org.biopax.paxtools.impl.level3
Class KPrimeImpl

java.lang.Object
  org.biopax.paxtools.impl.BioPAXElementImpl
      org.biopax.paxtools.impl.level3.L3ElementImpl
          org.biopax.paxtools.impl.level3.KPrimeImpl

All Implemented Interfaces:

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

@Entity
@Indexed
public class KPrimeImpl
extends L3ElementImpl
implements KPrime

See Also:

Serialized Form

Nested Class Summary

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

BioPAXElement.Key

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

SEARCH_FIELD_AVAILABILITY, SEARCH_FIELD_COMMENT, SEARCH_FIELD_EC_NUMBER, SEARCH_FIELD_KEYWORD, SEARCH_FIELD_NAME, SEARCH_FIELD_SEQUENCE, SEARCH_FIELD_TERM, SEARCH_FIELD_XREF_DB, SEARCH_FIELD_XREF_ID, SEARCH_INDEX_NAME

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

KPrimeImpl()

Method Summary

int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
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	getKPrime() The apparent equilibrium constant K'.
java.lang.Class<? extends KPrime>	getModelInterface() This method returns the actual model interface that a class implements.
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()
float	getTemperature()
protected boolean	semanticallyEquivalent(BioPAXElement element)
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	setKPrime(float prime) The apparent equilibrium constant K'.
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)
void	setTemperature(float temperature)

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, setProxyId, setRDFId, setVersion, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

addComment, getComment, removeComment

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

getAnnotations, getRDFId, isEquivalent

Constructor Detail

KPrimeImpl

public KPrimeImpl()

Method Detail

getModelInterface

public java.lang.Class<? extends KPrime> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class BioPAXElementImpl

Returns:

an integer that is same across all equivalent entities.

getIonicStrength

public float getIonicStrength()

Description copied from interface: KPrime

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

Specified by:

getIonicStrength in interface KPrime

Returns:

The ionic strength

setIonicStrength

public void setIonicStrength(float ionicStrength)

Description copied from interface: KPrime

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

Specified by:

setIonicStrength in interface KPrime

Parameters:

ionicStrength - The ionic strength

getKPrime

public float getKPrime()

Description copied from interface: KPrime

The apparent equilibrium constant K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate:

K' = [ADP][P_i]/[ATP],

The concentration of ATP refers to the total concentration of all of the following species:

[ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [MgHATP^-] + [Mg₂ATP].

The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm³) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]).

Specified by:

getKPrime in interface KPrime

Returns:

The apparent equilibrium constant K'

setKPrime

public void setKPrime(float prime)

Description copied from interface: KPrime

The apparent equilibrium constant K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate:

K' = [ADP][P_i]/[ATP],

The concentration of ATP refers to the total concentration of all of the following species:

[ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [MgHATP^-] + [Mg₂ATP].

The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm³) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). (Definition from EcoCyc)

Specified by:

setKPrime in interface KPrime

Parameters:

prime - The apparent equilibrium constant K'

getPh

public float getPh()

Description copied from interface: KPrime

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.

Specified by:

getPh in interface KPrime

Returns:

A measure of acidity and alkalinity of a solution

setPh

public void setPh(float ph)

Description copied from interface: KPrime

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.

Specified by:

setPh in interface KPrime

Parameters:

ph - A measure of acidity and alkalinity of a solution

getPMg

public float getPMg()

Specified by:

getPMg in interface KPrime

Returns:

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

setPMg

public void setPMg(float pMg)

Specified by:

setPMg in interface KPrime

Parameters:

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

getTemperature

public float getTemperature()

Specified by:

getTemperature in interface KPrime

Returns:

Temperature in Celsius

setTemperature

public void setTemperature(float temperature)

Specified by:

setTemperature in interface KPrime

Parameters:

temperature - Temperature in Celsius