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
See Also:

  • Constructor Details

    • QuatSymmetryParameters

      public QuatSymmetryParameters()

  • Method Details

    • getMinimumSequenceLength

      public int getMinimumSequenceLength()
      Returns:
      the minimumSequenceLength

    • setMinimumSequenceLength

      public void setMinimumSequenceLength(int minimumSequenceLength)
      Parameters:
      minimumSequenceLength - the minimumSequenceLength to set

    • getAbsoluteMinimumSequenceLength

      public int getAbsoluteMinimumSequenceLength()
      Returns:
      the absoluteMinimumSequenceLength

    • setAbsoluteMinimumSequenceLength

      public void setAbsoluteMinimumSequenceLength(int absoluteMinimumSequenceLength)
      Parameters:
      absoluteMinimumSequenceLength - the absoluteMinimumSequenceLength to set

    • getMinimumSequenceLengthFraction

      public double getMinimumSequenceLengthFraction()
      Returns:
      the minimumSequenceLengthFraction

    • setMinimumSequenceLengthFraction

      public void setMinimumSequenceLengthFraction(double minimumSequenceLengthFraction)
      Parameters:
      minimumSequenceLengthFraction - the minimumSequenceLengthFraction to set

    • getSequenceIdentityThresholds

      public double[] getSequenceIdentityThresholds()
      Returns:
      the sequenceIdentityThreshold

    • setSequenceIdentityThresholds

      public void setSequenceIdentityThresholds(double[] sequenceIdentityThresholds)
      Parameters:
      sequenceIdentityThresholds - the sequenceIdentityThresholds to set

    • getAlignmentFractionThreshold

      public double getAlignmentFractionThreshold()
      Returns:
      the alignmentFractionThreshold

    • setAlignmentFractionThreshold

      public void setAlignmentFractionThreshold(double alignmentFractionThreshold)
      Parameters:
      alignmentFractionThreshold - the alignmentFractionThreshold to set

    • 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)

    • getSequencePseudoSymmetryThreshold

      public double getSequencePseudoSymmetryThreshold()

    • setSequencePseudoSymmetryThreshold

      public void setSequencePseudoSymmetryThreshold(double sequencePseudoSymmetryThreshold)

    • getMaximumLocalCombinations

      public int getMaximumLocalCombinations()

    • setMaximumLocalCombinations

      public void setMaximumLocalCombinations(int maximumLocalCombinations)

    • getMaximumLocalResults

      public int getMaximumLocalResults()
      Returns:
      the maximumLocalResults

    • getMaximumLocalSubunits

      public int getMaximumLocalSubunits()
      Returns:
      the maximumLocalSubunits

    • setMaximumLocalSubunits

      public void setMaximumLocalSubunits(int maximumLocalSubunits)
      Parameters:
      maximumLocalSubunits - the maximumLocalSubunits to set

    • setMaximumLocalResults

      public void setMaximumLocalResults(int maximumLocalResults)
      Parameters:
      maximumLocalResults - the maximumLocalResults to set

    • isLocalSymmetry

      public boolean isLocalSymmetry()

    • setLocalSymmetry

      public void setLocalSymmetry(boolean localSymmetry)

    • getLocalTimeLimit

      public double getLocalTimeLimit()
      Returns:
      the localTimeLimit

    • setLocalTimeLimit

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

    • isOnTheFly

      public boolean isOnTheFly()
      Returns:
      true if Jmol on the fly bioassembly generation is used

    • setOnTheFly

      public void setOnTheFly(boolean useJmolBioAssemblies)
      Parameters:
      onTheFly - the onTheFly to set

    • isVerbose

      public boolean isVerbose()

    • setVerbose

      public void setVerbose(boolean verbose)

    • toString

      public String toString()
      Overrides:
      toString in class Object