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

Class QuatSymmetryParameters

java.lang.Object
org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
All Implemented Interfaces:
Serializable
public class QuatSymmetryParameters extends Object implements 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:

  • Constructor Details

  • Method Details

    • 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(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 String toString()
      Overrides:
      toString in class Object