SBML2Kintecus

Converts SBML Level 2 (all versions) and Level 3 core models to Kintecus MODEL.DAT / SPECIES.DAT / PARM.DAT. Supports mass-action and complex kinetic laws (Michaelis–Menten, Arrhenius, Hill) via Kintecus USER syntax. Python 3.9+, no dependencies.

Output files

File	Description
MODEL.DAT	Reaction mechanism (rate constant + equation per line)
SPECIES.DAT	Species initial conditions
PARM.DAT	Simulation parameters (temperature, time, accuracy, …)

Usage

# All defaults — writes MODEL.DAT, SPECIES.DAT, PARM.DAT in the current directory
python sbml2kintecus.py model.xml

# Explicit output paths
python sbml2kintecus.py model.xml -o MODEL.DAT -s SPECIES.DAT -p PARM.DAT

# Verbose warnings to stderr
python sbml2kintecus.py model.xml -v

Supported SBML L2 features

• Integer and fractional stoichiometry
• Reversible reactions split into separate forward / reverse lines
• stoichiometryMath referencing global parameters
• Rate constants from local kineticLaw/listOfParameters or the model-level listOfParameters (used when kinetic laws carry no local params)
• Outer compartment × rate MathML wrapping automatically stripped
• Multi-compartment models: species renamed speciesName{compartmentID}
• SBML <notes> section preserved as #-prefixed comments in MODEL.DAT
• All output files use Windows CRLF line endings (required by Kintecus)

Examples

Model	Source
Field-Noyes Oregonator (BZ reaction)	examples/BIOMD0000000040_oreg.xml
Legewie 2006 Apoptosis (non-competitive)	examples/BIOMD0000000103_url.xml

Pre-converted Kintecus files are in examples/oregonator/ and examples/apoptosis/.

Requirements

Python 3.9+ — standard library only (xml.etree.ElementTree, argparse, pathlib). No third-party packages required.