence. See the LICENCE file for details.