de.bioforscher.singa.structure.algorithms.superimposition

Class SubstructureSuperimposition

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposition

All Implemented Interfaces:

Superimposition<LeafSubstructure<?>>

public class SubstructureSuperimposition
extends Object
implements Superimposition<LeafSubstructure<?>>

An implementation of a Superimposition for AtomContainers.

Author:

fk

Field Summary

Fields inherited from interface de.bioforscher.singa.mathematics.algorithms.superimposition.Superimposition

RMSD_FORMAT_PATTERN

Constructor Summary

Constructors

Constructor and Description
SubstructureSuperimposition(double rmsd, Vector translation, Matrix rotation, List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, List<LeafSubstructure<?>> mappedCandidate, List<LeafSubstructure<?>> mappedFullCandidate)

Method Summary

Modifier and Type	Method and Description
List<LeafSubstructure<?>>	applyTo(List<LeafSubstructure<?>> candidate)
List<LeafSubstructure<?>>	getCandidate()
List<LeafSubstructure<?>>	getMappedCandidate()
List<LeafSubstructure<?>>	getMappedFullCandidate()
List<LeafSubstructure<?>>	getReference()
double	getRmsd()
Matrix	getRotation()
String	getStringRepresentation() Returns a string representation of the SubstructureSuperimposition, that is:
Vector	getTranslation()
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.bioforscher.singa.mathematics.algorithms.superimposition.Superimposition

getFormattedRmsd

Constructor Detail

SubstructureSuperimposition

public SubstructureSuperimposition(double rmsd,
                                   Vector translation,
                                   Matrix rotation,
                                   List<LeafSubstructure<?>> reference,
                                   List<LeafSubstructure<?>> candidate,
                                   List<LeafSubstructure<?>> mappedCandidate,
                                   List<LeafSubstructure<?>> mappedFullCandidate)

Method Detail

getReference

public List<LeafSubstructure<?>> getReference()

Specified by:

getReference in interface Superimposition<LeafSubstructure<?>>

getCandidate

public List<LeafSubstructure<?>> getCandidate()

Specified by:

getCandidate in interface Superimposition<LeafSubstructure<?>>

getStringRepresentation

public String getStringRepresentation()

Returns a string representation of the SubstructureSuperimposition, that is:

[RMSD]_[PDB-ID of mapped candidates]_[candidate residues]...

The ordering of LeafIdentifiers corresponds to the actual found optimal alignment to the reference. TODO move this to interface, as other superimpositions should also get a string representation.

Returns:

The full string representation of this SubstructureSuperimposition.

toString

public String toString()

Overrides:

toString in class Object

getRmsd

public double getRmsd()

Specified by:

getRmsd in interface Superimposition<LeafSubstructure<?>>

getTranslation

public Vector getTranslation()

Specified by:

getTranslation in interface Superimposition<LeafSubstructure<?>>

getRotation

public Matrix getRotation()

Specified by:

getRotation in interface Superimposition<LeafSubstructure<?>>

getMappedCandidate

public List<LeafSubstructure<?>> getMappedCandidate()

Specified by:

getMappedCandidate in interface Superimposition<LeafSubstructure<?>>

getMappedFullCandidate

public List<LeafSubstructure<?>> getMappedFullCandidate()

Specified by:

getMappedFullCandidate in interface Superimposition<LeafSubstructure<?>>

applyTo

public List<LeafSubstructure<?>> applyTo(List<LeafSubstructure<?>> candidate)

Specified by:

applyTo in interface Superimposition<LeafSubstructure<?>>