Class QuatSymmetryResults

java.lang.Object
org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults

public class QuatSymmetryResults extends Object
Holds the results of quaternary symmetry perception obtained with QuatSymmetryDetector.
Author:
Peter Rose, Aleix Lafita
  • Constructor Details

    • QuatSymmetryResults

      public QuatSymmetryResults(Stoichiometry stoichiometry, RotationGroup rotationGroup, SymmetryPerceptionMethod method)
      Constructor for rotational symmetries.
      Parameters:
      stoichiometry - Stoichiometry used to calculate symmetry
      rotationGroup -
      method -
    • QuatSymmetryResults

      public QuatSymmetryResults(Stoichiometry stoichiometry, HelixLayers helixLayers, SymmetryPerceptionMethod method)
      Constructor for roto-translational symmetries.
      Parameters:
      stoichiometry - Stoichiometry used to calculate symmetry
      helixLayers -
      method -
  • Method Details

    • isSupersededBy

      public boolean isSupersededBy(QuatSymmetryResults other)
      Determine if this symmetry result is a subset of the other Symmetry result. Checks the following conditions: - 'Other' includes all subunits of 'this'. - 'Other' has the same or higher order than 'this'. Special treatment for the helical symmetry: - 'Other' includes all subunits of 'this'. - 'this' may be Cn, as well as H Note that isSupersededBy establishes a partial order, i.e. for some symmetries A and B, neither A.isSupersededBy(B) nor B.isSupersededBy(A) may be true.
      Parameters:
      other - QuatSymmetryResults
      Returns:
      true if other supersedes this, false otherwise
    • getSubunitClusters

      public List<SubunitCluster> getSubunitClusters()
      Returns the List of SubunitCluster used to calculate symmetry.
      Returns:
      an unmodifiable view of the original List
    • getSubunits

      public List<Subunit> getSubunits()
      Returns the List of Subunits used to calculate symmetry.
      Returns:
      an unmodifiable view of the List
    • getSubunitCount

      public int getSubunitCount()
      Return the number of Subunits involved in the symmetry.
      Returns:
      the number of Subunits
    • getRotationGroup

      public RotationGroup getRotationGroup()
      Returns:
      rotation group (point group) information representing rotational quaternary symmetry.
    • getHelixLayers

      public HelixLayers getHelixLayers()
      Returns:
      helix layers (layer lines) as a list of helices that describe a helical structure.
    • getMethod

      public SymmetryPerceptionMethod getMethod()
      Returns:
      the method used for symmetry perception.
    • getSymmetry

      public String getSymmetry()
      Returns:
      the symmetry group symbol. For point groups returns the point group symbol and for helical symmetry returns "H".
    • getScores

      public QuatSymmetryScores getScores()
      Returns:
      the quaternary scores as an object
    • getStoichiometry

      public Stoichiometry getStoichiometry()
    • isPseudoStoichiometric

      public boolean isPseudoStoichiometric()
    • isLocal

      public boolean isLocal()
      A local result means that only a subset of the original Subunits was used for symmetry determination.
      Returns:
      true if local result, false otherwise
    • getStructure

      public Structure getStructure()
    • setStructure

      public void setStructure(Structure structure)
    • toString

      public String toString()
      Overrides:
      toString in class Object