Chemical reaction network theory analysis #117

Chemical reaction network theory analysis

Repository: RuleWorld/PyBioNetGen

Title: Add chemical reaction network theory analysis for generated BNGL networks

Motivation

BNGsim already computes conservation laws from the stoichiometry matrix, so conservation-law detection itself is not missing.

However, generated BioNetGen networks could support a broader set of structural chemical-reaction-network analyses, including:

• reaction complexes;
• linkage classes;
• strong linkage classes;
• weak reversibility;
• stoichiometric rank;
• deficiency;
• terminal strong linkage classes;
• network decomposition.

These properties can reveal qualitative model structure without simulation and are useful for understanding multistability, complex balancing, and network organization.

Proposed API

analysis = model.crnt()

analysis.stoichiometric_rank
analysis.deficiency
analysis.linkage_classes
analysis.weakly_reversible
analysis.conservation_laws

For rule-based models, this analysis would apply to the finite generated network and should state that explicitly.

Implementation

This could reuse:

• BioNetGen's generated species/reactions;
• BNGsim's stoichiometry representation where available;
• existing conservation-law information rather than recomputing it separately.

The first version does not need to implement every theorem from CRNT. Exposing a reliable structural representation and the common network invariants would already be useful.