org.biojava.nbio.structure.cluster

Class SubunitExtractor

java.lang.Object

org.biojava.nbio.structure.cluster.SubunitExtractor

public class SubunitExtractor
extends Object

The SubunitExtractor extracts the information of each protein Chain in a Structure and converts them into a List of Subunit.

Since:

5.0.0

Author:

Peter Rose, Aleix Lafita

Method Summary

Modifier and Type	Method and Description
static List<Subunit>	extractSubunits(Structure structure, int absMinLen, double fraction, int minLen) Extract the information of each protein Chain in a Structure and converts them into a List of Subunit.

Methods inherited from class java.lang.Object

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

Method Detail

extractSubunits

public static List<Subunit> extractSubunits(Structure structure,
                                            int absMinLen,
                                            double fraction,
                                            int minLen)

Extract the information of each protein Chain in a Structure and converts them into a List of Subunit. The name of the Subunits is set to Chain.getId().

Parameters:

structure - Structure object with protein Chains

absMinLen - SubunitClustererParameters.getAbsoluteMinimumSequenceLength()

fraction - SubunitClustererParameters.getMinimumSequenceLengthFraction()

minLen - SubunitClustererParameters.getMinimumSequenceLength()

Returns:

List of Subunits