Project overview

  ┌── __init__.py
  ├── model.py
  ├── protein.py
  ├── reaction.py
  ├── io.py
  ├── flux_analysis.py
  │ ┌── __init__.py
  │ ├── relaxation.py
  │ ├── pytfa.py
  ├─┴ integration
  │ ┌── __init__.py
  │ ├── experimental.py
  │ ├── molecular_weights.py
  │ ├── relaxation.py
  ├─┴ experimental
┌─┴ geckopy

geckopy/model.py

The Model class, which is derived from cobra.core.model.

• All methods that directly mention Reaction were overwritten. This would be also required if any component of cobrapy’s Model is derived in geckopy.

• Proteins were added to the population of the model.

• Pool constraint methods.

geckopy/protein.py

The Protein class is both represented as a constraint (the metabolite) and as a variable (the exchange pseudorreaction). Thus, it contains methods both from cobrapy’s Metabolite and Reaction.

geckopy/reaction.py

The class Reaction merely extends cobrapy’s Reaction to point to its proteins.

geckopy/io.py

Serialization and deserialization to SBML (adapting cobrapy:autoapi/cobra/io/sbml/index).

geckopy/flux_analysis.py

Cobrapy flux analysis functionality can generally be used for geckopy models but some care must be taken to make fair comparisons of flux variability analysis, as pointed by Domenzain et al., 2021. This submodule includes that and some utility functions to inspect and process the protein solution.

geckopy/integration/

Integration layer for pytfa. It includes relaxation algorithms for the integration of metabolomics with proteins.

geckopy/experimental/

Functionality for integration of experimental data. It includes the relaxation algorithms for proteomics experimental data and utility functions for the annotation of molecular weights from Uniprot accesion numbers.