mseditor

MSEditorAPI

A class of static methods that offer various editing features

remove_reactions()

staticMethod Removes a list of reactions from a model:

MSEditorAPI.remove_reactions(model, rxn_id_list = [])

  • model core.core.model.Model: The model that will be edited by removing a reaction.

  • rxn_id_list list: The IDs of all reaction that will be removed from the model.

edit_reaction()

staticMethod Defines genome features from a FASTA file:

MSEditorAPI.edit_reaction(model, rxn_id, direction=None, gpr=None)

  • model core.core.model.Model: The model that will be edited by removing a reaction.

  • rxn_id str: The ID of the reaction that will be edited.

  • direction str: The “=>”, “<=”, or “<=>” reaction direction that represents thermodynamic favorability.

  • gpr str: The reaction GPR that will be set in the COBRA model.

edit_biomass_compound()

staticMethod Adds a compound to the biomass reaction, or creates a biomass reaction with the compound where a biomass reaction is not defined:

MSEditorAPI.edit_biomass_compound(model,biomass_id,cpd_id,new_coef)

  • model core.core.model.Model: The model whose biomass reaction will be edited.

  • biomass_id & cpd_id str: The IDs of the biomass reaction and the compound that will be added to the biomass reaction.

  • new_coef float: The stoichiometric coefficient of the added compound to the biomass reaction.

compute_molecular_weight()

staticMethod Returns the molecular weight of a model metabolite:

met_mw = MSEditorAPI.compute_molecular_weight(model, metabolite_id)

  • model core.core.model.Model: The model that contains the metabolite and thus the molecular formula.

  • metabolite_id str: The ID of the metabolite whose MW will be calculated.

Returns met_mw float: The MW of the metabolite.

add_custom_reaction()

staticMethod Adds a reaction to the model with the parameterized characteristics:

MSEditorAPI.add_custom_reaction(model,rxn_id,MSEquation,gpr = None)

  • model core.core.model.Model: The model that will be expanded with the reaction.

  • rxn_id str: The ID of the reaction that will be added to the model.

  • MSEquation modelseedpy.core.mseditorapi.msequation: The ModelSEED reaction object that contains both the stoichiometry and direction.

  • gpr str: The reaction GPR that will be set in the COBRA model.

add_ms_reaction()

staticMethod Adds a reaction with ModelSEED parameters to a model:

MSEditorAPI.add_ms_reaction(model, rxn_id, modelseed, compartment_equivalents = {'0':'c0', '1':'e0'}, direction = '>')

  • model core.core.model.Model: The model that will be expanded with the reaction.

  • rxn_id str: The ID of the reaction that will be added to the model.

  • modelseed ModelSEED Database: The ModelSEED Database object that will be used to acquire reaction information.

  • compartment_equivalents dict: The compartments and their indicies that are used in the reaction.

  • direction str: The “<”, “=”, or “>” direction of the reaction.

copy_model_reactions()

staticMethod Adds specified reactions from a source model to a second model:

MSEditorAPI.copy_model_reactions(model,source_model,rxn_id_list = [])

  • model core.core.model.Model: The model that will be expanded with additional reactions.

  • source_model core.core.model.Model: The model whose reactions will be added to the model.

  • rxn_id_list list: The list of reactions that may be potentially added, provided that they are in the source_model.

copy_all_model_reactions()

staticMethod Adds all new reactions from a source model to a second model:

MSEditorAPI.copy_model_reactions(model,source_model)

  • model core.core.model.Model: The model that will be expanded with all new reactions.

  • source_model core.core.model.Model: The model whose reactions will be added to the model.

MSEquation

A class that constructs and organizes reaction information:

mse = MSEquation(stoichiometry, direction)

  • stoichiometry dict: The collection of stoichiometry (values) for all metabolites in the reaction (keys).

  • direction str: The “<”, “=”, or “>” reaction directionality.

build_from_palsson_string()

staticMethod Parses a BiGG-formatted reaction string into an amenable form for ModelSEEDpy:

reaction_object = MSEquation.build_from_palsson_string(equation_string, default_group='c')

  • equation_string str: The BiGG reaction string.

  • default_group str: The reactant identifier.

Returns reaction_object modelseedpy.core.mseditorapi.MSEquation: The MSEquation object version of a BiGG reaction.