Package org.biojava.nbio.structure.symmetry.core

Class QuatSymmetryResults

  • public class QuatSymmetryResults
extends java.lang.Object
    Holds the results of quaternary symmetry perception.
    Author:
    Peter Rose

    • Constructor Detail

      • QuatSymmetryResults

        public QuatSymmetryResults​(Subunits subunits,
                           RotationGroup rotationGroup,
                           java.lang.String method)

      • QuatSymmetryResults

        public QuatSymmetryResults​(Subunits subunits,
                           HelixLayers helixLayers,
                           java.lang.String method)

    • Method Detail

      • getSubunits

        public Subunits getSubunits()
        Returns protein subunit information that was used to determine symmetry information
        Returns:

      • getRotationGroup

        public RotationGroup getRotationGroup()
        Returns rotation group (point group) information representing rotational quaternary symmetry, see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
        Returns:
        rotation group

      • getMethod

        public java.lang.String getMethod()
        Returns name of method used for symmetry perception.
        Returns:
        method

      • getSymmetry

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

      • getAverageTraceRmsd

        @Deprecated
public double getAverageTraceRmsd()
        Deprecated.
        use getScores() instead.
        Returns the average Calpha trace RMSD for all symmetry operations
        Returns:

      • getAverageTraceTmScoreMin

        @Deprecated
public double getAverageTraceTmScoreMin()
        Deprecated.
        use getScores() instead.
        Returns the average Calpha trace Tm for all symmetry operations
        Returns:

      • getNucleicAcidChainCount

        public int getNucleicAcidChainCount()

      • getSequenceIdentityThreshold

        public double getSequenceIdentityThreshold()

      • setSequenceIdentityThreshold

        public void setSequenceIdentityThreshold​(double sequenceIdentityThreshold)

      • toString

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

      • isLocal

        public boolean isLocal()
        Return true
        Returns:

      • setLocal

        public void setLocal​(boolean local)

      • isPreferredResult

        public boolean isPreferredResult()

      • setPreferredResult

        public void setPreferredResult​(boolean preferredResult)