org.biopax.paxtools.impl.level3

Class DeltaGImpl

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.DeltaGImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, ChemicalConstant, DeltaG, Level3Element, UtilityClass

@Entity
 @Indexed
public class DeltaGImpl
extends ChemicalConstantImpl
implements DeltaG

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
DeltaGImpl()

Method Summary

Modifier and Type	Method and Description
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
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.
Class<? extends DeltaG>	getModelInterface() This method returns the actual model interface that a class implements.
protected boolean	semanticallyEquivalent(BioPAXElement element)
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.

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

DeltaGImpl

public DeltaGImpl()

Method Detail

getModelInterface

public Class<? extends DeltaG> 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.

getDeltaGPrime0

public float getDeltaGPrime0()

Description copied from interface: DeltaG

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).

Specified by:

getDeltaGPrime0 in interface DeltaG

Returns:

delta-G'^o for this condition

setDeltaGPrime0

public void setDeltaGPrime0(float deltaGPrime0)

Description copied from interface: DeltaG

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).

Specified by:

setDeltaGPrime0 in interface DeltaG

Parameters:

deltaGPrime0 - delta-G'^o for this condition