6.1.1.2.1.2. equilibrator_api.model.model
¶
a basic stoichiometric model with thermodynamics.
6.1.1.2.1.2.1. Module Contents¶
- class equilibrator_api.model.model.StoichiometricModel(S: pandas.DataFrame, compound_dict: Dict[str, equilibrator_cache.Compound], reaction_dict: Dict[str, equilibrator_cache.Reaction], comp_contrib: Optional[equilibrator_api.ComponentContribution] = None, standard_dg_primes: Optional[equilibrator_api.Q_] = None, dg_sigma: Optional[equilibrator_api.Q_] = None, bounds: Optional[equilibrator_api.model.Bounds] = None, config_dict: Optional[Dict[str, str]] = None)[source]¶
Bases:
object
A basic stoichiometric model with thermodynamics.
Designed as a base model for ‘Pathway’ which also includes flux directions and magnitudes.
- property compounds Iterable[equilibrator_cache.Compound] [source]¶
Get the list of Compound objects.
- property compound_df pandas.DataFrame [source]¶
Get a DataFrame with all the compound data.
- The columns are:
compound_id lower_bound upper_bound
- property reactions Iterable[equilibrator_cache.Reaction] [source]¶
Get the list of Reaction objects.
- property reaction_formulas Iterable[str] [source]¶
Iterate through all the reaction formulas.
- Returns
the reaction formulas
- property reaction_df pandas.DataFrame [source]¶
Get a DataFrame with all the reaction data.
- The columns are:
reaction_id reaction_formula standard_dg_prime
- update_standard_dgs() None [source]¶
Calculate the standard ΔG’ values and uncertainties.
Use the Component Contribution method.
- set_bounds(cid: str, lb: Optional[equilibrator_api.Q_] = None, ub: Optional[equilibrator_api.Q_] = None) None [source]¶
Set the lower and upper bound of a compound.
- Parameters
compound_id (str) – the compound ID
lb (Quantity, optional) – the new concentration lower bound (ignored if the value is None)
ub (Quantity, optional) – the new concentration upper bound (ignored if the value is None)
- get_bounds(cid: str) Tuple[equilibrator_api.Q_, equilibrator_api.Q_] [source]¶
Get the lower and upper bound of a compound.
- Parameters
compound_id (str) – the compound ID
- Returns
lb (Quantity, optional) – the new concentration lower bound (ignored if the value is None)
ub (Quantity, optional) – the new concentration upper bound (ignored if the value is None)
- property bounds Tuple[Iterable[equilibrator_api.Q_], Iterable[equilibrator_api.Q_]] [source]¶
Get the concentration bounds.
The order of compounds is according to the stoichiometric matrix index.
- Return type
tuple of (lower bounds, upper bounds)
- property ln_conc_lb numpy.array [source]¶
Get the log lower bounds on the concentrations.
The order of compounds is according to the stoichiometric matrix index.
- Return type
a NumPy array of the log lower bounds
- property ln_conc_ub numpy.ndarray [source]¶
Get the log upper bounds on the concentrations.
The order of compounds is according to the stoichiometric matrix index.
- Return type
a NumPy array of the log upper bounds
- property ln_conc_mu numpy.array [source]¶
Get mean of log concentration distribution based on the bounds.
The order of compounds is according to the stoichiometric matrix index.
- Return type
a NumPy array with the mean of the log concentrations
- property ln_conc_sigma numpy.array [source]¶
Get stdev of log concentration distribution based on the bounds.
- Return type
a NumPy array with the stdev of the log concentrations
- static read_thermodynamics(thermo_sbtab: equilibrator_api.model.SBtabTable, config_dict: Dict[str, str]) Dict[str, equilibrator_api.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
- Return type
A dictionary mapping reaction IDs to standard ΔG’ values.
- classmethod from_network_sbtab(filename: Union[str, equilibrator_api.model.SBtabDocument], comp_contrib: Optional[equilibrator_api.ComponentContribution] = None, freetext: bool = True, bounds: Optional[equilibrator_api.model.Bounds] = None) StoichiometricModel [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)
- Return type
a Pathway object
- classmethod from_sbtab(filename: Union[str, equilibrator_api.model.SBtabDocument], comp_contrib: Optional[equilibrator_api.ComponentContribution] = None) 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