6.1.2.3. equilibrator_api.phased_compound

inherit from equilibrator_cache.models.compound.Compound an add phases.

6.1.2.3.1. Module Contents

equilibrator_api.phased_compound.AQUEOUS_PHASE_NAME = aqueous

equilibrator_api.phased_compound.GAS_PHASE_NAME = gas

equilibrator_api.phased_compound.LIQUID_PHASE_NAME = liquid

equilibrator_api.phased_compound.SOLID_PHASE_NAME = solid

equilibrator_api.phased_compound.REDOX_PHASE_NAME = redox

equilibrator_api.phased_compound.PhaseInfo

equilibrator_api.phased_compound.PHASE_INFO_DICT

equilibrator_api.phased_compound.NON_AQUEOUS_COMPOUND_DICT

equilibrator_api.phased_compound.MicroSpecie

equilibrator_api.phased_compound.PHASED_COMPOUND_DICT

equilibrator_api.phased_compound.CARBONATE_INCHIS

class equilibrator_api.phased_compound.Condition(phase: str, abundance: equilibrator_api.ureg.Quantity = None)

Bases: object

A class for defining the conditions of a compound.

I.e. the phase and the abundance.

property phase → str

Return the phase.

property abundance → equilibrator_api.ureg.Quantity

Return the abundance.

property standard_abundance → equilibrator_api.ureg.Quantity

Return the standard abundance in this phase.

property physiolical_abundance → equilibrator_api.ureg.Quantity

Return the default physiological abundance in this phase.

property dimensionality → str

Return the dimensionality of the abundance in this phase.

E.g. [concentration] for aqueous phase, or [pressure] for gas phase. :return: the dimensionality in this phase, or None if abundance is fixed.

property ln_abundance → float

Return the log of the ratio between given and std abundances.

property ln_physiological_abundance → float

Return the log of the ratio between phys and std abundances.

reset_abundance() → None

Reset the abundance to standard abundance.

property is_physiological → bool

Return True iff the abundance is the same as the physiological.

Returns

True if the abundance is in physiological conditions,

or if the abundance if fixed in this phase anyway.

class equilibrator_api.phased_compound.PhasedCompound(compound: equilibrator_cache.Compound, condition: Condition = None)

Bases: object

A class that combines a equilibrator_api Compound and a Condition.

static get_default(compound: equilibrator_cache.Compound) → Condition

Get the default phase of a compound.

Parameters

compound – a Compound

Returns

the default phase

property atom_bag → dict

Get the compound’s atom bag.

property smiles → str

Get the compound’s InChI.

property inchi → str

Get the compound’s InChI.

property inchi_key → str

Get the compound’s InChIKey.

property id → int

Get the compound’s equilibrator internal ID.

property formula → str

Get the chemical formula.

property mass → float

Get the chemical molecular mass.

property phase → str

Get the phase.

property html_formula → str

Get the chemical formula.

property phase_shorthand → str

Get the phase shorthand (i.e. ‘l’ for liquid).

property possible_phases → Tuple[str]

Get the possible phases for this compound.

property abundance → equilibrator_api.ureg.Quantity

Get the abundance.

property ln_abundance → float

Return the log of the abundance (for thermodynamic calculations).

property ln_physiological_abundance → float

Return the log of the default physiological abundance.

property is_physiological → bool

Check if the abundance is physiological.

get_stored_standard_dgf_prime(p_h: equilibrator_api.ureg.Quantity, ionic_strength: equilibrator_api.ureg.Quantity, temperature: equilibrator_api.ureg.Quantity, p_mg: equilibrator_api.ureg.Quantity) → equilibrator_api.ureg.Quantity

Return the stored formation energy of this phased compound.

Only if it exists, otherwise return None (and we will use component-contribution later to get the reaction energy).

Parameters

• p_h –

• ionic_strength –

• temperature –

• p_mg –

Returns

standard_dgf_prime (in kJ/mol)

get_stored_standard_dgf() → equilibrator_api.ureg.Quantity

Return the stored formation energy of this phased compound.

Only if it exists, otherwise return None (and we will use component-contribution later to get the reaction energy).

Returns

standard_dgf (in kJ/mol)

get_stored_microspecie() → MicroSpecie

Get the stored microspecies (from the PHASED_COMPOUND_DICT).

Returns

The MicroSpecie namedtuple with the stored formation energy,

or None if this compound has no stored value at this phase.

serialize() → dict

Return a serialized version of all the compound thermo data.

Returns

a list of dictionaries with all the microspecies data

class equilibrator_api.phased_compound.Proton(compound: equilibrator_cache.Compound)

Bases: PhasedCompound

A class specifically for protons.

property abundance → equilibrator_api.ureg.Quantity

Get the abundance.

property ln_physiological_abundance → float

Return the log of the default physiological abundance.

property ln_abundance → float

Return the log of the abundance (for thermodynamic calculations).

class equilibrator_api.phased_compound.RedoxCarrier(compound: equilibrator_cache.Compound, potential: Optional[equilibrator_api.ureg.Quantity] = None)

Bases: PhasedCompound

A class specifically for redox carriers (with a given potential).

get_stored_standard_dgf_prime(p_h: equilibrator_api.ureg.Quantity, ionic_strength: equilibrator_api.ureg.Quantity, temperature: equilibrator_api.ureg.Quantity, p_mg: equilibrator_api.ureg.Quantity) → equilibrator_api.ureg.Quantity

Get the standard formation ΔG’.

get_stored_standard_dgf() → equilibrator_api.ureg.Quantity

Get the standard formation ΔG.

property atom_bag → dict

Get the compound’s atom bag.

property ln_abundance → float

Return the log of the abundance (for thermodynamic calculations).

property ln_physiological_abundance → float

Return the log of the default physiological abundance.

property is_physiological → bool

Check if the abundance is physiological.