14.1.5. cobra.manipulation package¶
14.1.5.1. Submodules¶
14.1.5.2. cobra.manipulation.annotate module¶
-
cobra.manipulation.annotate.add_SBO(model)[source]¶ 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
14.1.5.3. 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:
Modelgene_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.
-
cobra.manipulation.delete.get_compiled_gene_reaction_rules(cobra_model)[source]¶ 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.
-
cobra.manipulation.delete.prune_unused_metabolites(cobra_model)[source]¶ Remove metabolites that are not involved in any reactions
Parameters: cobra_model (cobra.Model) – the model to remove unused metabolites from Returns: list of metabolites that were removed Return type: list
-
cobra.manipulation.delete.prune_unused_reactions(cobra_model)[source]¶ Remove reactions that have no assigned metabolites
Parameters: cobra_model (cobra.Model) – the model to remove unused reactions from Returns: list of reactions that were removed Return type: list
14.1.5.4. 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.
-
cobra.manipulation.modify.convert_to_irreversible(cobra_model)[source]¶ 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.
-
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 an irreversible model made by convert_to_irreversible into a reversible model.
- cobra_model : cobra.Model
- A model which will be modified in place.
- update_solution: bool
- This option is ignored since model.solution was removed.