mstemplate¶

TemplateReactionType¶

A class that defines reaction types, where the attributes CONDITIONAL, UNIVERSAL, SPONTANEOUS, and GAPFILLING correspond to the strings "conditional", "universal", "spontaneous", and "gapfilling", respectively:

MSTemplateMetabolite¶

A function that assembles a unique list of features for the specified genome:

met_template = MSTemplateMetabolite(cpd_id, formula=None, name='', default_charge=None, mass=None,
                  delta_g=None, delta_g_error=None, is_cofactor=False, abbreviation='', aliases=None)

cpd_id, name, formula, abbreviation, & aliases str: The ID, name, formula, abbreviation, and alias of the ModelSEED compound that will be constructed into a template.
default_charge, mass, delta_g, & delta_g_error float: The charge, mass, \(\Delta\) g, and error in the \(\Delta\) g that describe the metabolite that will be constructed into a template.
is_cofactor bool: A description of whether the metabolite is a cofactor in metabolic reactions.

from_dict()¶

Returns a MSTemplateMetabolite object from a metabolite dictionary:

metabolite_template = met_template.from_dict(met_dict)

met_dict dict: A dictionary description of the ModelSEED compound that possesses the following keys "id", "formula", "name", "defaultCharge", "mass", "deltaG", "deltaGErr", "isCofactor", "abbreviation", & "aliases".

Returns metabolite_template modelseedpy.core.mstemplate.MSTemplateMetabolite: The metabolite object that embodies the content from the dictionary.

get_data()¶

Returns the metabolite template content.

met_template_dict = met_template.get_data()

Returns met_template_dict dict: A dictionary of the MSTemplateMetabolite content.

repr() & str() & _repr_html_()¶

Constructs strings of the metabolite template content.

met_template_str = met_template.__repr__()
met_template_str = met_template.__str__()
met_template_str = met_template.__repr_html__()

Returns met_template_str str: formulations of the MSTemplateMetabolite content.

MSTemplateSpecies¶

A class that defines a metabolite of a template:

met_template = MSTemplateSpecies(comp_cpd_id: str, charge: int, compartment: str, cpd_id, max_uptake=0, template=None)

cobra_cpd_id, compartment, & cpd_id str: The COBRA ID, compartment, and ModelSEED ID for the respective compound.
charge & max_uptake int: The compound charge and max uptake of the compound by the examined model.
template modelseedpy.core.mstemplate.MSTemplate: The model template in which the compound will be searched.

to_metabolite()¶

Creates a COBRA object for a ModelSEEDpy metabolite:

met = met_template.to_metabolite(index='0')

index string: The compartment index of the respective metabolite.

returns met cobra.core.metabolite.Metabolite: The COBRA metabolite object of the respective metabolite.

compound(), name(), & formula()¶

Property methods that return the object, name, or formula of the template compound, respectively:

template_compound = met_template.compound()
compound_name = met_template.name()
compound_formula = met_template.formula()

name() & formula()¶

Property setter methods that set the name or formula of the template compound, respectively:

met_template.name(name)
met_template.formula(formula)

name & formula string: The name and formula that will be assigned to the respective metabolite.

from_dict()¶

Returns methods that return the template compound object:

template_compound = met_template.from_dict(met_dict, template)

met_dict dict: A dictionary description of the ModelSEED compound that possesses the following keys "id", "charge", "templatecompartment_ref", & "templatecompound_ref".
template modelseedpy.core.mstemplate.MSTemplate: The model template in which the compound will be searched.

get_data()¶

Returns the metabolite template content.

met_template_dict = met_template.get_data()

Returns met_template_dict dict: A dictionary of the MSTemplateMetabolite content.

MSTemplateReaction¶

A class that defines a metabolite of a template:

rxn_template = MSTemplateSpecies(rxn_id: str, reference_id: str, name='', subsystem='', lower_bound=0.0,
                upper_bound=None,reaction_type=TemplateReactionType.CONDITIONAL, gapfill_direction='=',
                base_cost=1000, reverse_penalty=1000, forward_penalty=1000, status='OK')

rxn_id, reference_id, name, subsystem, & gapfill_direction str: The COBRA ID, KBase reference ID, name, subsystem, and gapfilling direction of the respective reaction.
lower_bound & upper_bound int: The reaction flux limitations.
reaction_type modelseedpy.core.mstemplate.TemplateReactionType: A description of the reaction type from the set of four options that are offered in the TemplateReactionType class.
base_cost, reverse_penalty, & forward_penalty float: defines the minimal flux cost and the specific costs of reverse and forward fluxes, respectively.
status str: specifies the gapfilling status.

gene_reaction_rule()¶

Property methods that return the gene complexes for the reaction:

gene_rules = rxn_template.gene_reaction_rule()

returns gene_rules str: The set of gene complexes, delimited by " or ".

compartment()¶

Property methods that return the interesting compartment of the respective reaction:

comptment = rxn_template.compartment()

returns comptment str: The interesting compartment character from the reaction.

to_reaction()¶

Creates a COBRA object for a ModelSEEDpy reaction:

reaction = rxn_template.to_reaction(model=None, index='0')

model cobra.core.model.Model: The CobraKBase model in which the examined reaction exists.
index string: The compartment within which the reaction executes.

returns reaction cobra.core.reaction.Reaction: The COBRA metabolite object of the respective metabolite.

from_dict()¶

Returns methods that return the template compound object and the name of the template compound, respectively:

reaction = rxn_template.from_dict(rxn_dict, template)

rxn_dict dict: A dictionary description of the ModelSEED reaction that possesses the following keys "id", "reaction_ref", "name", "type", "GapfillDirection", "base_cost", "reverse_penalty", "forward_penalty", & "status".
template modelseedpy.core.mstemplate.MSTemplate: The model template in which the reaction will be searched.

add_complexes() & get_complexes()¶

Concatenates a list of complexes to the existing list of complexes, and returns the list of complexes, respectively.

rxn_template.add_complexes(complex_list)
complexes = rxn_template.get_complexes()

complex_list list: The list of complexes that will be extended to the existing list of complexes.

returns complexes list: The collection of complexes in the MSTemplateReaction object.

cstoichiometry()¶

Property methods that return a dictionary of stoichiometric coefficients for each metabolite in the reaction:

rxn_stoichiometry = rxn_template.cstoichiometry()

returns rxn_stoichiometry dict: The stoichiometry of each metabolite in the reaction (value) for each metabolite ID and compartment as a tuple (key).

get_roles()¶

The set of all roles in all complexes are returned:

roles = rxn_template.get_roles()

returns roles set: The set of all roles in the complexes of the MSTemplateReaction object.

get_complex_roles()¶

The creates a dictionary of the roles for each complex:

roles = rxn_template.get_complex_roles()

returns roles dict: The set of all roles (keys) for each complex in the MSTemplateReaction object.

get_data()¶

Returns the reaction template content.

rxn_template_dict = rxn_template.get_data()

Returns rxn_template_dict dict: A dictionary of the MSTemplateReaction content.

NewModelTemplateRole¶

A class that defines a template role for a model:

new_model_tmp = NewModelTemplateRole(role_id, name, features=None, source='', aliases=None)

role_id & name str: The ID and name of the role that will be refined into a template.
features & aliases list: The collections of features and aliases of the role that will be translated into a template.
source str: The source of the role.

from_dict()¶

Returns a role template object that is constructed from a dictionary:

role_template = new_model_tmp.from_dict(role_dict)

role_dict dict: A dictionary description of the ModelSEED compound that possesses the following keys "id", "name", "features", "source", & "aliases".

Returns role_template modelseedpy.core.mstemplate.NewModelTemplateRole: A template role object.

get_data()¶

Returns the reaction template content.

role_template_dict = new_model_tmp.get_data()

Returns role_template_dict dict: A dictionary of the NewModelTemplateRole content.

repr() & str() & _repr_html_()¶

Constructs strings of the template content.

role_template_str = new_model_tmp.__repr__()
role_template_str = new_model_tmp.__str__()
role_template_str = new_model_tmp.__repr_html__()

Returns role_template_str str: formulations of the NewModelTemplateRole content.

NewModelTemplateComplex¶

A class that defines a template for a protein complex:

complex_template = NewModelTemplateComplex(complex_id, name, source='', reference='', confidence=0, template=None)

complex_id, name, source, reference str: The ID, name, source, and reference of the complex that will be refined into a template.
confidence int: A confidence rating of the
template modelseedpy.core.mstemplate.MSTemplate: The template upon which the complex will be added.

from_dict()¶

Returns a complex template object that is constructed from a dictionary:

complex = complex_template.from_dict(complex_dict, template)

complex_dict dict: A dictionary description of the ModelSEED compound that possesses the following keys "id", "name", "source", "reference", & "confidence".
template modelseedpy.core.mstemplate.MSTemplate: The template upon which the complex will be added.

Returns complex modelseedpy.core.mstemplate.NewModelTemplateComplex: A complex template object.

add_role()¶

Adds triggering and optional functions of a role to the dictionary of roles for the respective complex:

complex_template.add_role(role, triggering=True, optional=False)

role modelseedpy.core.mstemplate.NewModelTemplateRole: The role that will be added to the collection of roles for the complex.
triggering & optional bool: Descriptions of the role that will be added.

get_data()¶

Returns the complex template information:

complex_data = complex_template.get_data()

Returns complex_data dict: The complex template information.

repr() & str() & _repr_html_()¶

Constructs strings of the template content.

complex_template_str = complex_template.__repr__()
complex_template_str = complex_template.__str__()
complex_template_str = complex_template.__repr_html__()

Returns complex_template_str str: formulations of the NewModelTemplateComplex content.

MSTemplateCompartment¶

A class that defines template compartments:

complex_template = NewModelTemplateComplex(compartment_index: str, name: str, ph: float, hierarchy=0, aliases=None)

compartment_index & name str: The ID and name of the compartment that will be refined into a template.
ph float: The pH of the compartment.
hierarchy float: The pH of the compartment.
aliases list: The collection of alternative identifications for the compartment.

from_dict()¶

Returns a compartment template object that is constructed from a dictionary:

compartment = complex_template.from_dict(compartment_dict)

compartment_dict dict: A dictionary description of the ModelSEED compound that possesses the following keys "id", "name", "pH", "hierarchy", & "aliases".

Returns compartment modelseedpy.core.mstemplate.MSTemplateCompartment: A compartment template object.

get_data()¶

Returns the compartment template information:

complex_data = complex_template.get_data()

Returns complex_data dict: The complex template information.

MSTemplate¶

A class that defines model templates, while leveraging the aforementioned classes:

template = MSTemplate(template_id, name='', domain='', template_type='', version=1, info=None, args=None)

template_id, name, domain, & template_type str: The ID, name, domain, and type of the template that will be constructed.
version int: The version of the template.

add_compartments(), add_roles(), add_complexes(), add_compounds(), add_comp_compounds(), & add_reactions()¶

Functions that add compartments, roles, complexes, compartment compounds, and reactions, respectively, to the developing template. These functions will only add the provided values to the template when they are all unique:

template.add_compartments(compartments)
template.add_roles(roles)
template.add_complexes(complexes)
template.add_compounds(compounds)
template.add_comp_compounds(comp_compounds)
template.add_reactions(reactions)

compartments, roles, complexes, compounds, comp_compounds, & reactions list: The collections of compartments, roles, complexes, compounds, comp_compounds, and reactions that will be added to the template, provided that all list elements are not extant in the model.

get_complex_from_roles()¶

A function that yields a complex based upon a descriptive set of complex roles:

complex = template.get_complex_from_roles(roles)

roles list: The collection of complex roles that will be used to discern the associated complex.

Returns complex modelseedpy.core.mstemplate.NewModelTemplateComplex: The complex that is discerned from the collection of roles.

get_last_id_value()¶

A function that yields the largest id from a collection of COBRA objects:

last_id = template.get_complex_from_roles(objects)

objects list: The collection of COBRA objects whose IDs will be examined.

Returns last_id int: The largest ID from the collection of COBRA objects.

get_complex(), get_reaction(), & get_role()¶

A function that yields the largest id from a collection of COBRA objects:

complex = template.get_complex(obj_id)
reaction = template.get_reaction(obj_id)
role = template.get_role(obj_id)

obj_id str: The COBRA ID whose associated complex, reaction, and role will be examined.

Returns complex modelseedpy.core.mstemplate.NewModelTemplateComplex: The complex that matches the COBRA object ID. Returns reaction cobra.core.reaction.Reaction: The COBRA reaction that matches the ID. Returns role modelseedpy.core.mstemplate.NewModelTemplateRole: The role that matches the COBRA objects.

get_data()¶

A function that returns the template data:

template_data = template.get_data()

Returns template_data dict: The template data organized into a dictionary structure.

_repr_html_()¶

Constructs and returns strings of the template content:

template_html = template.__repr_html__()

Returns template_html str: A str of the template data organized into HTML.

MSTemplateBuilder¶

A class that defines model templates, while leveraging the aforementioned classes:

template = MSTemplateBuilder(template_id, name='', domain='', template_type='', version=1, info=None,
                biochemistry=None, biomasses=None, pathways=None, subsystems=None)

template_id, name, domain, & template_type str: The ID, name, domain, and type of the template that will be constructed.
version int: The version of the template.
info str: A description of the template that will be stored with the constructed template.

from_dict()¶

Returns a template builder object that is constructed from a dictionary:

builder = complex_template.from_dict(template_dict)

template_dict dict: A dictionary description of the template, which possesses keys of "id", "name", "domain", "type", "__VERSION__", "compartments", "roles", "complexes", "compounds", "compcompounds", "reactions", "biochemistry_ref", & "biomasses".

Returns builder modelseedpy.core.mstemplate.MSTemplateBuilder: The template builder object that was constructed from the dictionary.

from_template()¶

Returns a template builder object whose compartments are copied from an existing template:

builder = complex_template.from_dict(template)

template modelseedpy.core.mstemplate.MSTemplate: The template upon which the complex will be added.

Returns builder modelseedpy.core.mstemplate.MSTemplateBuilder: The template builder object that was partly copied from the existing template.

with_role()¶

Returns the complex reference for the given reaction and role IDs:

complex_ref = complex_template.with_role(template_rxn, role_ids, auto_complex=False)

template modelseedpy.core.mstemplate.MSTemplate: The template upon which the complex will be added.
role_ids list: The collection of role IDs for the complex that will identify the corresponding complex ID.
auto_complex bool: specifies whether a complex will be added from the roles if roles are not identified with an associated complex.

Returns complex_ref str: The complex reference path with the determined complex ID.

with_compartment()¶

Returns a matched compartment with the provided ID, otherwise the compartment is added to the MSTemplateBuilder object and the MSBuilder object is returned:

compartment = complex_template.with_compartment(cmp_id, name, ph=7, index='0')

cmp_id, name, & index str: The ID, name, and index of the compartment that will be returned or added to the template.
ph float: The pH of the corresponding compartment.

Returns compartment str: The compartment, or the first of numerous compartments, that matches the provided ID.

build()¶

The function that amalgamates the content of the MSTemplateBuilder object into a MSTemplate object:

template = complex_template.build()

Returns template modelseedpy.core.mstemplate.MSTemplate: The MSTemplate object that is constructed from the content of the MSTemplateBuilder object.

mstemplate¶

TemplateReactionType¶

MSTemplateMetabolite¶

from_dict()¶

get_data()¶

__repr__() & __str__() & _repr_html_()¶

MSTemplateSpecies¶

to_metabolite()¶

compound(), name(), & formula()¶

name() & formula()¶

from_dict()¶

get_data()¶

MSTemplateReaction¶

gene_reaction_rule()¶

compartment()¶

to_reaction()¶

from_dict()¶

add_complexes() & get_complexes()¶

cstoichiometry()¶

get_roles()¶

get_complex_roles()¶

get_data()¶

NewModelTemplateRole¶

from_dict()¶

get_data()¶

__repr__() & __str__() & _repr_html_()¶

NewModelTemplateComplex¶

from_dict()¶

add_role()¶

get_data()¶

__repr__() & __str__() & _repr_html_()¶

MSTemplateCompartment¶

from_dict()¶

get_data()¶

MSTemplate¶

add_compartments(), add_roles(), add_complexes(), add_compounds(), add_comp_compounds(), & add_reactions()¶

get_complex_from_roles()¶

get_last_id_value()¶

get_complex(), get_reaction(), & get_role()¶

get_data()¶

_repr_html_()¶

MSTemplateBuilder¶

from_dict()¶

from_template()¶

with_role()¶

with_compartment()¶

build()¶

repr() & str() & _repr_html_()¶

repr() & str() & _repr_html_()¶

repr() & str() & _repr_html_()¶