API reference
The API reference is generated from the docstrings of the package.
sbmlutils
The top level modules: the model definition, reading and writing, validation and the shared output.
| module |
description |
| factory |
the model definition and create_model, the entry point of the package |
| io |
reading and writing SBML |
| validation |
validation of a document against the SBML specification |
| parser |
SBML and antimony into a model definition |
| notes |
element documentation written as markdown |
| reaction_equation |
the stoichiometry of a reaction as a string |
| biomodels |
models from the BioModels database |
| cytoscape |
models rendered as a network in Cytoscape |
| console |
shared rich console |
| log |
logging of the package |
| utils |
meta ids and the frozen base class |
sbmlutils.comp
Hierarchical models with the comp package, see Model composition.
| module |
description |
| comp.comp |
ports, external model definitions and replacements |
| comp.flatten |
flattening a comp model into a single model |
sbmlutils.converters
Conversion of a model into another representation, see Converters.
sbmlutils.data
sbmlutils.fbc
Constraint based models, see Flux balance constraints.
| module |
description |
| fbc.fbc |
flux bounds and boundary conditions |
| fbc.cobra |
the bridge to cobrapy, the optional cobra extra |
sbmlutils.layout
sbmlutils.manipulation
Annotation of models, see Annotations. The qualifiers BQB, BQM and the ontology terms SBO are re-exported from pymetadata.
sbmlutils.report
The content of a model for a human reader, see Reports.