QuatSymmetryParameters (biojava 4.2.1 API)

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

All Implemented Interfaces:: Serializable

public class QuatSymmetryParameters
extends Object
implements Serializable

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
`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)`
`String`	`toString()`

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

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 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

getMinimumSequenceLength

setMinimumSequenceLength

getAbsoluteMinimumSequenceLength

setAbsoluteMinimumSequenceLength

getMinimumSequenceLengthFraction

setMinimumSequenceLengthFraction

getSequenceIdentityThresholds

setSequenceIdentityThresholds

getAlignmentFractionThreshold

setAlignmentFractionThreshold

getRmsdThreshold

setRmsdThreshold

getAngleThreshold

setAngleThreshold

getHelixRmsdThreshold

setHelixRmsdThreshold

getHelixRmsdToRiseRatio

setHelixRmsdToRiseRatio

getMinimumHelixRise

setMinimumHelixRise

getMinimumHelixAngle

setMinimumHelixAngle

getSequencePseudoSymmetryThreshold

setSequencePseudoSymmetryThreshold

getMaximumLocalCombinations

setMaximumLocalCombinations

getMaximumLocalResults

getMaximumLocalSubunits

setMaximumLocalSubunits

setMaximumLocalResults

isLocalSymmetry

setLocalSymmetry

getLocalTimeLimit

setLocalTimeLimit

isOnTheFly

setOnTheFly

isVerbose

setVerbose

toString