Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
 PREV CLASS   NEXT CLASS FRAMES    NO FRAMES    
SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

org.biopax.paxtools.impl.level3
Class DeltaGImpl

java.lang.Object
  extended by org.biopax.paxtools.impl.BioPAXElementImpl
      extended by org.biopax.paxtools.impl.level3.L3ElementImpl
          extended by org.biopax.paxtools.impl.level3.DeltaGImpl
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, BioPAXElement, DeltaG, Level3Element, UtilityClass
@Entity
@Indexed
public class DeltaGImpl
extends L3ElementImpl
implements DeltaG

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
DeltaGImpl()
           
 
Method Summary
 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.
 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).
 java.lang.Class<? extends DeltaG> 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()
          A measure of the concentration of magnesium (Mg) in solution.
 float getTemperature()
          Temperature in Celsius
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.
 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 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

DeltaGImpl

public DeltaGImpl()
Method Detail

getModelInterface

public java.lang.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
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.

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

getIonicStrength

public float getIonicStrength()
Description copied from interface: DeltaG
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 DeltaG
Returns:
the ionic strength for this condition

setIonicStrength

public void setIonicStrength(float ionicStrength)
Description copied from interface: DeltaG
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 DeltaG
Parameters:
ionicStrength - the ionic strength for this condition

getPh

public float getPh()
Description copied from interface: DeltaG
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)

Specified by:
getPh in interface DeltaG
Returns:
pH for this condition

setPh

public void setPh(float ph)
Description copied from interface: DeltaG
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)

Specified by:
setPh in interface DeltaG
Parameters:
ph - for this condition

getPMg

public float getPMg()
Description copied from interface: DeltaG
A measure of the concentration of magnesium (Mg) in solution. (pMg = -log10[Mg2+])

Specified by:
getPMg in interface DeltaG
Returns:
pMG for this condition

setPMg

public void setPMg(float pmg)
Description copied from interface: DeltaG
A measure of the concentration of magnesium (Mg) in solution. (pMg = -log10[Mg2+])

Specified by:
setPMg in interface DeltaG
Parameters:
pmg - for this condition

getTemperature

public float getTemperature()
Description copied from interface: DeltaG
Temperature in Celsius

Specified by:
getTemperature in interface DeltaG
Returns:
Temperature in Celsius for this condition

setTemperature

public void setTemperature(float temperature)
Description copied from interface: DeltaG
Temperature in Celsius

Specified by:
setTemperature in interface DeltaG
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
 PREV CLASS   NEXT CLASS FRAMES    NO FRAMES    
SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD
Copyright © 2011 BioPAX. All Rights Reserved.