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: equilibrator_api.ComponentContribution | None = None, standard_dg_primes: equilibrator_api.Q_ | None = None, dg_sigma: equilibrator_api.Q_ | None = None, bounds: equilibrator_api.model.Bounds | None = None, config_dict: Dict[str, str] | None = None)[source]
Bases:
objectA 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
- 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
- update_standard_dgs() None[source]
Calculate the standard ΔG’ values and uncertainties.
Use the Component Contribution method.
- set_bounds(cid: str, lb: equilibrator_api.Q_ | None = None, ub: equilibrator_api.Q_ | None = 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)
- 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: str | equilibrator_api.model.SBtabDocument, comp_contrib: equilibrator_api.ComponentContribution | None = None, freetext: bool = True, bounds: equilibrator_api.model.Bounds | None = 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: str | equilibrator_api.model.SBtabDocument, comp_contrib: equilibrator_api.ComponentContribution | None = 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: