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

Class ValidAlignmentGenerator

java.lang.Object

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

public class ValidAlignmentGenerator
extends Object

This class constructs valid alignments for the Fit3D algorithm.

Consider Q=(K,D,E,E,H) to be the query motif. Further, we allow exchanges that are:

  E(K1) = (H)
  E(E2) = (D,N)
  E(H)  = (K)
 

If we now consider T=(H,E,N,D,H) to be a target of unknown order to which Q should be matched, there are exactly two valid alignments:

  Q =   K | D | E | E | H
  T =   H1| D | E | N | H2
 

  Q =   K | D | E | E | H
  T =   H2| D | E | N | H1
 

Author:

sb

Constructor Summary

Constructors

Constructor and Description
ValidAlignmentGenerator(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)

Method Summary

Modifier and Type	Method and Description
List<List<de.bioforscher.singa.core.utility.Pair<LeafSubstructure<?>>>>	getValidAlignments()

Methods inherited from class java.lang.Object

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

Constructor Detail

ValidAlignmentGenerator

public ValidAlignmentGenerator(List<LeafSubstructure<?>> reference,
                               List<LeafSubstructure<?>> candidate)

Method Detail

getValidAlignments

public List<List<de.bioforscher.singa.core.utility.Pair<LeafSubstructure<?>>>> getValidAlignments()