Package 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 obtained with QuatSymmetryDetector.

Author:

Peter Rose, Aleix Lafita

Constructor Summary

Constructors

Constructor	Description
QuatSymmetryResults(Stoichiometry stoichiometry, HelixLayers helixLayers, SymmetryPerceptionMethod method)	Constructor for roto-translational symmetries.
QuatSymmetryResults(Stoichiometry stoichiometry, RotationGroup rotationGroup, SymmetryPerceptionMethod method)	Constructor for rotational symmetries.

Method Summary

Modifier and Type	Method	Description
HelixLayers	getHelixLayers()
SymmetryPerceptionMethod	getMethod()
RotationGroup	getRotationGroup()
QuatSymmetryScores	getScores()
Stoichiometry	getStoichiometry()
Structure	getStructure()
List<SubunitCluster>	getSubunitClusters()	Returns the List of SubunitCluster used to calculate symmetry.
int	getSubunitCount()	Return the number of Subunits involved in the symmetry.
List<Subunit>	getSubunits()	Returns the List of Subunits used to calculate symmetry.
String	getSymmetry()
boolean	isLocal()	A local result means that only a subset of the original Subunits was used for symmetry determination.
boolean	isPseudoStoichiometric()
boolean	isSupersededBy(QuatSymmetryResults other)	Determine if this symmetry result is a subset of the other Symmetry result.
void	setStructure(Structure structure)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

QuatSymmetryResults

public QuatSymmetryResults(Stoichiometry stoichiometry,
 RotationGroup rotationGroup,
 SymmetryPerceptionMethod method)

Constructor for rotational symmetries.

Parameters:

stoichiometry - Stoichiometry used to calculate symmetry

rotationGroup -

method -

QuatSymmetryResults

public QuatSymmetryResults(Stoichiometry stoichiometry,
 HelixLayers helixLayers,
 SymmetryPerceptionMethod method)

Constructor for roto-translational symmetries.

Parameters:

stoichiometry - Stoichiometry used to calculate symmetry

helixLayers -

method -

Method Details

isSupersededBy

public boolean isSupersededBy(QuatSymmetryResults other)

Determine if this symmetry result is a subset of the other Symmetry result. Checks the following conditions: - 'Other' includes all subunits of 'this'. - 'Other' has the same or higher order than 'this'. Special treatment for the helical symmetry: - 'Other' includes all subunits of 'this'. - 'this' may be Cn, as well as H Note that isSupersededBy establishes a partial order, i.e. for some symmetries A and B, neither A.isSupersededBy(B) nor B.isSupersededBy(A) may be true.

Parameters:

other - QuatSymmetryResults

Returns:

true if other supersedes this, false otherwise

getSubunitClusters

public List<SubunitCluster> getSubunitClusters()

Returns the List of SubunitCluster used to calculate symmetry.

Returns:

an unmodifiable view of the original List

getSubunits

public List<Subunit> getSubunits()

Returns the List of Subunits used to calculate symmetry.

Returns:

an unmodifiable view of the List

getSubunitCount

public int getSubunitCount()

Return the number of Subunits involved in the symmetry.

Returns:

the number of Subunits

getRotationGroup

public RotationGroup getRotationGroup()

Returns:

rotation group (point group) information representing rotational quaternary symmetry.

getHelixLayers

public HelixLayers getHelixLayers()

Returns:

helix layers (layer lines) as a list of helices that describe a helical structure.

getMethod

public SymmetryPerceptionMethod getMethod()

Returns:

the method used for symmetry perception.

getSymmetry

public String getSymmetry()

Returns:

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

getScores

public QuatSymmetryScores getScores()

Returns:

the quaternary scores as an object

getStoichiometry

public Stoichiometry getStoichiometry()

isPseudoStoichiometric

public boolean isPseudoStoichiometric()

isLocal

public boolean isLocal()

A local result means that only a subset of the original Subunits was used for symmetry determination.

Returns:

true if local result, false otherwise

getStructure

public Structure getStructure()

setStructure

public void setStructure(Structure structure)

toString

public String toString()

Overrides:

toString in class Object