cobra.core.model

Define the Model class.

Module Contents

Classes

Model

Class representation for a cobra model.

Attributes

logger
configuration

cobra.core.model.logger

cobra.core.model.configuration

class cobra.core.model.Model(id_or_model: Union[str, Model, None] = None, name: Optional[str] = None)

Bases: cobra.core.object.Object

Class representation for a cobra model.

Parameters

• id_or_model (str or Model, optional) – String to use as model id, or actual model to base new model one. If string, it is used as id. If model, a new model object is instantiated with the same properties as the original model (default None).

• name (str, optional) – Human readable string to be model description (default None).

reactions

A DictList where the key is the reaction identifier and the value a Reaction

Type

DictList

metabolites

A DictList where the key is the metabolite identifier and the value a Metabolite

Type

DictList

genes

A DictList where the key is the gene identifier and the value a Gene

Type

DictList

groups

A DictList where the key is the group identifier and the value a Group

Type

DictList

property solver: optlang.interface.Model

Get the attached solver instance.

The associated the solver object, which manages the interaction with the associated solver, e.g. glpk.

This property is useful for accessing the optimization problem directly and to define additional non-metabolic constraints.

Examples

>>> from cobra.io import load_model
>>> model = load_model("textbook")
>>> new = model.problem.Constraint(model.objective.expression, lb=0.99)
>>> model.solver.add(new)

property tolerance: float

Get the tolerance.

Returns

The tolerance of the mdoel.

Return type

float

property compartments: Dict

Return all metabolites’ compartments.

Returns

A dictionary of metabolite compartments, where the keys are the short version (one letter version) of the compartmetns, and the values are the full names (if they exist).

Return type

dict

property medium: Dict[str, float]

Get the constraints on the model exchanges.

model.medium returns a dictionary of the bounds for each of the boundary reactions, in the form of {rxn_id: bound}, where bound specifies the absolute value of the bound in direction of metabolite creation (i.e., lower_bound for met <–, upper_bound for met –>)

Returns

A dictionary with rxn.id (str) as key, bound (float) as value.

Return type

Dict[str, float]

property problem: optlang.interface

Get the interface to the model’s underlying mathematical problem.

Solutions to cobra models are obtained by formulating a mathematical problem and solving it. Cobrapy uses the optlang package to accomplish that and with this property you can get access to the problem interface directly.

Returns

The problem interface that defines methods for interacting with the problem and associated solver directly.

Return type

optlang.interface

property variables: optlang.container.Container

Get the mathematical variables in the cobra model.

In a cobra model, most variables are reactions. However, for specific use cases, it may also be useful to have other types of variables. This property defines all variables currently associated with the model’s problem.

Returns

A container with all associated variables.

Return type

optlang.container.Container

property constraints: optlang.container.Container

Get the constraints in the cobra model.

In a cobra model, most constraints are metabolites and their stoichiometries. However, for specific use cases, it may also be useful to have other types of constraints. This property defines all constraints currently associated with the model’s problem.

Returns

A container with all associated constraints.

Return type

optlang.container.Container

property boundary: List[cobra.core.reaction.Reaction]

Boundary reactions in the model.

Reactions that either have no substrate or product.

Returns

A list of reactions that either have no substrate or product and only one metabolite overall.

Return type

list

property exchanges: List[cobra.core.reaction.Reaction]

Exchange reactions in model.

Reactions that exchange mass with the exterior. Uses annotations and heuristics to exclude non-exchanges such as sink reactions.

Returns

A list of reactions that satisfy the conditions for exchange reactions.

Return type

list

See also

cobra.medium.find_boundary_types

property demands: List[cobra.core.reaction.Reaction]

Demand reactions in model.

Irreversible reactions that accumulate or consume a metabolite in the inside of the model.

Returns

A list of reactions that are demand reactions (reactions that accumulate/consume a metabolite irreversibly).

Return type

list

See also

cobra.medium.find_boundary_types

property sinks: List[cobra.core.reaction.Reaction]

Sink reactions in model.

Reversible reactions that accumulate or consume a metabolite in the inside of the model.

Returns

A list of reactions that are demand reactions (reactions that accumulate/consume a metabolite reversibly).

Return type

list

See also

cobra.medium.find_boundary_types

property objective: Union[optlang.Objective]

Get the solver objective.

With optlang, the objective is not limited to a simple linear summation of individual reaction fluxes, making the return value ambiguous.

Henceforth, use cobra.util.solver.linear_reaction_coefficients to get a dictionary of reactions with their linear coefficients (empty if there are none).

property objective_direction: str

Get the objective direction.

Returns

Objective direction as string. Should be “max” or “min”.

Return type

str

__setstate__(state: Dict) → None

Make sure all cobra.Objects in the model point to the model.

Parameters

state (dict) –

__getstate__() → Dict

Get state for serialization.

Ensures that the context stack is cleared prior to serialization, since partial functions cannot be pickled reliably.

Returns

odict – A dictionary of state, based on self.__dict__.

Return type

Dict

copy() → Model

Provide a partial ‘deepcopy’ of the Model.

All the Metabolite, Gene, and Reaction objects are created anew but in a faster fashion than deepcopy.

Returns

cobra.Model

Return type

new model copy

add_metabolites(metabolite_list: Union[List, cobra.core.metabolite.Metabolite]) → None

Add new metabolites to a model.

Will add a list of metabolites to the model object and add new constraints accordingly.

The change is reverted upon exit when using the model as a context.

Parameters

metabolite_list (list or Metabolite.) – A list of cobra.core.Metabolite objects. If it isn’t an iterable container, the metabolite will be placed into a list.

remove_metabolites(metabolite_list: Union[List, cobra.core.metabolite.Metabolite], destructive: bool = False) → None

Remove a list of metabolites from the the object.

The change is reverted upon exit when using the model as a context.

Parameters

• metabolite_list (list or Metaoblite) – A list of cobra.core.Metabolite objects. If it isn’t an iterable container, the metabolite will be placed into a list.

• destructive (bool, optional) – If False then the metabolite is removed from all associated reactions. If True then all associated reactions are removed from the Model (default False).

add_boundary(metabolite: cobra.core.metabolite.Metabolite, type: str = 'exchange', reaction_id: Optional[str] = None, lb: Optional[float] = None, ub: Optional[float] = None, sbo_term: Optional[str] = None) → cobra.core.reaction.Reaction

Add a boundary reaction for a given metabolite.

There are three different types of pre-defined boundary reactions: exchange, demand, and sink reactions. An exchange reaction is a reversible, unbalanced reaction that adds to or removes an extracellular metabolite from the extracellular compartment. A demand reaction is an irreversible reaction that consumes an intracellular metabolite. A sink is similar to an exchange but specifically for intracellular metabolites, i.e., a reversible reaction that adds or removes an intracellular metabolite.

If you set the reaction type to something else, you must specify the desired identifier of the created reaction along with its upper and lower bound. The name will be given by the metabolite name and the given type.

The change is reverted upon exit when using the model as a context.

Parameters

• metabolite (cobra.Metabolite) – Any given metabolite. The compartment is not checked but you are encouraged to stick to the definition of exchanges and sinks.

• type ({"exchange", "demand", "sink"}) – Using one of the pre-defined reaction types is easiest. If you want to create your own kind of boundary reaction choose any other string, e.g., ‘my-boundary’ (default “exchange”).

• reaction_id (str, optional) – The ID of the resulting reaction. This takes precedence over the auto-generated identifiers but beware that it might make boundary reactions harder to identify afterwards when using model.boundary or specifically model.exchanges etc. (default None).

• lb (float, optional) – The lower bound of the resulting reaction (default None).

• ub (float, optional) – The upper bound of the resulting reaction (default None).

• sbo_term (str, optional) – A correct SBO term is set for the available types. If a custom type is chosen, a suitable SBO term should also be set (default None).

Returns

The created boundary reaction.

Return type

cobra.Reaction

Examples

>>> from cobra.io load_model
>>> model = load_model("textbook")
>>> demand = model.add_boundary(model.metabolites.atp_c, type="demand")
>>> demand.id
'DM_atp_c'
>>> demand.name
'ATP demand'
>>> demand.bounds
(0, 1000.0)
>>> demand.build_reaction_string()
'atp_c --> '

add_reactions(reaction_list: Iterable[cobra.core.reaction.Reaction]) → None

Add reactions to the model.

Reactions with identifiers identical to a reaction already in the model are ignored.

The change is reverted upon exit when using the model as a context.

Parameters

reaction_list (list) – A list of cobra.Reaction objects

remove_reactions(reactions: Union[str, cobra.core.reaction.Reaction, List[Union[str, cobra.core.reaction.Reaction]]], remove_orphans: bool = False) → None

Remove reactions from the model.

The change is reverted upon exit when using the model as a context.

Parameters

• reactions (list or reaction or str) – A list with reactions (cobra.Reaction), or their id’s, to remove. Reaction will be placed in a list. Str will be placed in a list and used to find the reaction in the model.

• remove_orphans (bool, optional) – Remove orphaned genes and metabolites from the model as well (default False).

add_groups(group_list: Union[str, cobra.core.group.Group, List[cobra.core.group.Group]]) → None

Add groups to the model.

Groups with identifiers identical to a group already in the model are ignored.

If any group contains members that are not in the model, these members are added to the model as well. Only metabolites, reactions, and genes can have groups.

Parameters

group_list (list or str or Group) – A list of cobra.Group objects to add to the model. Can also be a single group or a string representing group id. If the input is not a list, a warning is raised.

remove_groups(group_list: Union[str, cobra.core.group.Group, List[cobra.core.group.Group]]) → None

Remove groups from the model.

Members of each group are not removed from the model (i.e. metabolites, reactions, and genes in the group stay in the model after any groups containing them are removed).

Parameters

group_list (list or str or Group) –

A list of cobra.Group objects to remove from the model. Can also be a single group or a string representing group id. If the input is not a list,

a warning is raised.

get_associated_groups(element: Union[cobra.core.reaction.Reaction, cobra.core.gene.Gene, cobra.core.metabolite.Metabolite]) → List[cobra.core.group.Group]

Get list of groups for element.

Returns a list of groups that an element (reaction, metabolite, gene) is associated with.

Parameters

element (cobra.Reaction, cobra.Metabolite, or cobra.Gene) –

Returns

All groups that the provided object is a member of

Return type

list of cobra.Group

add_cons_vars(what: Union[List[cobra.util.solver.CONS_VARS], Tuple[cobra.util.solver.CONS_VARS]], **kwargs) → None

Add constraints and variables to the model’s mathematical problem.

Useful for variables and constraints that can not be expressed with reactions and simple lower and upper bounds.

Additions are reversed upon exit if the model itself is used as context.

Parameters

• what (list or tuple of optlang variables or constraints.) – The variables or constraints to add to the model. Must be of class optlang.interface.Variable or optlang.interface.Constraint.

• **kwargs (keyword arguments) – Passed to solver.add()

remove_cons_vars(what: Union[List[cobra.util.solver.CONS_VARS], Tuple[cobra.util.solver.CONS_VARS]]) → None

Remove variables and constraints from problem.

Remove variables and constraints from the model’s mathematical problem.

Remove variables and constraints that were added directly to the model’s underlying mathematical problem. Removals are reversed upon exit if the model itself is used as context.

Parameters

what (list or tuple of optlang variables or constraints.) – The variables or constraints to add to the model. Must be of class optlang.interface.Variable or optlang.interface.Constraint.

_populate_solver(reaction_list: List[cobra.core.reaction.Reaction], metabolite_list: Optional[List[cobra.core.metabolite.Metabolite]] = None) → None

Populate attached solver with constraints and variables.

Populate attached solver with constraints and variables that model the provided reactions.

Parameters

• reaction_list (list) – A list of cobra.Reaction to add to the solver. This list will be constrained.

• metabolite_list (list, optional) – A list of cobra.Metabolite to add to the solver. This list will be constrained (default None).

slim_optimize(error_value: Optional[float] = float('nan'), message: Optional[str] = None) → float

Optimize model without creating a solution object.

Creating a full solution object implies fetching shadow prices and flux values for all reactions and metabolites from the solver object. This necessarily takes some time and in cases where only one or two values are of interest, it is recommended to instead use this function which does not create a solution object returning only the value of the objective. Note however that the optimize() function uses efficient means to fetch values so if you need fluxes/shadow prices for more than say 4 reactions/metabolites, then the total speed increase of slim_optimize versus optimize is expected to be small or even negative depending on how you fetch the values after optimization.

Parameters

• error_value (float, None) – The value to return if optimization failed due to e.g. infeasibility. If None, raise OptimizationError if the optimization fails (default float(“nan”)).

• message (str, optional) – Error message to use if the model optimization did not succeed (default None).

Returns

The objective value. Returns the error value if optimization failed and error_value was not None.

Return type

float

Raises

OptimizationError – If error_value was set as None and the optimization fails.

optimize(objective_sense: Optional[str] = None, raise_error: bool = False) → cobra.Solution

Optimize the model using flux balance analysis.

Parameters

• objective_sense ({None, 'maximize' 'minimize'}, optional) – Whether fluxes should be maximized or minimized. In case of None, the previous direction is used (default None).

• raise_error (bool) –

  If true, raise an OptimizationError if solver status is not

  optimal (default False).

Return type

Solution

Notes

Only the most commonly used parameters are presented here. Additional parameters for cobra.solvers may be available and specified with the appropriate keyword argument.

repair(rebuild_index: bool = True, rebuild_relationships: bool = True) → None

Update all indexes and pointers in a model.

Parameters

• rebuild_index (bool) – rebuild the indices kept in reactions, metabolites and genes

• rebuild_relationships (bool) – reset all associations between genes, metabolites, model and then re-add them.

summary(solution: Optional[cobra.Solution] = None, fva: Union[pandas.DataFrame, float, None] = None) → cobra.summary.ModelSummary

Create a summary of the exchange fluxes of the model.

Parameters

• solution (cobra.Solution, optional) – A previous model solution to use for generating the summary. If None, the summary method will generate a parsimonious flux distribution (default None).

• fva (pd.DataFrame or float, optional) – Whether or not to include flux variability analysis in the output. If given, fva should either be a previous FVA solution matching the model or a float between 0 and 1 representing the fraction of the optimum objective to be searched (default None).

Return type

cobra.ModelSummary

See also

Reaction.summary, Metabolite.summary

__enter__() → Model

Record future changes to the model.

Record all future changes to the model, undoing them when a call to __exit__ is received. Creates a new context and adds it to the stack.

Returns

Returns the model with context added.

Return type

cobra.Model

__exit__(type, value, traceback) → None

Pop the top context manager and trigger the undo functions.

merge(right: Model, prefix_existing: Optional[str] = None, inplace: bool = True, objective: str = 'left') → Model

Merge two models to create a model with the reactions from both models.

Custom constraints and variables from right models are also copied to left model, however note that, constraints and variables are assumed to be the same if they have the same name.

Parameters

• right (cobra.Model) – The model to add reactions from

• prefix_existing (string or optional) – Prefix the reaction identifier in the right that already exist in the left model with this string (default None).

• inplace (bool) – Add reactions from right directly to left model object. Otherwise, create a new model leaving the left model untouched. When done within the model as context, changes to the models are reverted upon exit (default True).

• objective ({"left", "right", "sum"}) – One of “left”, “right” or “sum” for setting the objective of the resulting model to that of the corresponding model or the sum of both (default “left”).

Returns

The merged model.

Return type

cobra.Model

_repr_html_() → str

Get HTML represenation of the model.

Returns

Model representation as HTML string.

Return type

str