Package org.biojava.nbio.structure.align.quaternary

Class QsAlignResult

java.lang.Object
org.biojava.nbio.structure.align.quaternary.QsAlignResult
public class QsAlignResult extends Object
Result of a Quaternary Structure Alignment QsAlign. The QsAlignResult holds the original inputs of the algorithm and the results and scores of the alignment.
Since:
5.0.0
Author:
Aleix Lafita

  • Constructor Details

  • Method Details

    • getSubunits1

      public List<Subunit> getSubunits1()
      Original Subunits of the first group.
      Returns:
      an unmodifiable view of the original List

    • getSubunits2

      public List<Subunit> getSubunits2()
      Original Subunits of the second group.
      Returns:
      an unmodifiable view of the original List

    • getSubunitMap

      public Map<Integer,Integer> getSubunitMap()
      Map of Subunit equivalencies from the first to the second group.
      Returns:
      an unmodifiable view of the original Map

    • setSubunitMap

      public void setSubunitMap(Map<Integer,Integer> subunitMap)
      Map of Subunit equivalencies from the first to the second group.
      Parameters:
      subunitMap -

    • length

      public int length()
      The length of the alignment is the number of Subunit equivalencies it contains. This is equivalent to the size of the Subunit Map.
      Returns:
      length of the alignment

    • getTransform

      public javax.vecmath.Matrix4d getTransform()
      The transformation 4D matrix that needs to be applied to the second group of Subunits to superimpose them onto the first group of Subunits, given the equivalent residues in the SubunitCluster and the Subunit equivalencies.

      This is equivalent to multipleAlignment.getBlockSet(0).getTransformations().get(1).

      Returns:
      Matrix4d

    • getRmsd

      public double getRmsd()
      The RMSD between the equivalent residues of the equivalent Subunits after superposition of the Subunit groups. This is equivalent to multipleAlignment.getScore(MultipleAlignmentScorer.RMSD).
      Returns:
      rmsd

    • getRelation

      public QsRelation getRelation()
      The quaternary structure relation QsRelation between the two groups of Subunits.
      Returns:
      relation

    • setRelation

      public void setRelation(QsRelation relation)
      The quaternary structure relation QsRelation between the two groups of Subunits.
      Parameters:
      relation -

    • getAlignment

      public MultipleAlignment getAlignment()
      The alignment that specifies the residue equivalencies of the equivalent Subunits.
      Returns:
      alignment as a MultipleAlignment object

    • setAlignment

      public void setAlignment(MultipleAlignment alignment)
      The alignment that specifies the residue equivalencies of the equivalent Subunits.
      Parameters:
      alignment - a MultipleAlignment object

    • getAlignedSubunits1

      public List<Subunit> getAlignedSubunits1()
      Return the aligned subunits of the first Subunit group, in the alignment order.
      Returns:
      a List of Subunits in the alignment order

    • getAlignedSubunits2

      public List<Subunit> getAlignedSubunits2()
      Return the aligned subunits of the second Subunit group, in the alignment order.
      Returns:
      a List of Subunits in the alignment order

    • setClusters

      public void setClusters(List<SubunitCluster> clusters)

    • getAlignedAtomsForSubunits1

      public Atom[] getAlignedAtomsForSubunits1(int index)

    • getAlignedAtomsForSubunits2

      public Atom[] getAlignedAtomsForSubunits2(int index)

    • toString

      public String toString()
      Overrides:
      toString in class Object