psamm.datasource.sbml – SBML model parser

Parser for SBML model files

class psamm.datasource.sbml.FluxBoundEntry(reader, namespace, root)

Flux bound defined with FBC

class psamm.datasource.sbml.ObjectiveEntry(reader, namespace, root)

Flux objective defined with FBC

exception psamm.datasource.sbml.ParseError

Error parsing SBML file

class psamm.datasource.sbml.ReactionEntry(reader, root)

Reaction entry in SBML file

equation

Reaction equation is a Reaction object

id

Reaction ID

kinetic_law_reaction_parameters

Iterator over the values of kinetic law reaction parameters

name

Reaction name

properties

All reaction properties as a dict

reversible

Whether the reaction is reversible

class psamm.datasource.sbml.SBMLReader(file, strict=False, ignore_boundary=False)

Reader of SBML model files

The constructor takes a file-like object which will be parsed as XML and then as SBML according to the specification. If the strict parameter is set to False, the parser will revert to a more lenient parsing which is required for many older models. This tries to mimic the inconsistencies employed by COBRA when parsing models.

If ignore_boundary is True, the species that are marked as boundary conditions will simply be dropped from the species list and from the reaction equations.

flux_bounds

Iterator over FluxBoundEntry

get_objective(objective_id)

Return ObjectiveEntry corresponding to objective_id

get_reaction(reaction_id)

Return ReactionEntry corresponding to reaction_id

get_species(species_id)

Return SpeciesEntry corresponding to species_id

id

Model ID

name

Model name

objectives

Iterator over ObjectiveEntry

reactions

Iterator over ReactionEntries

species

Iterator over SpeciesEntries

This will not yield boundary condition species if those are ignored.

class psamm.datasource.sbml.SBMLWriter

Writer of SBML files

write_model(file, model)

Write a given model to file

class psamm.datasource.sbml.SpeciesEntry(reader, root)

Species entry in the SBML file

boundary

Whether this compound is a boundary condition

charge

Species charge

compartment

Species compartment

formula

Species formula

name

Species name

properties

All species properties as a dict