cobra.io.dict ============= .. py:module:: cobra.io.dict .. autoapi-nested-parse:: Provide functions for cobrapy objects to generic Python objects and vice-versa. Attributes ---------- .. autoapisummary:: cobra.io.dict._REQUIRED_REACTION_ATTRIBUTES cobra.io.dict._ORDERED_OPTIONAL_REACTION_KEYS cobra.io.dict._OPTIONAL_REACTION_ATTRIBUTES cobra.io.dict._REQUIRED_METABOLITE_ATTRIBUTES cobra.io.dict._ORDERED_OPTIONAL_METABOLITE_KEYS cobra.io.dict._OPTIONAL_METABOLITE_ATTRIBUTES cobra.io.dict._REQUIRED_GENE_ATTRIBUTES cobra.io.dict._ORDERED_OPTIONAL_GENE_KEYS cobra.io.dict._OPTIONAL_GENE_ATTRIBUTES cobra.io.dict._ORDERED_OPTIONAL_MODEL_KEYS cobra.io.dict._OPTIONAL_MODEL_ATTRIBUTES Functions --------- .. autoapisummary:: cobra.io.dict._fix_type cobra.io.dict._update_optional cobra.io.dict._metabolite_to_dict cobra.io.dict._metabolite_from_dict cobra.io.dict._gene_to_dict cobra.io.dict.gene_from_dict cobra.io.dict._reaction_to_dict cobra.io.dict._reaction_from_dict cobra.io.dict.model_to_dict cobra.io.dict.model_from_dict Module Contents --------------- .. py:data:: _REQUIRED_REACTION_ATTRIBUTES :value: ['id', 'name', 'metabolites', 'lower_bound', 'upper_bound', 'gene_reaction_rule'] .. py:data:: _ORDERED_OPTIONAL_REACTION_KEYS :value: ['objective_coefficient', 'subsystem', 'notes', 'annotation'] .. py:data:: _OPTIONAL_REACTION_ATTRIBUTES .. py:data:: _REQUIRED_METABOLITE_ATTRIBUTES :value: ['id', 'name', 'compartment'] .. py:data:: _ORDERED_OPTIONAL_METABOLITE_KEYS :value: ['charge', 'formula', '_bound', 'notes', 'annotation'] .. py:data:: _OPTIONAL_METABOLITE_ATTRIBUTES .. py:data:: _REQUIRED_GENE_ATTRIBUTES :value: ['id', 'name'] .. py:data:: _ORDERED_OPTIONAL_GENE_KEYS :value: ['notes', 'annotation'] .. py:data:: _OPTIONAL_GENE_ATTRIBUTES .. py:data:: _ORDERED_OPTIONAL_MODEL_KEYS :value: ['name', 'compartments', 'notes', 'annotation'] .. py:data:: _OPTIONAL_MODEL_ATTRIBUTES .. py:function:: _fix_type(value: Union[str, float, bool, Set, Dict]) -> Union[str, float, bool, List, collections.OrderedDict] Convert possible types to correct Python types. :param value: The value to fix type for. :type value: str, float, bool, set, dict :returns: The fixed type for the value. :rtype: str, float, bool, list, dict .. py:function:: _update_optional(cobra_object: cobra.Object, new_dict: Dict, optional_attribute_dict: Dict, ordered_keys: Sequence) -> None Update `new_dict` with optional attributes from `cobra_object`. :param cobra_object: The cobra Object to update optional attributes from. :type cobra_object: cobra.Object :param new_dict: The dictionary to update optional attributes for. :type new_dict: dict :param optional_attribute_dict: The dictionary to use as default value lookup store. :type optional_attribute_dict: dict :param ordered_keys: The keys to update values for. :type ordered_keys: list, tuple :raises IndexError: If key in `ordered_keys` is not found in `optional_attribute_dict`. :raises AttributeError: If key in `ordered_keys` is not found in `cobra_object`. .. py:function:: _metabolite_to_dict(metabolite: cobra.core.Metabolite) -> collections.OrderedDict Convert a cobra Metabolite object to dictionary. :param metabolite: The cobra.Metabolite to convert to dictionary. :type metabolite: cobra.Metabolite :returns: The converted dictionary object. :rtype: dict .. seealso:: :py:obj:`_metabolite_from_dict` Convert a dictionary to cobra Metabolite object. .. py:function:: _metabolite_from_dict(metabolite: Dict) -> cobra.core.Metabolite Convert a dictionary to cobra Metabolite object. :param metabolite: The dictionary to convert to cobra.Metabolite . :type metabolite: dict :rtype: cobra.Metabolite .. seealso:: :py:obj:`_metabolite_to_dict` Convert a cobra Metabolite object to dictionary. .. py:function:: _gene_to_dict(gene: cobra.core.Gene) -> collections.OrderedDict Convert a cobra Gene object to dictionary. :param gene: The cobra.Gene to convert to dictionary. :type gene: cobra.Gene :returns: The converted dictionary object. :rtype: dict .. seealso:: :py:obj:`_gene_from_dict` Convert a dictionary to cobra Gene object. .. py:function:: gene_from_dict(gene: Dict) -> cobra.core.Gene Convert a dictionary to cobra Gene object. :param gene: The dictionary to convert to cobra.Gene . :type gene: dict :returns: The converted cobra.Gene object. :rtype: cobra.Gene .. seealso:: :py:obj:`_gene_to_dict` Convert a cobra Gene object to a dictionary. .. py:function:: _reaction_to_dict(reaction: cobra.core.Reaction) -> collections.OrderedDict Convert a cobra Reaction object to a dictionary. :param reaction: The cobra.Reaction to convert to dictionary. :type reaction: cobra.Reaction :returns: The converted dictionary object. :rtype: dict .. seealso:: :py:obj:`_reaction_from_dict` Convert a dictionary to a cobra Reaction object. .. py:function:: _reaction_from_dict(reaction: Dict, model: cobra.core.Model) -> cobra.core.Reaction Convert a dictionary to a cobra Reaction object. :param reaction: The dictionary to convert to cobra.Reaction . :type reaction: dict :param model: The model to which the reaction should associate with. :type model: cobra.Model :returns: The converted cobra.Reaction object. :rtype: cobra.Reaction .. seealso:: :py:obj:`_reaction_to_dict` Convert a cobra Reaction object to a dictionary. .. py:function:: model_to_dict(model: cobra.core.Model, sort: bool = False) -> collections.OrderedDict Convert a cobra Model to a dictionary. :param model: The model to reformulate as a dict. :type model: cobra.Model :param sort: Whether to sort the metabolites, reactions, and genes or maintain the order defined in the model (default False). :type sort: bool, optional :returns: A dictionary with keys: 'genes', 'compartments', 'id', 'metabolites', 'notes' and 'reactions'; where 'metabolites', 'genes' and 'metabolites' are in turn lists of dictionaries holding all attributes to form the corresponding object. :rtype: OrderedDict .. seealso:: :py:obj:`model_from_dict` Convert a dictionary to a cobra Model. .. py:function:: model_from_dict(obj: Dict) -> cobra.core.Model Build a cobra Model from a dictionary. Models stored in JSON are first formulated as a dictionary that can be read to a cobra Model using this function. :param obj: A dictionary with keys: 'genes', 'compartments', 'id', 'metabolites', 'notes' and 'reactions'; where 'metabolites', 'genes' and 'metabolites' are in turn lists of dictionaries holding all attributes to form the corresponding object. :type obj: dict :returns: The generated model. :rtype: cobra.Model :raises ValueError: If `obj` has no 'reactions' attribute. .. seealso:: :py:obj:`model_to_dict` Convert a cobra Model to a dictionary.