org.biojava.nbio.structure.cluster

Class SubunitClusterUtils

java.lang.Object

org.biojava.nbio.structure.cluster.SubunitClusterUtils

public class SubunitClusterUtils
extends Object

Some utility methods commonly used for Subunit clusters. They take as input a List of SubunitCluster, the output of the SubunitClusterer.

Since:

5.0.0

Author:

Aleix Lafita

Method Summary

Modifier and Type	Method and Description
static String	getStoichiometryString(List<SubunitCluster> clusters) Return a canonical String representation of the stoichiometry of a group of Subunits.
static boolean	isPseudoStoichiometric(List<SubunitCluster> clusters) A pseudostoichiometric SubunitCluster was obtained using the SubunitClustererMethod.STRUCTURE similarity, or SubunitClustererMethod.SEQUENCE similarity with low scores.
static List<SubunitCluster>	orderByStoichiometry(List<SubunitCluster> clusters) Order clusters by the number of subunits (decreasing) and assign alphabetic characters in order.

Methods inherited from class java.lang.Object

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

Method Detail

getStoichiometryString

public static String getStoichiometryString(List<SubunitCluster> clusters)

Return a canonical String representation of the stoichiometry of a group of Subunits.

This method only uses alphabetic charaters for Subunit ids. For stoichiometries with a large number of entities, when all alphabetic characters are used, they will restart from the beginning.

Parameters:

clusters - List of Subunit clusters

Returns:

String representation of the stoichiometry

orderByStoichiometry

public static List<SubunitCluster> orderByStoichiometry(List<SubunitCluster> clusters)

Order clusters by the number of subunits (decreasing) and assign alphabetic characters in order.

This method makes an alpha-identifier a property of a cluster, which is useful for local symmetries, whose stoichiometries will be consistent with respect to the global clustering.

Parameters:

clusters - List of Subunit clusters

Returns:

Ordered list of Subunit clusters with alpha-identifiers.

isPseudoStoichiometric

public static boolean isPseudoStoichiometric(List<SubunitCluster> clusters)

A pseudostoichiometric SubunitCluster was obtained using the SubunitClustererMethod.STRUCTURE similarity, or SubunitClustererMethod.SEQUENCE similarity with low scores.

Parameters:

clusters -

Returns:

true if any of the clusters is pseudostoichiometric, false otherwise