Class QuatSymmetryResults


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

      • 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 Detail

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

        public java.util.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.
      • getSymmetry

        public java.lang.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
      • 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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object