Class QuatSymmetryParameters
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
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- All Implemented Interfaces:
java.io.Serializable
public class QuatSymmetryParameters extends java.lang.Object implements java.io.Serializable
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description QuatSymmetryParameters()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getAbsoluteMinimumSequenceLength()
double
getAlignmentFractionThreshold()
double
getAngleThreshold()
double
getHelixRmsdThreshold()
double
getHelixRmsdToRiseRatio()
double
getLocalTimeLimit()
int
getMaximumLocalCombinations()
int
getMaximumLocalResults()
int
getMaximumLocalSubunits()
double
getMinimumHelixAngle()
double
getMinimumHelixRise()
int
getMinimumSequenceLength()
double
getMinimumSequenceLengthFraction()
double
getRmsdThreshold()
double[]
getSequenceIdentityThresholds()
double
getSequencePseudoSymmetryThreshold()
boolean
isLocalSymmetry()
boolean
isOnTheFly()
boolean
isVerbose()
void
setAbsoluteMinimumSequenceLength(int absoluteMinimumSequenceLength)
void
setAlignmentFractionThreshold(double alignmentFractionThreshold)
void
setAngleThreshold(double angleThreshold)
void
setHelixRmsdThreshold(double helixRmsdThreshold)
void
setHelixRmsdToRiseRatio(double helixRmsdToRiseRatio)
void
setLocalSymmetry(boolean localSymmetry)
void
setLocalTimeLimit(double localTimeLimit)
void
setMaximumLocalCombinations(int maximumLocalCombinations)
void
setMaximumLocalResults(int maximumLocalResults)
void
setMaximumLocalSubunits(int maximumLocalSubunits)
void
setMinimumHelixAngle(double minimumHelixAngle)
void
setMinimumHelixRise(double minimumHelixRise)
void
setMinimumSequenceLength(int minimumSequenceLength)
void
setMinimumSequenceLengthFraction(double minimumSequenceLengthFraction)
void
setOnTheFly(boolean useJmolBioAssemblies)
void
setRmsdThreshold(double rmsdThreshold)
void
setSequenceIdentityThresholds(double[] sequenceIdentityThresholds)
void
setSequencePseudoSymmetryThreshold(double sequencePseudoSymmetryThreshold)
void
setVerbose(boolean verbose)
java.lang.String
toString()
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Method Detail
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getMinimumSequenceLength
public int getMinimumSequenceLength()
- Returns:
- the minimumSequenceLength
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setMinimumSequenceLength
public void setMinimumSequenceLength(int minimumSequenceLength)
- Parameters:
minimumSequenceLength
- the minimumSequenceLength to set
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getAbsoluteMinimumSequenceLength
public int getAbsoluteMinimumSequenceLength()
- Returns:
- the absoluteMinimumSequenceLength
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setAbsoluteMinimumSequenceLength
public void setAbsoluteMinimumSequenceLength(int absoluteMinimumSequenceLength)
- Parameters:
absoluteMinimumSequenceLength
- the absoluteMinimumSequenceLength to set
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getMinimumSequenceLengthFraction
public double getMinimumSequenceLengthFraction()
- Returns:
- the minimumSequenceLengthFraction
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setMinimumSequenceLengthFraction
public void setMinimumSequenceLengthFraction(double minimumSequenceLengthFraction)
- Parameters:
minimumSequenceLengthFraction
- the minimumSequenceLengthFraction to set
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getSequenceIdentityThresholds
public double[] getSequenceIdentityThresholds()
- Returns:
- the sequenceIdentityThreshold
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setSequenceIdentityThresholds
public void setSequenceIdentityThresholds(double[] sequenceIdentityThresholds)
- Parameters:
sequenceIdentityThresholds
- the sequenceIdentityThresholds to set
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getAlignmentFractionThreshold
public double getAlignmentFractionThreshold()
- Returns:
- the alignmentFractionThreshold
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setAlignmentFractionThreshold
public void setAlignmentFractionThreshold(double alignmentFractionThreshold)
- Parameters:
alignmentFractionThreshold
- the alignmentFractionThreshold to set
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getRmsdThreshold
public double getRmsdThreshold()
- Returns:
- the rmsdThreshold
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setRmsdThreshold
public void setRmsdThreshold(double rmsdThreshold)
- Parameters:
rmsdThreshold
- the rmsdThreshold to set
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getAngleThreshold
public double getAngleThreshold()
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setAngleThreshold
public void setAngleThreshold(double angleThreshold)
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getHelixRmsdThreshold
public double getHelixRmsdThreshold()
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setHelixRmsdThreshold
public void setHelixRmsdThreshold(double helixRmsdThreshold)
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getHelixRmsdToRiseRatio
public double getHelixRmsdToRiseRatio()
- Returns:
- the helixRmsdToRiseRatio
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setHelixRmsdToRiseRatio
public void setHelixRmsdToRiseRatio(double helixRmsdToRiseRatio)
- Parameters:
helixRmsdToRiseRatio
- the helixRmsdToRiseRatio to set
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getMinimumHelixRise
public double getMinimumHelixRise()
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setMinimumHelixRise
public void setMinimumHelixRise(double minimumHelixRise)
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getMinimumHelixAngle
public double getMinimumHelixAngle()
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setMinimumHelixAngle
public void setMinimumHelixAngle(double minimumHelixAngle)
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getSequencePseudoSymmetryThreshold
public double getSequencePseudoSymmetryThreshold()
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setSequencePseudoSymmetryThreshold
public void setSequencePseudoSymmetryThreshold(double sequencePseudoSymmetryThreshold)
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getMaximumLocalCombinations
public int getMaximumLocalCombinations()
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setMaximumLocalCombinations
public void setMaximumLocalCombinations(int maximumLocalCombinations)
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getMaximumLocalResults
public int getMaximumLocalResults()
- Returns:
- the maximumLocalResults
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getMaximumLocalSubunits
public int getMaximumLocalSubunits()
- Returns:
- the maximumLocalSubunits
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setMaximumLocalSubunits
public void setMaximumLocalSubunits(int maximumLocalSubunits)
- Parameters:
maximumLocalSubunits
- the maximumLocalSubunits to set
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setMaximumLocalResults
public void setMaximumLocalResults(int maximumLocalResults)
- Parameters:
maximumLocalResults
- the maximumLocalResults to set
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isLocalSymmetry
public boolean isLocalSymmetry()
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setLocalSymmetry
public void setLocalSymmetry(boolean localSymmetry)
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getLocalTimeLimit
public double getLocalTimeLimit()
- Returns:
- the localTimeLimit
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setLocalTimeLimit
public void setLocalTimeLimit(double localTimeLimit)
- Parameters:
localTimeLimit
- the localTimeLimit to set
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isOnTheFly
public boolean isOnTheFly()
- Returns:
- true if Jmol on the fly bioassembly generation is used
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setOnTheFly
public void setOnTheFly(boolean useJmolBioAssemblies)
- Parameters:
onTheFly
- the onTheFly to set
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isVerbose
public boolean isVerbose()
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setVerbose
public void setVerbose(boolean verbose)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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