Class QuatSymmetryParameters
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
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- 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 theQuatSymmetryDetector
.- Author:
- Peter Rose, Aleix Lafita
- 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 double
getAngleThreshold()
double
getHelixRmsdThreshold()
double
getHelixRmsdToRiseRatio()
double
getLocalTimeLimit()
double
getLocalTimeStart()
int
getMaximumLocalCombinations()
double
getMinimumHelixAngle()
double
getMinimumHelixRise()
double
getRmsdThreshold()
boolean
isLocalLimitsExceeded()
boolean
isLocalLimitsExceeded(Set<?> combinations)
boolean
isOnTheFly()
On-the-fly Jmol bioassembly generation.void
setAngleThreshold(double angleThreshold)
void
setHelixRmsdThreshold(double helixRmsdThreshold)
void
setHelixRmsdToRiseRatio(double helixRmsdToRiseRatio)
void
setLocalTimeLimit(double localTimeLimit)
void
setMaximumLocalCombinations(int maximumLocalCombinations)
void
setMinimumHelixAngle(double minimumHelixAngle)
void
setMinimumHelixRise(double minimumHelixRise)
void
setOnTheFly(boolean useJmolBioAssemblies)
On-the-fly Jmol bioassembly generation.void
setRmsdThreshold(double rmsdThreshold)
String
toString()
void
useLocalTimeLimit(double localTimeStart)
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Constructor Detail
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QuatSymmetryParameters
public QuatSymmetryParameters()
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Method Detail
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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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getMaximumLocalCombinations
public int getMaximumLocalCombinations()
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setMaximumLocalCombinations
public void setMaximumLocalCombinations(int maximumLocalCombinations)
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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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getLocalTimeStart
public double getLocalTimeStart()
- Returns:
- the localTimeStart
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useLocalTimeLimit
public void useLocalTimeLimit(double localTimeStart)
- Parameters:
localTimeStart
- the time when local calculations started
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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
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isLocalLimitsExceeded
public boolean isLocalLimitsExceeded()
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isOnTheFly
public boolean isOnTheFly()
On-the-fly Jmol bioassembly generation.- Returns:
- true if Jmol on the fly bioassembly generation is used
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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
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