Package org.biojava.nbio.structure.asa

Class GroupAsa

java.lang.Object

org.biojava.nbio.structure.asa.GroupAsa

All Implemented Interfaces:

Serializable

public class GroupAsa
extends Object
implements Serializable

A class to store the results of ASA calculations, it can hold ASA values per atom present in Group

Author:

duarte_j

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
GroupAsa(Group g)

Method Summary

Modifier and Type	Method	Description
void	addAtomAsaC(double asa)
void	addAtomAsaU(double asa)
Object	clone()
double	getAsaC()	Returns the ASA of the residue in the complexed state
double	getAsaU()	Returns the ASA of the residue in the uncomplexed state
List<Double>	getAtomAsaCs()
List<Double>	getAtomAsaUs()
double	getBsa()	Returns the BSA value for this group, i.e. the difference between ASA uncomplexed and ASA complexed
double	getBsaToAsaRatio()	Returns the bsa/asa(uncomplexed) ratio, i.e. the ratio of burial of a residue upon complexation
Group	getGroup()
double	getRelativeAsaC()	Returns the relative (complexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)
double	getRelativeAsaU()	Returns the relative (uncomplexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)
void	setAsaC(double asaC)
void	setAsaU(double asaU)
void	setAtomAsaCs(List<Double> atomAsaCs)
void	setAtomAsaUs(List<Double> atomAsaUs)

Methods inherited from class java.lang.Object

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

Constructor Detail

GroupAsa

public GroupAsa(Group g)

Method Detail

getGroup

public Group getGroup()

getAsaU

public double getAsaU()

Returns the ASA of the residue in the uncomplexed state

Returns:

setAsaU

public void setAsaU(double asaU)

getAsaC

public double getAsaC()

Returns the ASA of the residue in the complexed state

Returns:

setAsaC

public void setAsaC(double asaC)

addAtomAsaU

public void addAtomAsaU(double asa)

addAtomAsaC

public void addAtomAsaC(double asa)

getAtomAsaUs

public List<Double> getAtomAsaUs()

setAtomAsaUs

public void setAtomAsaUs(List<Double> atomAsaUs)

getAtomAsaCs

public List<Double> getAtomAsaCs()

setAtomAsaCs

public void setAtomAsaCs(List<Double> atomAsaCs)

getBsa

public double getBsa()

Returns the BSA value for this group, i.e. the difference between ASA uncomplexed and ASA complexed

Returns:

getBsaToAsaRatio

public double getBsaToAsaRatio()

Returns the bsa/asa(uncomplexed) ratio, i.e. the ratio of burial of a residue upon complexation

Returns:

getRelativeAsaU

public double getRelativeAsaU()

Returns the relative (uncomplexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)

Returns:

getRelativeAsaC

public double getRelativeAsaC()

Returns the relative (complexed) ASA, i.e. the ASA of the residue with respect to its ASA in an extended tri-peptide conformation (GLY-x-GLY)

Returns:

clone

public Object clone()

Overrides:

clone in class Object