6.1.2.2. equilibrator_api.component_contribution
A wrapper for the GibbeEnergyPredictor in component-contribution.
6.1.2.2.1. Module Contents
- equilibrator_api.component_contribution.find_most_abundant_ms(cpd: equilibrator_cache.Compound, p_h: equilibrator_api.Q_, p_mg: equilibrator_api.Q_, ionic_strength: equilibrator_api.Q_, temperature: equilibrator_api.Q_) equilibrator_cache.CompoundMicrospecies [source]
Find the most abundant microspecies based on transformed energies.
- equilibrator_api.component_contribution.predict_protons_and_charge(rxn: equilibrator_api.phased_reaction.PhasedReaction, p_h: equilibrator_api.Q_, p_mg: equilibrator_api.Q_, ionic_strength: equilibrator_api.Q_, temperature: equilibrator_api.Q_) Tuple[float, float, float] [source]
Find the #protons and charge of a transport half-reaction.
- class equilibrator_api.component_contribution.ComponentContribution(rmse_inf: equilibrator_api.Q_ = default_rmse_inf, ccache: equilibrator_cache.CompoundCache | None = None, predictor: component_contribution.predict.GibbsEnergyPredictor | None = None)[source]
Bases:
object
A wrapper class for GibbsEnergyPredictor.
Also holds default conditions for compounds in the different phases.
- static legacy() ComponentContribution [source]
Initialize a ComponentContribution object with the legacy version.
The legacy version is intended for compatibility with older versions of equilibrator api (0.2.x - 0.3.1). Starting from 0.3.2, there is a significant change in the predictions caused by an improved Mg2+ concentration model.
- Return type:
A ComponentContribution object
- static initialize_custom_version(rmse_inf: equilibrator_api.Q_ = default_rmse_inf, ccache_settings: component_contribution.ZenodoSettings = DEFAULT_COMPOUND_CACHE_SETTINGS, cc_params_settings: component_contribution.ZenodoSettings = DEFAULT_CC_PARAMS_SETTINGS) ComponentContribution [source]
Initialize ComponentContribution object with custom Zenodo versions.
- Parameters:
rmse_inf (Quantity, optional) – Set the factor by which to multiply the error covariance matrix for reactions outside the span of Component Contribution. (Default value: 1e-5 kJ/mol)
settings (ZenodoSettings) – The doi, filename and md5 of the
- Return type:
A ComponentContribution object
- get_compound(compound_id: str) equilibrator_cache.Compound | None [source]
Get a Compound using the DB namespace and its accession.
- Returns:
cpd
- Return type:
Compound
- get_compound_by_inchi(inchi: str) equilibrator_cache.Compound | None [source]
Get a Compound using InChI.
- Returns:
cpd
- Return type:
Compound
- search_compound_by_inchi_key(inchi_key: str) List[equilibrator_cache.Compound] [source]
Get a Compound using InChI.
- Returns:
cpd
- Return type:
Compound
- search_compound(query: str) None | equilibrator_cache.Compound [source]
Try to find the compound that matches the name best.
- Parameters:
query (str) – an (approximate) compound name
- Returns:
cpd – the best match
- Return type:
Compound
- parse_reaction_formula(formula: str) equilibrator_api.phased_reaction.PhasedReaction [source]
Parse reaction text using exact match.
- Parameters:
formula (str) – a string containing the reaction formula
- Returns:
rxn
- Return type:
- search_reaction(formula: str) equilibrator_api.phased_reaction.PhasedReaction [source]
Search a reaction written using compound names (approximately).
- Parameters:
formula (str) – a string containing the reaction formula
- Returns:
rxn
- Return type:
- balance_by_oxidation(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.phased_reaction.PhasedReaction [source]
Convert an unbalanced reaction into an oxidation reaction.
By adding H2O, O2, Pi, CO2, and NH4+ to both sides.
- get_oxidation_reaction(compound: equilibrator_cache.Compound) equilibrator_api.phased_reaction.PhasedReaction [source]
Generate an oxidation Reaction for a single compound.
Generate a Reaction object which represents the oxidation reaction of this compound using O2. If there are N atoms, the product must be NH3 (and not N2) to represent biological processes. Other atoms other than C, N, H, and O will raise an exception.
- standard_dg_formation(compound: equilibrator_cache.Compound) Tuple[float | None, numpy.ndarray | None] [source]
Get the (mu, sigma) predictions of a compound’s formation energy.
- Parameters:
compound (Compound) – a Compound object
- Returns:
mu (float) – the mean of the standard formation Gibbs energy estimate
sigma_fin (array) – a vector representing the square root of the covariance matrix (uncertainty)
sigma_inf (array) – a vector representing the infinite-uncertainty eigenvalues of the covariance matrix
- standard_dg(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Measurement [source]
Calculate the chemical reaction energies of a reaction.
- Returns:
standard_dg – the dG0 in kJ/mol and standard error. To calculate the 95% confidence interval, use the range -1.96 to 1.96 times this value
- Return type:
ureg.Measurement
- standard_dg_multi(reactions: List[equilibrator_api.phased_reaction.PhasedReaction], uncertainty_representation: str = 'cov') Tuple[numpy.ndarray, numpy.ndarray] [source]
Calculate the chemical reaction energies of a list of reactions.
Using the major microspecies of each of the reactants.
- Parameters:
reactions (List[PhasedReaction]) – a list of PhasedReaction objects to estimate
uncertainty_representation (str) – which representation to use for the uncertainties. cov would return a full covariance matrix. precision would return the precision matrix (i.e. the inverse of the covariance matrix). sqrt would return a sqaure root of the covariance, based on the uncertainty vectors. fullrank would return a full-rank square root of the covariance which is a compressed form of the sqrt result. (Default value: cov)
- Returns:
standard_dg (Quantity) – the estimated standard reaction Gibbs energies based on the the major microspecies
dg_uncertainty (Quantity) – the uncertainty matrix (in either ‘cov’, ‘sqrt’ or ‘fullrank’ format)
- standard_dg_prime(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Measurement [source]
Calculate the transformed reaction energies of a reaction.
- Returns:
standard_dg – the dG0_prime in kJ/mol and standard error. To calculate the 95% confidence interval, use the range -1.96 to 1.96 times this value
- Return type:
ureg.Measurement
- dg_prime(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Measurement [source]
Calculate the dG’0 of a single reaction.
- Returns:
dg – the dG_prime in kJ/mol and standard error. To calculate the 95% confidence interval, use the range -1.96 to 1.96 times this value
- Return type:
ureg.Measurement
- standard_dg_prime_multi(reactions: List[equilibrator_api.phased_reaction.PhasedReaction], uncertainty_representation: str = 'cov', minimize_norm: bool = False) Tuple[equilibrator_api.Q_, equilibrator_api.Q_] [source]
Calculate the transformed reaction energies of a list of reactions.
- Parameters:
reactions (List[PhasedReaction]) – a list of PhasedReaction objects to estimate
uncertainty_representation (str) – which representation to use for the uncertainties. cov would return a full covariance matrix. precision would return the precision matrix (i.e. the inverse of the covariance matrix). sqrt would return a sqaure root of the covariance, based on the uncertainty vectors. fullrank would return a full-rank square root of the covariance which is a compressed form of the sqrt result. (Default value: cov)
minimize_norm (bool) – if True, use an orthogonal projection to minimize the norm2 of the result vector (keeping it within the finite-uncertainty sub-space, i.e. only moving along eigenvectors with infinite uncertainty).
- Returns:
standard_dg_prime (Quantity) – the CC estimation of the reactions’ standard transformed energies
dg_uncertainty (Quantity) – the uncertainty co-variance matrix (in either ‘cov’, ‘sqrt’ or ‘fullrank’ format)
- physiological_dg_prime(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Measurement [source]
Calculate the dG’m of a single reaction.
Assume all aqueous reactants are at 1 mM, gas reactants at 1 mbar and the rest at their standard concentration.
- Returns:
standard_dg_primes (ndarray) – a 1D NumPy array containing the CC estimates for the reactions’ physiological dG’
dg_sigma (ndarray) – the second is a 2D numpy array containing the covariance matrix of the standard errors of the estimates. one can use the eigenvectors of the matrix to define a confidence high-dimensional space, or use dg_sigma as the covariance of a Gaussian used for sampling (where ‘standard_dg_primes’ is the mean of that Gaussian).
- dgf_prime_sensitivity_to_p_h(compound: equilibrator_cache.Compound) equilibrator_api.ureg.Quantity [source]
Calculate the sensitivity of the chemical formation energy to pH.
- Returns:
The derivative of \(\Delta G_f\) with respect to pH, in kJ/mol.
- Return type:
Quantity
- dg_prime_sensitivity_to_p_h(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Quantity [source]
Calculate the sensitivity of the chemical reaction energy to pH.
- Returns:
The derivative of \(\Delta G_r\) with respect to pH, in kJ/mol.
- Return type:
Quantity
- ln_reversibility_index(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Measurement [source]
Calculate the reversibility index (ln Gamma) of a single reaction.
- Returns:
ln_RI – the reversibility index (in natural log scale).
- Return type:
ureg.Measurement
- standard_e_prime(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Measurement [source]
Calculate the E’0 of a single half-reaction.
- Returns:
standard_e_prime (ureg.Measurement)
the estimated standard electrostatic potential of reaction and
E0_uncertainty is the standard deviation of estimation. Multiply it
by 1.96 to get a 95% confidence interval (which is the value shown on
eQuilibrator).
- physiological_e_prime(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Measurement [source]
Calculate the E’0 of a single half-reaction.
- Returns:
physiological_e_prime (ureg.Measurement)
the estimated physiological electrostatic potential of reaction and
E0_uncertainty is the standard deviation of estimation. Multiply it
by 1.96 to get a 95% confidence interval (which is the value shown on
eQuilibrator).
- e_prime(reaction: equilibrator_api.phased_reaction.PhasedReaction) equilibrator_api.ureg.Measurement [source]
Calculate the E’0 of a single half-reaction.
- Returns:
e_prime (ureg.Measurement)
the estimated electrostatic potential of reaction and
E0_uncertainty is the standard deviation of estimation. Multiply it
by 1.96 to get a 95% confidence interval (which is the value shown on
eQuilibrator).
- dg_analysis(reaction: equilibrator_api.phased_reaction.PhasedReaction) Iterable[Dict[str, object]] [source]
Get the analysis of the component contribution estimation process.
- Return type:
the analysis results as a list of dictionaries
- is_using_group_contribution(reaction: equilibrator_api.phased_reaction.PhasedReaction) bool [source]
Check whether group contribution is needed to get this reactions’ dG.
- Return type:
true iff group contribution is needed
- multicompartmental_standard_dg_prime(reaction_inner: equilibrator_api.phased_reaction.PhasedReaction, reaction_outer: equilibrator_api.phased_reaction.PhasedReaction, e_potential_difference: equilibrator_api.Q_, p_h_outer: equilibrator_api.Q_, ionic_strength_outer: equilibrator_api.Q_, p_mg_outer: equilibrator_api.Q_ = default_physiological_p_mg, tolerance: float = 0.0) equilibrator_api.ureg.Measurement [source]
Calculate the transformed energies of a multi-compartmental reaction.
Based on the equations from Harandsdottir et al. 2012 (https://doi.org/10.1016/j.bpj.2012.02.032)
- Parameters:
reaction_inner (PhasedReaction) – the inner compartment half-reaction
reaction_outer (PhasedReaction) – the outer compartment half-reaction
e_potential_difference (Quantity) – the difference in electro-static potential between the outer and inner compartments
p_h_outer (Quantity) – the pH in the outside compartment
ionic_strength_outer (Quantity) – the ionic strength outside
p_mg_outer (Quantity (optional)) – the pMg in the outside compartment
tolerance (Float (optional)) – tolerance for identifying inbalance between inner and outer reactions (default = 0)
- Returns:
standard_dg_prime – the transport reaction Gibbs free energy change
- Return type:
Measurement
- static parse_formula_side(s: str) Dict[str, float] [source]
Parse one side of the reaction formula.
- static create_stoichiometric_matrix_from_reaction_formulas(formulas: Iterable[str]) pandas.DataFrame [source]
Build a stoichiometric matrix.
- Parameters:
formulas (Iterable[str]) – String representations of the reactions.
- Returns:
The stoichiometric matrix as a DataFrame whose indexes are the compound IDs and its columns are the reaction IDs (in the same order as the input).
- Return type:
DataFrame
- create_stoichiometric_matrix_from_reaction_objects(reactions: Iterable[equilibrator_api.phased_reaction.PhasedReaction]) pandas.DataFrame [source]
Build a stoichiometric matrix.
- Parameters:
reactions (Iterable[PhasedReaction]) – The collection of reactions to build a stoichiometric matrix from.
- Returns:
The stoichiometric matrix as a DataFrame whose indexes are the compounds and its columns are the reactions (in the same order as the input).
- Return type:
DataFrame