micom.util

Holds utility functions for other modules.

Module Contents

Functions

is_active_demand(r)	Check if a reaction is a demand reaction.
fix_demands(model)	Check for forced sinks and demands and deactivates them.
download_model(url[, folder])	Download a model.
_read_model(file)	Read a model from a local file.
load_model(filepath)	Load a cobra model from several file types.
load_pickle(filename)	Load a community model from a pickled version.
serialize_models(files[, dir])	Convert several models to Python pickles.
chr_or_input(m)	Return ascii character for the ordinal or the original string.
clean_ids(id)	Clean ids up a bit.
compartment_id(micom_obj)	Get the compartment id for a cobra object and prune the prefix if needed.
join_models(model_files[, id])	Join several models into one.
fluxes_from_primals(model, info)	Extract a list of fluxes from the model primals.
add_var_from_expression(model, name, expr[, lb, ub])	Add a variable to a model equaling an expression.
ex_metabolite(model, rid)	Get the metabolite from an exchange reaction ID.
check_modification(community)	Check whether a community already carries a modification.
_format_min_growth(min_growth, taxa)	Format min_growth into a pandas series.
_apply_min_growth(community, min_growth[, atol, rtol])	Set minimum growth constraints on a model.
adjust_solver_config(solver)	Adjust the optlang solver configuration for larger problems.
reset_min_community_growth(com)	Reset the lower bound for the community growth.

Attributes

_read_funcs
COMPARTMENT_RE

micom.util._read_funcs

micom.util.COMPARTMENT_RE = '(_{}$)|([^a-zA-Z0-9 :]{}[^a-zA-Z0-9 :]$)'

micom.util.is_active_demand(r)

Check if a reaction is a demand reaction.

micom.util.fix_demands(model)

Check for forced sinks and demands and deactivates them.

micom.util.download_model(url, folder='.')

Download a model.

micom.util._read_model(file)

Read a model from a local file.

micom.util.load_model(filepath)

Load a cobra model from several file types.

micom.util.load_pickle(filename)

Load a community model from a pickled version.

Parameters:

filename (str) – The file the community is stored in.

Returns:

The loaded community model.

Return type:

micom.Community

micom.util.serialize_models(files, dir='.')

Convert several models to Python pickles.

micom.util.chr_or_input(m)

Return ascii character for the ordinal or the original string.

micom.util.clean_ids(id)

Clean ids up a bit.

micom.util.compartment_id(micom_obj)

Get the compartment id for a cobra object and prune the prefix if needed.

micom.util.join_models(model_files, id=None)

Join several models into one.

This requires all the models to use the same ID system.

Parameters:

• model_files (list of strings) – The files to be joined.

• id (str) – The new ID for the model. Will be the ID of the first model if None.

Returns:

The joined cobra Model.

Return type:

cobra.Model

micom.util.fluxes_from_primals(model, info)

Extract a list of fluxes from the model primals.

micom.util.add_var_from_expression(model, name, expr, lb=None, ub=None)

Add a variable to a model equaling an expression.

micom.util.ex_metabolite(model, rid)

Get the metabolite from an exchange reaction ID.

micom.util.check_modification(community)

Check whether a community already carries a modification.

Parameters:

community (micom.Community) – The community class to check.

Raises:

ValueError – If the community already carries a modification and adding another would not be safe.

micom.util._format_min_growth(min_growth, taxa)

Format min_growth into a pandas series.

Parameters:

• min_growth (positive float or array-like object.) – The minimum growth rate for each individual in the community. Either a single value applied to all individuals or one value for each.

• taxa (array-like) – The ID for each individual model in the community.

Returns:

A pandas Series mapping each individual to its minimum growth rate.

Return type:

pandas.Series

micom.util._apply_min_growth(community, min_growth, atol=1e-06, rtol=1e-06)

Set minimum growth constraints on a model.

Will integrate with the context.

micom.util.adjust_solver_config(solver)

Adjust the optlang solver configuration for larger problems.

micom.util.reset_min_community_growth(com)

Reset the lower bound for the community growth.