Class QuatSymmetryParameters
java.lang.Object
org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters
- All Implemented Interfaces:
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:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
double
double
double
double
int
double
double
double
boolean
boolean
isLocalLimitsExceeded
(Set<?> combinations) boolean
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) toString()
void
useLocalTimeLimit
(double localTimeStart)
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Constructor Details
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QuatSymmetryParameters
public QuatSymmetryParameters()
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Method Details
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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() -
setAngleThreshold
public void setAngleThreshold(double angleThreshold) -
getHelixRmsdThreshold
public double getHelixRmsdThreshold() -
setHelixRmsdThreshold
public void setHelixRmsdThreshold(double helixRmsdThreshold) -
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() -
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
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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
- 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() -
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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toString
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