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

Class QsAlignParameters

java.lang.Object
org.biojava.nbio.structure.align.quaternary.QsAlignParameters
public class QsAlignParameters extends Object
The parameter bean for the QsAlign algorithm.
Since:
5.0.0
Author:
Aleix Lafita

  • Constructor Summary

    Constructors
    Constructor
    Description
    QsAlignParameters()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    double
    getdCutoff()
    The maximum allowed distance between the centroids of two equivalent Subunits, in A.
    double
    getMaxOrientationAngle()
    The maximum orientation angle between two equivalent Subunits, in radians.
    double
    getMaxRmsd()
    The maximum allowed RMSD of the alignment, in A.
    void
    setdCutoff(double dCutoff)
    The maximum allowed distance between the centroids of two equivalent Subunits, in A.
    void
    setMaxOrientationAngle(double maxOrientationAngle)
    The maximum orientation angle between two equivalent Subunits, in radians.
    void
    setMaxRmsd(double maxRmsd)
    The maximum allowed RMSD of the alignment, in A.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

  • Method Details

    • getdCutoff

      public double getdCutoff()
      The maximum allowed distance between the centroids of two equivalent Subunits, in A.
      Returns:
      dCutoff

    • setdCutoff

      public void setdCutoff(double dCutoff)
      The maximum allowed distance between the centroids of two equivalent Subunits, in A.
      Parameters:
      dCutoff -

    • getMaxRmsd

      public double getMaxRmsd()
      The maximum allowed RMSD of the alignment, in A.
      Returns:
      maxRmsd

    • setMaxRmsd

      public void setMaxRmsd(double maxRmsd)
      The maximum allowed RMSD of the alignment, in A.
      Parameters:
      maxRmsd -

    • getMaxOrientationAngle

      public double getMaxOrientationAngle()
      The maximum orientation angle between two equivalent Subunits, in radians. Range [0, Pi].
      Returns:
      the maximum orientation angle

    • setMaxOrientationAngle

      public void setMaxOrientationAngle(double maxOrientationAngle)
      The maximum orientation angle between two equivalent Subunits, in radians. Range [0, Pi].
      Parameters:
      maxOrientationAngle - maximum orientation angle