14.1.5. cobra.manipulation package Submodules cobra.manipulation.annotate module


adds SBO terms for demands and exchanges

This works for models which follow the standard convention for constructing and naming these reactions.

The reaction should only contain the single metabolite being exchanged, and the id should be EX_metid or DM_metid cobra.manipulation.delete module

cobra.manipulation.delete.delete_model_genes(cobra_model, gene_list, cumulative_deletions=True, disable_orphans=False)[source]

delete_model_genes will set the upper and lower bounds for reactions catalysed by the genes in gene_list if deleting the genes means that the reaction cannot proceed according to cobra_model.reactions[:].gene_reaction_rule

cumulative_deletions: False or True. If True then any previous deletions will be maintained in the model.

cobra.manipulation.delete.find_gene_knockout_reactions(cobra_model, gene_list, compiled_gene_reaction_rules=None)[source]

identify reactions which will be disabled when the genes are knocked out

cobra_model: Model

gene_list: iterable of Gene

compiled_gene_reaction_rules: dict of {reaction_id: compiled_string}
If provided, this gives pre-compiled gene_reaction_rule strings. The compiled rule strings can be evaluated much faster. If a rule is not provided, the regular expression evaluation will be used. Because not all gene_reaction_rule strings can be evaluated, this dict must exclude any rules which can not be used with eval.

Generates a dict of compiled gene_reaction_rules

Any gene_reaction_rule expressions which cannot be compiled or do not evaluate after compiling will be excluded. The result can be used in the find_gene_knockout_reactions function to speed up evaluation of these rules.


Removes metabolites that aren’t involved in any reactions in the model

cobra_model: A Model object.


Removes reactions from cobra_model.

cobra_model: A Model object.

reactions_to_prune: None, a string matching a reaction.id, a cobra.Reaction, or as list of the ids / Reactions to remove from cobra_model. If None then the function will delete reactions that have no active metabolites in the model.

cobra.manipulation.delete.remove_genes(cobra_model, gene_list, remove_reactions=True)[source]

remove genes entirely from the model

This will also simplify all gene_reaction_rules with this gene inactivated.


Undoes the effects of a call to delete_model_genes in place.

cobra_model: A cobra.Model which will be modified in place cobra.manipulation.modify module

cobra.manipulation.modify.canonical_form(model, objective_sense='maximize', already_irreversible=False, copy=True)[source]

Return a model (problem in canonical_form).

Converts a minimization problem to a maximization, makes all variables positive by making reactions irreversible, and converts all constraints to <= constraints.

model: class:~cobra.core.Model. The model/problem to convert.

objective_sense: str. The objective sense of the starting problem, either ‘maximize’ or ‘minimize’. A minimization problems will be converted to a maximization.

already_irreversible: bool. If the model is already irreversible, then pass True.

copy: bool. Copy the model before making any modifications.


Split reversible reactions into two irreversible reactions

These two reactions will proceed in opposite directions. This guarentees that all reactions in the model will only allow positive flux values, which is useful for some modeling problems.

cobra_model: A Model object which will be modified in place.


makes all ids SBML compliant

cobra.manipulation.modify.initialize_growth_medium(cobra_model, the_medium='MgM', external_boundary_compartment='e', external_boundary_reactions=None, reaction_lower_bound=0.0, reaction_upper_bound=1000.0, irreversible=False, reactions_to_disable=None)[source]

Sets all of the input fluxes to the model to zero and then will initialize the input fluxes to the values specified in the_medium if it is a dict or will see if the model has a composition dict and use that to do the initialization.

cobra_model: A cobra.Model object.

the_medium: A string, or a dictionary. If a string then the initialize_growth_medium function expects that the_model has an attribute dictionary called media_compositions, which is a dictionary of dictionaries for various medium compositions. Where a medium composition is a dictionary of external boundary reaction ids for the medium components and the external boundary fluxes for each medium component.

external_boundary_compartment: None or a string. If not None then it specifies the compartment in which to disable all of the external systems boundaries.

external_boundary_reactions: None or a list of external_boundaries that are to have their bounds reset. This acts in conjunction with external_boundary_compartment.

reaction_lower_bound: Float. The default value to use for the lower bound for the boundary reactions.

reaction_upper_bound: Float. The default value to use for the upper bound for the boundary.

irreversible: Boolean. If the model is irreversible then the medium composition is taken as the upper bound

reactions_to_disable: List of reactions for which the upper and lower bounds are disabled. This is superceded by the contents of media_composition

cobra.manipulation.modify.rename_genes(cobra_model, rename_dict)[source]

renames genes in a model from the rename_dict

cobra.manipulation.modify.revert_to_reversible(cobra_model, update_solution=True)[source]

This function will convert a reversible model made by convert_to_irreversible into a reversible model.

cobra_model: A cobra.Model which will be modified in place. cobra.manipulation.validate module

cobra.manipulation.validate.check_reaction_bounds(model)[source] Module contents