1.1.1.2.1.2. equilibrator_api.model.model¶
a basic stoichiometric model with thermodynamics.
1.1.1.2.1.2.1. Module Contents¶
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class
equilibrator_api.model.model.StoichiometricModel(reactions: List[Reaction], comp_contrib: Optional[ComponentContribution] = None, standard_dg_primes: Optional[Q_] = None, dg_sigma: Optional[Q_] = None, bounds: Optional[Bounds] = None, config_dict: Optional[Dict[str, str]] = None, compound_id_mapping: Callable[[Compound], str] = None)[source]¶ Bases:
objectA basic stoichiometric model with thermodynamics.
Designed as a base model for ‘Pathway’ which also includes flux directions and magnitudes.
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update_standard_dgs(self) → None[source]¶ Calculate the standard ΔG’ values and uncertainties.
Use the Component Contribution method.
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set_compound_ids(self, mapping: Callable[[Compound], str] = None) → None[source]¶ Use alternative compound names for outputs such as plots.
- Parameters
mapping (callable, optional) – a function mapping compounds to their names in the model
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property
bounds(self) → Tuple[Iterable[float], Iterable[float]][source]¶ Get the concentration bounds.
The order of compounds is according to the stoichiometric matrix index.
- Returns
- Return type
tuple of (lower bounds, upper bounds)
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property
ln_conc_lb(self) → numpy.array[source]¶ Get the log lower bounds on the concentrations.
The order of compounds is according to the stoichiometric matrix index.
- Returns
- Return type
a NumPy array of the log lower bounds
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property
ln_conc_ub(self) → numpy.ndarray[source]¶ Get the log upper bounds on the concentrations.
The order of compounds is according to the stoichiometric matrix index.
- Returns
- Return type
a NumPy array of the log upper bounds
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static
get_compounds(reactions: Iterable[Reaction]) → List[Compound][source]¶ Get a unique list of all compounds in all reactions.
- Parameters
reactions – an iterator of reactions
- Returns
a list of unique compounds
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property
reaction_ids(self) → Iterable[str][source]¶ Iterate through all the reaction IDs.
- Returns
the reaction IDs
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property
reaction_formulas(self) → Iterable[str][source]¶ Iterate through all the reaction formulas.
- Returns
the reaction formulas
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static
read_thermodynamics(thermo_sbtab: equilibrator_api.model.SBtabTable, config_dict: Dict[str, str]) → Dict[str, Q_][source]¶ Read the ‘thermodynamics’ table from an SBtab.
- Parameters
thermo_sbtab (SBtabTable) – A SBtabTable containing the thermodynamic data
config_dict (dict) – A dictionary containing the configuration arguments
- Returns
- Return type
A dictionary mapping reaction IDs to standard ΔG’ values.
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classmethod
from_network_sbtab(cls, filename: Union[str, SBtabDocument], comp_contrib: Optional[ComponentContribution] = None, freetext: bool = True, bounds: Optional[Bounds] = None) → object[source]¶ Initialize a Pathway object using a ‘network’-only SBtab.
- Parameters
filename (str, SBtabDocument) – a filename containing an SBtabDocument (or the SBtabDocument object itself) defining the network (topology) only
comp_contrib (ComponentContribution, optional) – a ComponentContribution object needed for parsing and searching the reactions. also used to set the aqueous parameters (pH, I, etc.)
freetext (bool, optional) – a flag indicating whether the reactions are given as free-text (i.e. common names for compounds) or by standard database accessions (Default value: True)
bounds (Bounds, optional) – bounds on metabolite concentrations (by default uses the “data/cofactors.csv” file in equilibrator-api)
- Returns
- Return type
a Pathway object
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classmethod
from_sbtab(cls, filename: Union[str, SBtabDocument], comp_contrib: Optional[ComponentContribution] = None) → equilibrator_api.model.model.StoichiometricModel[source]¶ Parse and SBtabDocument and return a StoichiometricModel.
- Parameters
filename (str or SBtabDocument) – a filename containing an SBtabDocument (or the SBtabDocument object itself) defining the pathway
comp_contrib (ComponentContribution, optional) – a ComponentContribution object needed for parsing and searching the reactions. also used to set the aqueous parameters (pH, I, etc.)
- Returns
stoich_model – A StoichiometricModel object based on the configuration SBtab
- Return type
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