6.1.1.3.1.2. pytfa.io.dict

Make the model serializable

6.1.1.3.1.2.1. Module Contents

6.1.1.3.1.2.1.1. Functions

get_all_subclasses(cls)

make_subclasses_dict(cls)

get_model_variable_subclasses()

get_model_constraint_subclasses()

metabolite_thermo_to_dict(metthermo)

var_to_dict(variable)

cons_to_dict(constraint)

archive_variables(var_dict)

archive_constraints(cons_dict)

archive_compositions(compositions)

Turns a peptide compositions dict of the form:

_stoichiometry_to_dict(stoichiometric_dict)

Turns a stoichiometric compositions dict of the form:

get_solver_string(model)

obj_to_dict(model)

model_to_dict(model)

param model

_add_thermo_reaction_info(rxn, rxn_dict)

_add_thermo_metabolite_info(met, met_dict)

model_from_dict(obj, solver=None, custom_hooks=None)

Custom_hooks looks like

rebuild_obj_from_dict(new, objective_dict)

add_custom_classes(model, custom_hooks)

Allows custom variable serialization

get_hook_dict(model, custom_hooks)

init_thermo_model_from_dict(new, obj)

rebuild_compositions(new, compositions_dict)

Performs the reverse operation of :func:archive_compositions

_rebuild_stoichiometry(new, stoich)

Performs the reverse operation of :func:_stoichiometry_to_dict

6.1.1.3.1.2.1.2. Attributes

BASE_NAME2HOOK

SOLVER_DICT

pytfa.get_all_subclasses(cls)
pytfa.make_subclasses_dict(cls)
pytfa.get_model_variable_subclasses()
pytfa.get_model_constraint_subclasses()
pytfa.BASE_NAME2HOOK
pytfa.SOLVER_DICT
pytfa.metabolite_thermo_to_dict(metthermo)
pytfa.var_to_dict(variable)
pytfa.cons_to_dict(constraint)
pytfa.archive_variables(var_dict)
pytfa.archive_constraints(cons_dict)
pytfa.archive_compositions(compositions)

Turns a peptide compositions dict of the form: { ‘b3991’: defaultdict(int,

{<Metabolite ala__L_c at 0x7f7d25504f28>: -42,

<Metabolite arg__L_c at 0x7f7d2550bcf8>: -11, <Metabolite asn__L_c at 0x7f7d2550beb8>: -6, …}),

…}

to:

{ ‘b3991’: defaultdict(int,,
{‘ala__L_c’: -42,

‘arg__L_c’: -11, ‘asn__L_c’: -6,

…}),

…} :param compositions: :return:

pytfa._stoichiometry_to_dict(stoichiometric_dict)

Turns a stoichiometric compositions dict of the form: ‘b3991’: defaultdict(int,

{<Metabolite ala__L_c at 0x7f7d25504f28>: -42,

<Metabolite arg__L_c at 0x7f7d2550bcf8>: -11, <Metabolite asn__L_c at 0x7f7d2550beb8>: -6, …})

to:

‘b3991’: defaultdict(int,,
{‘ala__L_c’: -42,

‘arg__L_c’: -11, ‘asn__L_c’: -6,

…})

pytfa.get_solver_string(model)
pytfa.obj_to_dict(model)
pytfa.model_to_dict(model)
Parameters

model

Returns

pytfa._add_thermo_reaction_info(rxn, rxn_dict)
pytfa._add_thermo_metabolite_info(met, met_dict)
pytfa.model_from_dict(obj, solver=None, custom_hooks=None)

Custom_hooks looks like

custom_hooks = {<EnzymeVariable Class at 0xffffff> : 'enzymes',
                ... }
Parameters
  • obj

  • solver

  • custom_hooks

Returns

pytfa.rebuild_obj_from_dict(new, objective_dict)
pytfa.add_custom_classes(model, custom_hooks)

Allows custom variable serialization

Parameters
  • model

  • base_classes

  • base_hooks

  • custom_hooks

Returns

pytfa.get_hook_dict(model, custom_hooks)
pytfa.init_thermo_model_from_dict(new, obj)
pytfa.rebuild_compositions(new, compositions_dict)

Performs the reverse operation of :func:archive_compositions

Parameters
  • new

  • compositions_dict

Returns

pytfa._rebuild_stoichiometry(new, stoich)

Performs the reverse operation of :func:_stoichiometry_to_dict

Parameters
  • new

  • stoich

Returns