Source code for cobra.core.Model

from warnings import warn
from copy import deepcopy, copy

from six import iteritems, string_types

from ..solvers import optimize
from .Object import Object
from .Solution import Solution
from .Reaction import Reaction
from .DictList import DictList


# Note, when a reaction is added to the Model it will no longer keep personal
# instances of its Metabolites, it will reference Model.metabolites to improve
# performance.  When doing this, take care to monitor metabolite coefficients.
# Do the same for Model.reactions[:].genes and Model.genes

[docs]class Model(Object): """Metabolic Model Refers to Metabolite, Reaction, and Gene Objects. """
[docs] def __setstate__(self, state): """Make sure all cobra.Objects in the model point to the model""" self.__dict__.update(state) for y in ['reactions', 'genes', 'metabolites']: for x in getattr(self, y): x._model = self if not hasattr(self, "name"): self.name = None
def __init__(self, id_or_model=None, name=None): if isinstance(id_or_model, Model): Object.__init__(self, name=name) self.__setstate__(id_or_model.__dict__) if not hasattr(self, "name"): self.name = None else: Object.__init__(self, id_or_model, name=name) self._trimmed = False self._trimmed_genes = [] self._trimmed_reactions = {} self.genes = DictList() self.reactions = DictList() # A list of cobra.Reactions self.metabolites = DictList() # A list of cobra.Metabolites # genes based on their ids {Gene.id: Gene} self.compartments = {} self.solution = Solution(None) self.media_compositions = {} @property def description(self): warn("description deprecated") return self.name if self.name is not None else "" @description.setter def description(self, value): self.name = value warn("description deprecated")
[docs] def __add__(self, other_model): """Adds two models. + The issue of reactions being able to exists in multiple Models now arises, the same for metabolites and such. This might be a little difficult as a reaction with the same name / id in two models might have different coefficients for their metabolites due to pH and whatnot making them different reactions. """ new_model = self.copy() new_reactions = deepcopy(other_model.reactions) new_model.add_reactions(new_reactions) new_model.id = self.id + '_' + other_model.id return new_model
[docs] def __iadd__(self, other_model): """Adds a Model to this model += The issue of reactions being able to exists in multiple Models now arises, the same for metabolites and such. This might be a little difficult as a reaction with the same name / id in two models might have different coefficients for their metabolites due to pH and whatnot making them different reactions. """ new_reactions = deepcopy(other_model.reactions) self.add_reactions(new_reactions) self.id = self.id + '_' + other_model.id return self
[docs] def copy(self): """Provides a partial 'deepcopy' of the Model. All of the Metabolite, Gene, and Reaction objects are created anew but in a faster fashion than deepcopy """ new = self.__class__() do_not_copy_by_ref = {"metabolites", "reactions", "genes", "notes", "annotation"} for attr in self.__dict__: if attr not in do_not_copy_by_ref: new.__dict__[attr] = self.__dict__[attr] new.notes = deepcopy(self.notes) new.annotation = deepcopy(self.annotation) new.metabolites = DictList() do_not_copy_by_ref = {"_reaction", "_model"} for metabolite in self.metabolites: new_met = metabolite.__class__() for attr, value in iteritems(metabolite.__dict__): if attr not in do_not_copy_by_ref: new_met.__dict__[attr] = copy( value) if attr == "formula" else value new_met._model = new new.metabolites.append(new_met) new.genes = DictList() for gene in self.genes: new_gene = gene.__class__(None) for attr, value in iteritems(gene.__dict__): if attr not in do_not_copy_by_ref: new_gene.__dict__[attr] = copy( value) if attr == "formula" else value new_gene._model = new new.genes.append(new_gene) new.reactions = DictList() do_not_copy_by_ref = {"_model", "_metabolites", "_genes"} for reaction in self.reactions: new_reaction = reaction.__class__() for attr, value in iteritems(reaction.__dict__): if attr not in do_not_copy_by_ref: new_reaction.__dict__[attr] = copy(value) new_reaction._model = new new.reactions.append(new_reaction) # update awareness for metabolite, stoic in iteritems(reaction._metabolites): new_met = new.metabolites.get_by_id(metabolite.id) new_reaction._metabolites[new_met] = stoic new_met._reaction.add(new_reaction) for gene in reaction._genes: new_gene = new.genes.get_by_id(gene.id) new_reaction._genes.add(new_gene) new_gene._reaction.add(new_reaction) return new
[docs] def add_metabolites(self, metabolite_list): """Will add a list of metabolites to the the object, if they do not exist and then expand the stochiometric matrix metabolite_list: A list of :class:`~cobra.core.Metabolite` objects """ if not hasattr(metabolite_list, '__iter__'): metabolite_list = [metabolite_list] # First check whether the metabolites exist in the model metabolite_list = [x for x in metabolite_list if x.id not in self.metabolites] for x in metabolite_list: x._model = self self.metabolites += metabolite_list
[docs] def add_reaction(self, reaction): """Will add a cobra.Reaction object to the model, if reaction.id is not in self.reactions. reaction: A :class:`~cobra.core.Reaction` object """ self.add_reactions([reaction])
[docs] def add_reactions(self, reaction_list): """Will add a cobra.Reaction object to the model, if reaction.id is not in self.reactions. reaction_list: A list of :class:`~cobra.core.Reaction` objects """ try: reaction_list = DictList(reaction_list) except TypeError: # This function really should not used for single reactions reaction_list = DictList([reaction_list]) warn("Use add_reaction for single reactions") # Only add the reaction if one with the same ID is not already # present in the model. reactions_in_model = [ i.id for i in reaction_list if self.reactions.has_id( i.id)] if len(reactions_in_model) > 0: raise Exception("Reactions already in the model: " + ", ".join(reactions_in_model)) # Add reactions. Also take care of genes and metabolites in the loop for reaction in reaction_list: reaction._model = self # the reaction now points to the model # keys() is necessary because the dict will be modified during # the loop for metabolite in list(reaction._metabolites.keys()): # if the metabolite is not in the model, add it # should we be adding a copy instead. if not self.metabolites.has_id(metabolite.id): self.metabolites.append(metabolite) metabolite._model = self # this should already be the case. Is it necessary? metabolite._reaction = set([reaction]) # A copy of the metabolite exists in the model, the reaction # needs to point to the metabolite in the model. else: stoichiometry = reaction._metabolites.pop(metabolite) model_metabolite = self.metabolites.get_by_id( metabolite.id) reaction._metabolites[model_metabolite] = stoichiometry model_metabolite._reaction.add(reaction) for gene in list(reaction._genes): # If the gene is not in the model, add it if not self.genes.has_id(gene.id): self.genes.append(gene) gene._model = self # this should already be the case. Is it necessary? gene._reaction = set([reaction]) # Otherwise, make the gene point to the one in the model else: model_gene = self.genes.get_by_id(gene.id) if model_gene is not gene: reaction._dissociate_gene(gene) reaction._associate_gene(model_gene) self.reactions += reaction_list
[docs] def to_array_based_model(self, deepcopy_model=False, **kwargs): """Makes a :class:`~cobra.core.ArrayBasedModel` from a cobra.Model which may be used to perform linear algebra operations with the stoichiomatric matrix. deepcopy_model: Boolean. If False then the ArrayBasedModel points to the Model """ from .ArrayBasedModel import ArrayBasedModel return ArrayBasedModel(self, deepcopy_model=deepcopy_model, **kwargs)
[docs] def optimize(self, objective_sense='maximize', **kwargs): r"""Optimize model using flux balance analysis objective_sense: 'maximize' or 'minimize' solver: 'glpk', 'cglpk', 'gurobi', 'cplex' or None quadratic_component: None or :class:`scipy.sparse.dok_matrix` The dimensions should be (n, n) where n is the number of reactions. This sets the quadratic component (Q) of the objective coefficient, adding :math:`\\frac{1}{2} v^T \cdot Q \cdot v` to the objective. tolerance_feasibility: Solver tolerance for feasibility. tolerance_markowitz: Solver threshold during pivot time_limit: Maximum solver time (in seconds) .. NOTE :: Only the most commonly used parameters are presented here. Additional parameters for cobra.solvers may be available and specified with the appropriate keyword argument. """ solution = optimize(self, objective_sense=objective_sense, **kwargs) self.solution = solution return solution
[docs] def remove_reactions(self, reactions, delete=True, remove_orphans=False): """remove reactions from the model reactions: [:class:`~cobra.core.Reaction.Reaction`] or [str] The reactions (or their id's) to remove delete: Boolean Whether or not the reactions should be deleted after removal. If the reactions are not deleted, those objects will be recreated with new metabolite and gene objects. remove_orphans: Boolean Remove orphaned genes and metabolites from the model as well """ if isinstance(reactions, string_types) or hasattr(reactions, "id"): warn("need to pass in a list") reactions = [reactions] for reaction in reactions: try: reaction = self.reactions[self.reactions.index(reaction)] except ValueError: warn('%s not in %s' % (reaction, self)) else: if delete: reaction.delete(remove_orphans=remove_orphans) else: reaction.remove_from_model(remove_orphans=remove_orphans)
[docs] def repair(self, rebuild_index=True, rebuild_relationships=True): """Update all indexes and pointers in a model""" if rebuild_index: # DictList indexes self.reactions._generate_index() self.metabolites._generate_index() self.genes._generate_index() if rebuild_relationships: for met in self.metabolites: met._reaction.clear() for gene in self.genes: gene._reaction.clear() for rxn in self.reactions: for met in rxn._metabolites: met._reaction.add(rxn) for gene in rxn._genes: gene._reaction.add(rxn) # point _model to self for l in (self.reactions, self.genes, self.metabolites): for e in l: e._model = self if self.solution is None: self.solution = Solution(None) return
[docs] def change_objective(self, objectives): """Change the model objective""" self.objective = objectives
@property def objective(self): return {reaction: reaction.objective_coefficient for reaction in self.reactions if reaction.objective_coefficient != 0} @objective.setter def objective(self, objectives): # set all objective coefficients to 0 initially for x in self.reactions: x.objective_coefficient = 0. # case of a single reaction if isinstance(objectives, string_types) or \ isinstance(objectives, Reaction): self.reactions.get_by_id(str(objectives)).objective_coefficient = 1 elif isinstance(objectives, int): self.reactions[objectives].objective_coefficient = 1 # case of an iterable else: for reaction_id in objectives: if isinstance(reaction_id, int): # index in a list reaction = self.reactions[reaction_id] else: reaction = self.reactions.get_by_id(str(reaction_id)) # objective coefficient obtained from a dict, and is 1. if # from a list. reaction.objective_coefficient = objectives[reaction_id] \ if hasattr(objectives, "items") else 1.
[docs] def summary(self, **kwargs): """Print a summary of the input and output fluxes of the model. This method requires the model to have been previously solved. threshold: float tolerance for determining if a flux is zero (not printed) fva: int or None Whether or not to calculate and report flux variability in the output summary floatfmt: string format method for floats, passed to tabulate. Default is '.3g'. """ try: from ..flux_analysis.summary import model_summary return model_summary(self, **kwargs) except ImportError: warn('Summary methods require pandas/tabulate')