de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics

Class FofanovEstimation

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.fit3d.statistics.FofanovEstimation

All Implemented Interfaces:

StatisticalModel

public class FofanovEstimation
extends Object
implements StatisticalModel

An estimation method of the statistical significance of matches produced by the Fit3D algorithm. According to:

     Fofanov, V. et al.
     A statistical model to correct systematic bias introduced by algorithmic thresholds in protein structural
     comparison algorithms.
     Bioinformatics and Biomedicine Workshops, 2008. BIBMW 2008. IEEE International Conference on, 2008, 1-8
 

Author:

fk

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_REFERENCE_SIZE The number of chains in the BLASTe-80 nrpdb dataset according to VAST as of 2017-10-17.

Constructor Summary

Constructors

Constructor and Description
FofanovEstimation(double rmsdCutoff)
FofanovEstimation(double rmsdCutoff, int referenceSize, double modelCorrectnessCutoff)

Method Summary

Modifier and Type	Method and Description
void	calculatePvalues(List<Fit3DMatch> matches)
static double	determineEpsilon(int numberOfAtoms, double modelCorrectnessCutoff) This calculates the cutoff epsilon up to which the RMSD distribution should be sampled for a desired model correctness.
static double	determineEpsilon(StructuralMotif queryMotif, double modelCorrectnessCutoff) This calculates the cutoff epsilon up to which the RMSD distribution should be sampled for a desired model correctness.
double	getModelCorrectnessCutoff()
void	incrementGs()
void	incrementNs()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_REFERENCE_SIZE

public static final int DEFAULT_REFERENCE_SIZE

The number of chains in the BLASTe-80 nrpdb dataset according to VAST as of 2017-10-17.

See Also:

Constant Field Values

Constructor Detail

FofanovEstimation

public FofanovEstimation(double rmsdCutoff)

FofanovEstimation

public FofanovEstimation(double rmsdCutoff,
                         int referenceSize,
                         double modelCorrectnessCutoff)

Method Detail

determineEpsilon

public static double determineEpsilon(StructuralMotif queryMotif,
                                      double modelCorrectnessCutoff)

This calculates the cutoff epsilon up to which the RMSD distribution should be sampled for a desired model correctness.

 epsilon = model_correctness * sqrt(n_atoms(query))
 

Parameters:

queryMotif - The StructuralMotif used as query for the Fit3D alignment.

modelCorrectnessCutoff - The desired model correctness.

Returns:

The epsilon up to which RMSD distribution should be sampled to guarantee model correctness (the RMSD cutoff that should be used for Fit3D).

determineEpsilon

public static double determineEpsilon(int numberOfAtoms,
                                      double modelCorrectnessCutoff)

This calculates the cutoff epsilon up to which the RMSD distribution should be sampled for a desired model correctness.

 epsilon = model_correctness * sqrt(n_atoms(query))
 

Parameters:

numberOfAtoms - The number of atoms used to represent the query for the Fit3D alignment.

modelCorrectnessCutoff - The desired model correctness.

Returns:

The epsilon up to which RMSD distribution should be sampled to guarantee model correctness (the RMSD cutoff that should be used for Fit3D).

getModelCorrectnessCutoff

public double getModelCorrectnessCutoff()

incrementNs

public void incrementNs()

incrementGs

public void incrementGs()

calculatePvalues

public void calculatePvalues(List<Fit3DMatch> matches)
                      throws IOException,
                             InterruptedException

Specified by:

calculatePvalues in interface StatisticalModel

Throws:

IOException

InterruptedException