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.ChemicalConstantImpl

org.biopax.paxtools.impl.level3.KPrimeImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, ChemicalConstant, KPrime, Level3Element, UtilityClass

@Entity
 @Indexed
public class KPrimeImpl
extends ChemicalConstantImpl
implements KPrime

See Also:

Serialized Form

Field Summary

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

FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
KPrimeImpl()

Method Summary

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

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

getIonicStrength, getPh, getPMg, getTemperature, setIonicStrength, setPh, setPMg, setTemperature

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

addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment

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

equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

getIonicStrength, getPh, getPMg, getTemperature, setIonicStrength, setPh, setPMg, setTemperature

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 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

Overrides:

getModelInterface in class ChemicalConstantImpl

Returns:

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

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class ChemicalConstantImpl

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 ChemicalConstantImpl

Returns:

an integer that is same across all equivalent entities.

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'