QuatSymmetryParameters (biojava 5.0.0 API)

java.lang.Object
- org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters

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 the QuatSymmetryDetector.

Author:

Peter Rose, Aleix Lafita

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

QuatSymmetryParameters()

Constructors
Constructor and Description
`QuatSymmetryParameters()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - QuatSymmetryParameters
```
public QuatSymmetryParameters()
```
- Method Detail
  - 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)
```
  - getMaximumLocalCombinations
```
public int getMaximumLocalCombinations()
```
  - setMaximumLocalCombinations
```
public void setMaximumLocalCombinations(int maximumLocalCombinations)
```
  - getLocalTimeLimit
```
public double getLocalTimeLimit()
```
    Returns:
    
    the localTimeLimit
  - setLocalTimeLimit
```
public void setLocalTimeLimit(double localTimeLimit)
```
    Parameters:
    
    localTimeLimit - the localTimeLimit to set
  - getLocalTimeStart
```
public double getLocalTimeStart()
```
    Returns:
    
    the localTimeStart
  - useLocalTimeLimit
```
public void useLocalTimeLimit(double localTimeStart)
```
    Parameters:
    
    localTimeStart - the time when local calculations started
  - 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
  - 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
  - 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
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class QuatSymmetryParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

QuatSymmetryParameters

Method Detail

getRmsdThreshold

setRmsdThreshold

getAngleThreshold

setAngleThreshold

getHelixRmsdThreshold

setHelixRmsdThreshold

getHelixRmsdToRiseRatio

setHelixRmsdToRiseRatio

getMinimumHelixRise

setMinimumHelixRise

getMinimumHelixAngle

setMinimumHelixAngle

getMaximumLocalCombinations

setMaximumLocalCombinations

getLocalTimeLimit

setLocalTimeLimit

getLocalTimeStart

useLocalTimeLimit

isLocalLimitsExceeded

isLocalLimitsExceeded

isOnTheFly

setOnTheFly

toString