Package semanticSBML :: Module sbmlmisc

Module sbmlmisc

Functions

get_elementtype2database()
i think this functions should be replaced with the appropriate functions in the annotation module

source code

setintersection(set1, set2)
TODO replace this funciton with python native function

source code

get_element_by_id(model, id)
get element from libsbml model, no matter which type

source code

get_element_by_annotation(model, anno)
get element from libsbml model, by annotation

source code

get_annotation_for_id(id)

source code

unify_reaction_scheme_delimiter(string)

source code

parse_reaction_scheme(string)
Extracts the list of reactants and products and stoichimetries from a reaction string

source code

make_valid_xml_id(id)
eliminate forbidden characters from designated xml id

source code

reassign_annotations(model)
reassigns all the annotations in the model (to update models to new annotation syntax)

source code

make_meta_ids(model)
Assign id to metaid if metaid is not set

source code

bool

has_celld_annotations(document)
does the document contain cell designer annotations

source code

libsbml.Model

remove_all_celld_annotations(document)
Remove all celldesigner annotations from model

source code

Iterator

get_participants(reaction)
get iterator for the reaction participants (reactants + products)

source code

is_enzyme(species)

source code

get_enzyme_for_reaction(reaction, create=False)

source code

Variables

[hide private]

error = '%s\n\nsemanticSBML requires libSBML version 3.4 and t...

__package__ = 'semanticSBML'

Imports: annotate, libSBAnnotation, xmlobject, re, libsbml

Function Details

[hide private]

setintersection(set1, set2)

source code


TODO replace this funciton with python native function

this is what the python doc says:

S.intersection(T)        S & T                    new set with elements
                                                  common to S and T

make_meta_ids(model)

source code

Assign id to metaid if metaid is not set

Parameters:

model (libsbml.Model)

remove_all_celld_annotations(document)

source code

Remove all celldesigner annotations from model

Parameters:

document (libsbml.Model or libsbml do)

Returns: libsbml.Model

get_participants(reaction)

source code

get iterator for the reaction participants (reactants + products)

Parameters:

reaction (libsbml.Reaction)

Returns: Iterator

Variables Details

[hide private]

error

Value:

'''%s

semanticSBML requires libSBML version 3.4 and the libSBML Python bindi
ngs.
Get libSBML from:

    https://sourceforge.net/projects/sbml/files/libsbml/

...