org.biojava.nbio.structure.symmetry.internal

Class CeSymmResult

java.lang.Object

org.biojava.nbio.structure.symmetry.internal.CeSymmResult

public class CeSymmResult
extends Object

This Class stores all the relevant information of an internal symmetry result obtained with CeSymm. The purpose is to carry all the information packed during the calculations and return a single object.

Since:

4.2.0

Author:

Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
CeSymmResult()

Method Summary

Modifier and Type	Method and Description
Atom[]	getAtoms()
SymmetryAxes	getAxes()
MultipleAlignment	getMultipleAlignment()
CESymmParameters	getParams()
String	getReason() Return a String describing the reasons for the CE-Symm final decision in this particular result.
List<StructureIdentifier>	getRepeatsID() Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.
AFPChain	getSelfAlignment()
StructureIdentifier	getStructureId()
String	getSymmGroup()
int	getSymmLevels()
int	getSymmOrder() Return the symmetry order determined by the order detector if the symmetry is significant.
CESymmParameters.SymmetryType	getType()
boolean	isRefined()
boolean	isSignificant() Conditions checked are: score above the threshold, order higher than 1 and refinement succeeded.
void	setAtoms(Atom[] atoms)
void	setAxes(SymmetryAxes axes)
void	setMultipleAlignment(MultipleAlignment multipleAlignment)
void	setParams(CESymmParameters params)
void	setRefined(boolean refined)
void	setSelfAlignment(AFPChain selfAlignment)
void	setStructureId(StructureIdentifier structureId)
void	setSymmGroup(String symmGroup)
void	setSymmLevels(int symmLevels)
void	setSymmOrder(int symmOrder)
void	setType(CESymmParameters.SymmetryType type)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

CeSymmResult

public CeSymmResult()

Method Detail

isSignificant

public boolean isSignificant()

Conditions checked are: score above the threshold, order higher than 1 and refinement succeeded.

Returns:

true if significant, false otherwise

getRepeatsID

public List<StructureIdentifier> getRepeatsID()
                                       throws StructureException

Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.

Returns:

List of StructureIdentifiers or null if not defined

Throws:

StructureException

toString

public String toString()

Overrides:

toString in class Object

getMultipleAlignment

public MultipleAlignment getMultipleAlignment()

setMultipleAlignment

public void setMultipleAlignment(MultipleAlignment multipleAlignment)

getSelfAlignment

public AFPChain getSelfAlignment()

setSelfAlignment

public void setSelfAlignment(AFPChain selfAlignment)

getParams

public CESymmParameters getParams()

setParams

public void setParams(CESymmParameters params)

getAxes

public SymmetryAxes getAxes()

setAxes

public void setAxes(SymmetryAxes axes)

getSymmOrder

public int getSymmOrder()

Return the symmetry order determined by the order detector if the symmetry is significant. Return 1 otherwise.

Returns:

the order of symmetry if the result is significant

setSymmOrder

public void setSymmOrder(int symmOrder)

isRefined

public boolean isRefined()

setRefined

public void setRefined(boolean refined)

getSymmGroup

public String getSymmGroup()

setSymmGroup

public void setSymmGroup(String symmGroup)

getType

public CESymmParameters.SymmetryType getType()

setType

public void setType(CESymmParameters.SymmetryType type)

getAtoms

public Atom[] getAtoms()

setAtoms

public void setAtoms(Atom[] atoms)

getSymmLevels

public int getSymmLevels()

setSymmLevels

public void setSymmLevels(int symmLevels)

getStructureId

public StructureIdentifier getStructureId()

setStructureId

public void setStructureId(StructureIdentifier structureId)

getReason

public String getReason()

Return a String describing the reasons for the CE-Symm final decision in this particular result.

Returns:

String decision reason