org.biojava.nbio.structure.symmetry.core

Class QuatSymmetryResults

java.lang.Object

org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

public class QuatSymmetryResults
extends Object

Holds the results of quaternary symmetry perception.

Author:

Peter Rose

Constructor Summary

Constructors

Constructor and Description
QuatSymmetryResults(Subunits subunits, HelixLayers helixLayers, String method)
QuatSymmetryResults(Subunits subunits, RotationGroup rotationGroup, String method)

Method Summary

Modifier and Type	Method and Description
double	getAverageTraceRmsd() Deprecated. use getScores() instead.
double	getAverageTraceTmScoreMin() Deprecated. use getScores() instead.
HelixLayers	getHelixLayers()
String	getMethod() Returns name of method used for symmetry perception.
int	getNucleicAcidChainCount()
RotationGroup	getRotationGroup() Returns rotation group (point group) information representing rotational quaternary symmetry, see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
QuatSymmetryScores	getScores()
double	getSequenceIdentityThreshold()
Subunits	getSubunits() Returns protein subunit information that was used to determine symmetry information
String	getSymmetry() Returns the symmetry group.
boolean	isLocal() Return true
boolean	isPreferredResult()
void	setLocal(boolean local)
void	setPreferredResult(boolean preferredResult)
void	setSequenceIdentityThreshold(double sequenceIdentityThreshold)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

QuatSymmetryResults

public QuatSymmetryResults(Subunits subunits,
                           RotationGroup rotationGroup,
                           String method)

QuatSymmetryResults

public QuatSymmetryResults(Subunits subunits,
                           HelixLayers helixLayers,
                           String method)

Method Detail

getSubunits

public Subunits getSubunits()

Returns protein subunit information that was used to determine symmetry information

Returns:

getRotationGroup

public RotationGroup getRotationGroup()

Returns rotation group (point group) information representing rotational quaternary symmetry, see http://en.wikipedia.org/wiki/Rotation_group_SO(3)

Returns:

rotation group

getHelixLayers

public HelixLayers getHelixLayers()

getMethod

public String getMethod()

Returns name of method used for symmetry perception.

Returns:

method

getSymmetry

public String getSymmetry()

Returns the symmetry group. For point groups returns the point group symbol and for helical symmetry returns "H".

Returns:

symmetry symbol

getScores

public QuatSymmetryScores getScores()

getAverageTraceRmsd

@Deprecated
public double getAverageTraceRmsd()

Deprecated. use getScores() instead.

Returns the average Calpha trace RMSD for all symmetry operations

Returns:

getAverageTraceTmScoreMin

@Deprecated
public double getAverageTraceTmScoreMin()

Deprecated. use getScores() instead.

Returns the average Calpha trace Tm for all symmetry operations

Returns:

getNucleicAcidChainCount

public int getNucleicAcidChainCount()

getSequenceIdentityThreshold

public double getSequenceIdentityThreshold()

setSequenceIdentityThreshold

public void setSequenceIdentityThreshold(double sequenceIdentityThreshold)

toString

public String toString()

Overrides:

toString in class Object

isLocal

public boolean isLocal()

Return true

Returns:

setLocal

public void setLocal(boolean local)

isPreferredResult

public boolean isPreferredResult()

setPreferredResult

public void setPreferredResult(boolean preferredResult)