de.bioforscher.singa.structure.algorithms.superimposition.scores

Class PsScore

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.scores.PsScore

public class PsScore
extends Object

An implementation of the score to assess the similarity of aligned ligand binding site environments:

     Gao, M., and Skolnick, J. (2013). APoc: large-scale identification of similar protein pockets.
     Bioinformatics, 29(5), 597-604.
 

Author:

fk

Method Summary

Modifier and Type	Method and Description
double	getScore()
double	getSignificance()
static PsScore	of(SubstructureSuperimposition substructureSuperimposition, int referenceLength, int queryLength) Calculates the PsScore for the given SubstructureSuperimposition.
String	toString()

Methods inherited from class java.lang.Object

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

Method Detail

of

public static PsScore of(SubstructureSuperimposition substructureSuperimposition,
                         int referenceLength,
                         int queryLength)

Calculates the PsScore for the given SubstructureSuperimposition.

Parameters:

substructureSuperimposition - The SubstructureSuperimposition for which the score should be calculated.

referenceLength - The length of the reference ligand binding site.

queryLength - The length of the query ligand binding site.

Returns:

The calculated PsScore.

getScore

public double getScore()

getSignificance

public double getSignificance()

toString

public String toString()

Overrides:

toString in class Object