Class QuatSymmetryParameters

  • All Implemented Interfaces:
    java.io.Serializable

    public class QuatSymmetryParameters
    extends java.lang.Object
    implements java.io.Serializable
    The QuatSymmetryParameters specify the options used for the detection of quaternary symmetry in structures using the QuatSymmetryDetector.
    Author:
    Peter Rose, Aleix Lafita
    See Also:
    Serialized Form
    • Constructor Detail

      • QuatSymmetryParameters

        public QuatSymmetryParameters()
    • Method Detail

      • getRmsdThreshold

        public double getRmsdThreshold()
        Returns:
        the rmsdThreshold
      • setRmsdThreshold

        public void setRmsdThreshold​(double rmsdThreshold)
        Parameters:
        rmsdThreshold - the rmsdThreshold to set
      • getAngleThreshold

        public double getAngleThreshold()
      • setAngleThreshold

        public void setAngleThreshold​(double angleThreshold)
      • getHelixRmsdThreshold

        public double getHelixRmsdThreshold()
      • setHelixRmsdThreshold

        public void setHelixRmsdThreshold​(double helixRmsdThreshold)
      • getHelixRmsdToRiseRatio

        public double getHelixRmsdToRiseRatio()
        Returns:
        the helixRmsdToRiseRatio
      • setHelixRmsdToRiseRatio

        public void setHelixRmsdToRiseRatio​(double helixRmsdToRiseRatio)
        Parameters:
        helixRmsdToRiseRatio - the helixRmsdToRiseRatio to set
      • getMinimumHelixRise

        public double getMinimumHelixRise()
      • setMinimumHelixRise

        public void setMinimumHelixRise​(double minimumHelixRise)
      • getMinimumHelixAngle

        public double getMinimumHelixAngle()
      • setMinimumHelixAngle

        public void setMinimumHelixAngle​(double minimumHelixAngle)
      • getMaximumLocalCombinations

        public int getMaximumLocalCombinations()
      • setMaximumLocalCombinations

        public void setMaximumLocalCombinations​(int maximumLocalCombinations)
      • getLocalTimeLimit

        public double getLocalTimeLimit()
        Returns:
        the localTimeLimit
      • setLocalTimeLimit

        public void setLocalTimeLimit​(double localTimeLimit)
        Parameters:
        localTimeLimit - the localTimeLimit to set
      • getLocalTimeStart

        public double getLocalTimeStart()
        Returns:
        the localTimeStart
      • useLocalTimeLimit

        public void useLocalTimeLimit​(double localTimeStart)
        Parameters:
        localTimeStart - the time when local calculations started
      • isLocalLimitsExceeded

        public boolean isLocalLimitsExceeded​(java.util.Set<?> combinations)
        Parameters:
        combinations - a set of combinations considered fo far by the local symmetry search
        Returns:
        true, if the number of combinations
      • isLocalLimitsExceeded

        public boolean isLocalLimitsExceeded()
      • isOnTheFly

        public boolean isOnTheFly()
        On-the-fly Jmol bioassembly generation.
        Returns:
        true if Jmol on the fly bioassembly generation is used
      • setOnTheFly

        public void setOnTheFly​(boolean useJmolBioAssemblies)
        On-the-fly Jmol bioassembly generation.
        Parameters:
        useJmolBioAssemblies - true if Jmol on the fly bioassembly generation is used, false otherwise
      • toString

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