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

Class Fit3DSiteAlignment

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3DSiteAlignment

All Implemented Interfaces:

Fit3D

public class Fit3DSiteAlignment
extends Object
implements Fit3D

An implementation of an algorithm for pairwise comparision of structure sites (e.g. binding sites) that are not equal in size. This method iteratively extends a seed alignment until one site is fully aligned or a cutoff score is reached. Internally the Fit3DAlignment algorithm is used if exchanges should be considered.

Author:

fk

Constructor Summary

Constructors

Constructor and Description
Fit3DSiteAlignment(Fit3DBuilder.Builder builder)

Method Summary

Modifier and Type	Method and Description
String	getAlignmentString() Returns a string that represents the alignment.
double	getFraction() Returns the fraction of aligned residues, in respect to the smaller site.
List<Fit3DMatch>	getMatches() Returns the matches that were found by this Fit3D search.
PsScore	getPsScore() Returns the PsScore of aligned residues (only available for Fit3DSiteAlignment.
XieScore	getXieScore() Returns the XieScore of aligned residues (only available for Fit3DSiteAlignment.
void	writeMatches(Path outputDirectory) Writes the matches that were found by this Fit3D search to the specified directory.

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.bioforscher.singa.structure.algorithms.superimposition.fit3d.Fit3D

writeMatches, writeSummaryFile

Constructor Detail

Fit3DSiteAlignment

public Fit3DSiteAlignment(Fit3DBuilder.Builder builder)
                   throws SubstructureSuperimpositionException

Throws:

SubstructureSuperimpositionException

Method Detail

getPsScore

public PsScore getPsScore()

Description copied from interface: Fit3D

Returns the PsScore of aligned residues (only available for Fit3DSiteAlignment.

Specified by:

getPsScore in interface Fit3D

Returns:

The PsScore of residues that were aligned.

getXieScore

public XieScore getXieScore()

Description copied from interface: Fit3D

Returns the XieScore of aligned residues (only available for Fit3DSiteAlignment.

Specified by:

getXieScore in interface Fit3D

Returns:

The XieScore of residues that were aligned.

getAlignmentString

public String getAlignmentString()

Description copied from interface: Fit3D

Returns a string that represents the alignment. This is only available for the Fit3DSiteAlignment.

Specified by:

getAlignmentString in interface Fit3D

Returns:

The alignment in string representation.

writeMatches

public void writeMatches(Path outputDirectory)

Description copied from interface: Fit3D

Writes the matches that were found by this Fit3D search to the specified directory. All matches are aligned to the query motif.

Specified by:

writeMatches in interface Fit3D

Parameters:

outputDirectory - The directory where the matches should be written.

getMatches

public List<Fit3DMatch> getMatches()

Description copied from interface: Fit3D

Returns the matches that were found by this Fit3D search.

Specified by:

getMatches in interface Fit3D

Returns:

The matches found in the target structure(s).

getFraction

public double getFraction()

Returns the fraction of aligned residues, in respect to the smaller site.

Specified by:

getFraction in interface Fit3D

Returns:

The fractions of matches that were aligned.