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sbmlinfo

Creates dictionary of information for given model.

The model dictionary can be used for rendering the HTML report. The information can be serialized to JSON for later rendering in web app.

SBMLDocumentInfo 

SBMLDocumentInfo(doc)

Class for collecting information in JSON on an SBMLDocument to create reports.

A single document can contain multiple models or be a hierarchical model (comp package).

Initialize SBMLDocumentInfo.

from_sbml staticmethod 

from_sbml(source)

Read model info from SBML.

to_json 

to_json(strip=True, indent=2)

Serialize to JSON representation.

create_info 

create_info()

Create information dictionary for report rendering.

model_dict 

model_dict(model)

Create information for a given model.

add_compartment_links(compartments, species, reactions)

Add species and reaction links to compartment.

add_species_links(species, reactions)

Add reaction links to species.

sbase_dict classmethod 

sbase_dict(sbase, include_sbo_cvterm=True)

Info dictionary for SBase.

:param sbase: SBase instance for which info dictionary is to be created :param include_sbo_cvterm: whether the returned cvterms synthesize a BQB_IS entry for the sboTerm, for a reader which wants the sboTerm surfaced alongside the real annotations, such as the sbml4humans report. sbmlutils.parser reads the real CVTerms only, since it builds a Model which is written back out, and the sboTerm is already carried by the sboTerm attribute. :return info dictionary for item

sbaseref_dict 

sbaseref_dict(sbaseref)

Info dictionary for SBaseRef.

:param sbaseref: SBaseRef instance for which information dictionary is created :return: information dictionary for SBaseRef

cvterms classmethod 

cvterms(sbase, include_sbo_cvterm=True)

Parse CVTerms information.

:param sbase: SBase instance :param include_sbo_cvterm: whether a BQB_IS entry is synthesized for the sboTerm when it is not already among the real CVTerms, see sbase_dict

model_history classmethod 

model_history(sbase)

Parse model history information.

:return

document 

document(doc)

Info for SBMLDocument.

:param doc: SBMLDocument :return: information dictionary for SBMLDocument

model 

model(model)

Info for SBML Model.

:param model: Model :return: information dictionary for Model

function_definitions 

function_definitions(model)

Information dictionaries for FunctionDefinitions.

:return: list of info dictionaries for FunctionDefinitions

unit_definitions 

unit_definitions(model)

Information for UnitDefinitions.

:return: list of info dictionaries for UnitDefinitions

compartments 

compartments(model, assignments)

Information for Compartments.

:return: list of info dictionaries for Compartments

species 

species(model, assignments)

Information for Species.

:return: list of info dictionaries for Species

parameters 

parameters(model, assignments)

Information for SBML Parameters.

:return: list of info dictionaries for Reactions

initial_assignments 

initial_assignments(model)

Information for InitialAssignments.

:return: list of info dictionaries for InitialAssignments

rules 

rules(model)

Information for Rules.

:return: list of info dictionaries for Rules

constraints 

constraints(model)

Information for Constraints.

:return: list of info dictionaries for Constraints

reactions 

reactions(model)

Information dictionaries for ListOfReactions.

:return: list of info dictionaries for Reactions

-- take a look at local parameter once

events 

events(model)

Information dictionaries for Events.

:return: list of info dictionaries for Events

model_definitions 

model_definitions()

Information for comp:ModelDefinitions.

:return: list of info dictionaries for comp:ModelDefinitions

submodels 

submodels(model)

Information dictionaries for comp:Submodels.

:return: list of info dictionaries for comp:Submodels

ports 

ports(model)

Information for comp:Ports.

:return: list of info dictionaries for comp:Ports

gene_products 

gene_products(model)

Information dictionaries for GeneProducts.

:return: list of info dictionaries for Reactions

objectives 

objectives(model)

Information dictionaries for Objectives.

:return: list of info dictionaries for Objectives

clean_empty 

clean_empty(d)

Remove empty fields from JSON.

Reducing to core information.