org.biopax.paxtools.model.level3
Interface DeltaG

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Level3Element, java.io.Serializable, UtilityClass

All Known Implementing Classes:

DeltaGImpl

public interface DeltaG
extends UtilityClass

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).

This property may have multiple values, representing different measurements for delta-G'^o obtained under the different experimental conditions listed in the 5-tuple.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

float	getDeltaGPrime0() 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.
float	getIonicStrength() 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).
float	getPh() 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.
float	getPMg() A measure of the concentration of magnesium (Mg) in solution.
float	getTemperature() Temperature in Celsius
void	setDeltaGPrime0(float deltaGPrime0) 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.
void	setIonicStrength(float ionicStrength) 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).
void	setPh(float ph) 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.
void	setPMg(float pmg) A measure of the concentration of magnesium (Mg) in solution.
void	setTemperature(float temperature) Temperature in Celsius

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getDeltaGPrime0

float getDeltaGPrime0()

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).

Returns:

delta-G'^o for this condition

setDeltaGPrime0

void setDeltaGPrime0(float deltaGPrime0)

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).

Parameters:

deltaGPrime0 - delta-G'^o for this condition

getIonicStrength

float getIonicStrength()

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

Returns:

the ionic strength for this condition

setIonicStrength

void setIonicStrength(float ionicStrength)

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

Parameters:

ionicStrength - the ionic strength for this condition

getPh

float getPh()

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)

Returns:

pH for this condition

setPh

void setPh(float ph)

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)

Parameters:

ph - for this condition

getPMg

float getPMg()

A measure of the concentration of magnesium (Mg) in solution. (pMg = -log₁₀[Mg²⁺])

Returns:

pMG for this condition

setPMg

void setPMg(float pmg)

A measure of the concentration of magnesium (Mg) in solution. (pMg = -log₁₀[Mg²⁺])

Parameters:

pmg - for this condition

getTemperature

float getTemperature()

Temperature in Celsius

Returns:

Temperature in Celsius for this condition

setTemperature

void setTemperature(float temperature)

Temperature in Celsius