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

Class ValidCandidateGenerator

java.lang.Object

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

public class ValidCandidateGenerator
extends Object

This class constructs valid candidates for the Fit3D algorithm.

Consider Q=(H,D,S) to be the query motif of size k. Further, we allow exchanges that are:

  E(H) = (E)
 

For a given extracted environment N=(H,E,D1,S1,D2,H2,S2) only the following candidates of size k are generated to be then aligned to the query motif:

  C1 =   H | D1 | S1
  C2 =   H | D1 | S2
  C3 =   H | D2 | S1
  C4 =   H | D2 | S2
  C5 =   Q | D1 | S1
  C6 =   Q | D1 | S2
  C7 =   Q | D2 | S1
  C8 =   Q | D2 | S2
 

Author:

sb

Constructor Summary

Constructors

Constructor and Description
ValidCandidateGenerator(List<LeafSubstructure<?>> queryMotif, List<LeafSubstructure<?>> environment)

Method Summary

Modifier and Type	Method and Description
Set<Set<LeafSubstructure<?>>>	getValidCandidates()

Methods inherited from class java.lang.Object

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

Constructor Detail

ValidCandidateGenerator

public ValidCandidateGenerator(List<LeafSubstructure<?>> queryMotif,
                               List<LeafSubstructure<?>> environment)

Method Detail

getValidCandidates

public Set<Set<LeafSubstructure<?>>> getValidCandidates()