psamm.datasource.sbml
– SBML model parser¶
Parser for SBML model files.
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class
psamm.datasource.sbml.
CompartmentEntry
(reader, root, filemark=None)¶ Compartment entry in the SBML file
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properties
¶ All compartment properties as a dict.
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class
psamm.datasource.sbml.
FluxBoundEntry
(reader, namespace, root)¶ Flux bound defined with FBC
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class
psamm.datasource.sbml.
ObjectiveEntry
(reader, namespace, root)¶ Flux objective defined with FBC
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exception
psamm.datasource.sbml.
ParseError
¶ Error parsing SBML file
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class
psamm.datasource.sbml.
ReactionEntry
(reader, root, filemark=None)¶ Reaction entry in SBML file
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id
¶ Reaction ID
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kinetic_law_reaction_parameters
¶ Iterator over the values of kinetic law reaction parameters
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name
¶ Reaction name
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properties
¶ All reaction properties as a dict
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reversible
¶ Whether the reaction is reversible
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class
psamm.datasource.sbml.
SBMLReader
(file, strict=False, ignore_boundary=False, context=None)¶ 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
isTrue
, the species that are marked as boundary conditions will simply be dropped from the species list and from the reaction equations.-
compartments
¶ Iterator over
CompartmentEntry
entries.
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flux_bounds
¶ Iterator over
FluxBoundEntry
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get_compartment
(compartment_id)¶ Return
CompartmentEntry
corresponding to id.
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get_objective
(objective_id)¶ Return
ObjectiveEntry
corresponding to objective_id
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get_reaction
(reaction_id)¶ Return
ReactionEntry
corresponding to reaction_id
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get_species
(species_id)¶ Return
SpeciesEntry
corresponding to species_id
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id
¶ Model ID
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name
¶ Model name
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objectives
¶ Iterator over
ObjectiveEntry
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reactions
¶ Iterator over
ReactionEntries
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species
¶ Iterator over
SpeciesEntries
This will not yield boundary condition species if those are ignored.
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class
psamm.datasource.sbml.
SBMLWriter
(cobra_flux_bounds=False)¶ Writer of SBML files
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write_model
(file, model, pretty=False)¶ Write a given model to file
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class
psamm.datasource.sbml.
SpeciesEntry
(reader, root, filemark=None)¶ Species entry in the SBML file
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boundary
¶ Whether this compound is a boundary condition
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charge
¶ Species charge
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compartment
¶ Species compartment
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formula
¶ Species formula
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name
¶ Species name
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properties
¶ All species properties as a dict
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