DeltaG#

class biopax-explorer.biopax.deltag.DeltaG(*args, **kwargs)[source]#

Bases: UtilityClass

Class DeltaG

Definition: Standard transformed Gibbs energy change for a reaction written in

terms of biochemical reactants. Usage: Delta-G is represented as a 5-tuple of delta-G’⁰, temperature, ionic strength , pH, and pMg . A conversion in BioPAX may have multiple Delta-G values, representing different measurements for delta-G’⁰ obtained under the different experimental conditions.

code generator : rdfobj (author F.Moreews 2023-2024).

Methods

get_comment()	Attribute _comment getter
get_deltaGPrime0()	Attribute _deltaGPrime0 getter
get_ionicStrength()	Attribute _ionicStrength getter
get_pMg()	Attribute _pMg getter
get_ph()	Attribute _ph getter
get_temperature()	Attribute _temperature getter

attribute_type_by_name
get_uri_string
object_attributes
set_comment
set_deltaGPrime0
set_ionicStrength
set_pMg
set_ph
set_temperature
set_uri_string
to_json
type_attributes

Methods Summary

attribute_type_by_name()
get_deltaGPrime0()	Attribute _deltaGPrime0 getter
get_ionicStrength()	Attribute _ionicStrength getter
get_pMg()	Attribute _pMg getter
get_ph()	Attribute _ph getter
get_temperature()	Attribute _temperature getter
get_uri_string()
object_attributes()
set_deltaGPrime0(value)
set_ionicStrength(value)
set_pMg(value)
set_ph(value)
set_temperature(value)
set_uri_string(uristr)
to_json()
type_attributes()

Methods Documentation

attribute_type_by_name()[source]#

get_deltaGPrime0()[source]#

Attribute _deltaGPrime0 getter

For biochemical reactions, this property refers to the standard transformed

Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G’^o. delta-G’^o = -RT lnK’ and delta-G’^o = delta-H’^o - T delta-S’^o delta-G’^o has units of kJ/mol. Like K’, it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G’^o T I pH pMg).

get_ionicStrength()[source]#

Attribute _ionicStrength getter

The ionic strength is defined as half of the total sum of the concentration (ci)

of every ionic species (i) in the solution times the square of its charge (zi). For example, the ionic strength of a 0.1 M solution of CaCl2 is 0.5 x (0.1 x 22 + 0.2 x 12) = 0.3 M

get_pMg()[source]#

Attribute _pMg getter

A measure of the concentration of magnesium (Mg) in solution. (pMg =

-log₁₀[Mg²⁺])

get_ph()[source]#

Attribute _ph getter

A measure of acidity and alkalinity of a solution that is a number on a scale on

which a value of 7 represents neutrality and lower numbers indicate increasing acidity and higher numbers increasing alkalinity and on which each unit of change represents a tenfold change in acidity or alkalinity and that is the negative logarithm of the effective hydrogen-ion concentration or hydrogen-ion activity in gram equivalents per liter of the solution. (Definition from Merriam-Webster Dictionary)

get_temperature()[source]#

Attribute _temperature getter

Temperature in Celsius

get_uri_string()[source]#

object_attributes()[source]#

set_deltaGPrime0(value)[source]#

set_ionicStrength(value)[source]#

set_pMg(value)[source]#

set_ph(value)[source]#

set_temperature(value)[source]#

set_uri_string(uristr)[source]#

to_json()[source]#

type_attributes()[source]#