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

Class QuatSymmetryParameters

  • All Implemented Interfaces:
    java.io.Serializable
    public class QuatSymmetryParameters
extends java.lang.Object
implements java.io.Serializable
    See Also:
    Serialized Form

    • Constructor Detail

      • QuatSymmetryParameters

        public QuatSymmetryParameters()

    • Method Detail

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