template

Template()

This class reformats metabolites into compounds and reactions into an amenable format for templates:

from modelseedpy.core import Template
bioplate = Template()

convert_template_compound()

A compound is reformatted for addition to a template:

met = bioplate.convert_template_compound(cpdid, index)

  • cpdid cobra.core.model.Metabolite: The compound that will be formatted for addition to a complate.

  • index int: The index of a respective compound, which will be the suffix of the reformatted compound ID.

returns met cobra.core.model.Metabolite: The reformatted compound for addition to a model template.

convert_template_reaction()

A reaction is reformatted for addition to a template:

rxn = bioplate.convert_template_reaction(model, rxnid, index, for_gapfilling=True)

  • model cobra.core.model.Model: The COBRA model that contains the reactions which are to be reformatted for the template.

  • rxnid str: The ID for the reaction that will be reformatted.

  • index int: The index of a respective reactuin, which will be the suffix of the reformatted reaction ID and the constituent metabolite IDs.

  • for_gapfilling bool: specifies whether the reaction direction for gapfilling or not gapfilling is used in the formatted reaction.

returns rxn cobra.core.model.Reaction: The reformatted reaction for addition to a model template.

Accessible content

The BilevelPkg class contains a couple of accessible content that may be useful for subsequent post-processing or troubleshooting:

  • compounds, compcompounds, & reactions DictList: The assemblies of base compounds, compartmentalized compounds, and reactions that were reformatted by the functions.