SubunitClustererParameters (biojava-structure 5.0.0-alpha8 API)

java.lang.Object
- org.biojava.nbio.structure.cluster.SubunitClustererParameters

All Implemented Interfaces:

Serializable
```
public class SubunitClustererParameters
extends Object
implements Serializable
```
The SubunitClustererParameters specifies the options used for the clustering of the subunits in structures using the SubunitClusterer.

Since:

5.0.0

Author:

Peter Rose, Aleix Lafita

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

SubunitClustererParameters()

Constructors
Constructor and Description
`SubunitClustererParameters()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`getAbsoluteMinimumSequenceLength()` If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
`SubunitClustererMethod`	`getClustererMethod()` Method to cluster subunits.
`double`	`getCoverageThreshold()` The minimum coverage of the sequence alignment between two subunits to be clustered together.
`int`	`getMinimumSequenceLength()` Get the minimum number of residues of a subunits to be considered in the clusters.
`double`	`getMinimumSequenceLengthFraction()` If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
`double`	`getRmsdThreshold()` Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
`double`	`getSequenceIdentityThreshold()` Sequence identity threshold to consider for the subunits clustering.
`boolean`	`isInternalSymmetry()` The internal symmetry option divides each `Subunit` of each `SubunitCluster` into its internally symmetric repeats.
`void`	`setAbsoluteMinimumSequenceLength(int absoluteMinimumSequenceLength)` If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
`void`	`setClustererMethod(SubunitClustererMethod method)` Method to cluster subunits.
`void`	`setCoverageThreshold(double coverageThreshold)` The minimum coverage of the sequence alignment between two subunits to be clustered together.
`void`	`setInternalSymmetry(boolean internalSymmetry)` The internal symmetry option divides each `Subunit` of each `SubunitCluster` into its internally symmetric repeats.
`void`	`setMinimumSequenceLength(int minimumSequenceLength)` Set the minimum number of residues of a subunits to be considered in the clusters.
`void`	`setMinimumSequenceLengthFraction(double minimumSequenceLengthFraction)` If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
`void`	`setRmsdThreshold(double rmsdThreshold)` Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
`void`	`setSequenceIdentityThreshold(double sequenceIdentityThreshold)` Sequence identity threshold to consider for the sequence subunit clustering.
`String`	`toString()`

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

- Constructor Detail
  - SubunitClustererParameters
```
public SubunitClustererParameters()
```
- Method Detail
  - getMinimumSequenceLength
```
public int getMinimumSequenceLength()
```
    Get the minimum number of residues of a subunits to be considered in the clusters.
    
    Returns:
    
    minimumSequenceLength
  - setMinimumSequenceLength
```
public void setMinimumSequenceLength(int minimumSequenceLength)
```
    Set the minimum number of residues of a subunits to be considered in the clusters.
    
    Parameters:
    
    minimumSequenceLength -
  - getAbsoluteMinimumSequenceLength
```
public int getAbsoluteMinimumSequenceLength()
```
    If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
    This adaptive feature allows the consideration of structures mainly constructed by very short chains, such as collagen (1A3I)
    
    Returns:
    
    the absoluteMinimumSequenceLength
  - setAbsoluteMinimumSequenceLength
```
public void setAbsoluteMinimumSequenceLength(int absoluteMinimumSequenceLength)
```
    If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
    This adaptive feature allows the consideration of structures mainly constructed by very short chains, such as collagen (1A3I)
    
    Parameters:
    
    absoluteMinimumSequenceLength -
  - getMinimumSequenceLengthFraction
```
public double getMinimumSequenceLengthFraction()
```
    If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
    This adaptive feature allows the consideration of structures mainly constructed by very short chains, such as collagen (1A3I)
    
    Returns:
    
    the minimumSequenceLengthFraction
  - setMinimumSequenceLengthFraction
```
public void setMinimumSequenceLengthFraction(double minimumSequenceLengthFraction)
```
    If the shortest subunit sequence length is higher or equal the minimumSequenceLengthFraction times the median subunit sequence length, then the minimumSequenceLength is set to shortest subunit sequence length, but not shorter than the absoluteMinimumSequenceLength.
    This adaptive feature allows the consideration of structures mainly constructed by very short chains, such as collagen (1A3I)
    
    Parameters:
    
    minimumSequenceLengthFraction -
  - getSequenceIdentityThreshold
```
public double getSequenceIdentityThreshold()
```
    Sequence identity threshold to consider for the subunits clustering.
    Two subunits with sequence identity equal or higher than the threshold will be clustered together.
    
    Returns:
    
    sequenceIdentityThreshold
  - setSequenceIdentityThreshold
```
public void setSequenceIdentityThreshold(double sequenceIdentityThreshold)
```
    Sequence identity threshold to consider for the sequence subunit clustering.
    Two subunits with sequence identity equal or higher than the threshold will be clustered together.
    
    Parameters:
    
    sequenceIdentityThreshold -
  - getRmsdThreshold
```
public double getRmsdThreshold()
```
    Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
    
    Returns:
    
    rmsdThreshold
  - setRmsdThreshold
```
public void setRmsdThreshold(double rmsdThreshold)
```
    Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
    
    Parameters:
    
    rmsdThreshold -
  - getCoverageThreshold
```
public double getCoverageThreshold()
```
    The minimum coverage of the sequence alignment between two subunits to be clustered together.
    
    Returns:
    
    coverageThreshold
  - setCoverageThreshold
```
public void setCoverageThreshold(double coverageThreshold)
```
    The minimum coverage of the sequence alignment between two subunits to be clustered together.
    
    Parameters:
    
    coverageThreshold -
  - getClustererMethod
```
public SubunitClustererMethod getClustererMethod()
```
    Method to cluster subunits.
    
    Returns:
    
    ChainClustererMethod
  - setClustererMethod
```
public void setClustererMethod(SubunitClustererMethod method)
```
    Method to cluster subunits.
    
    Parameters:
    
    SubunitClustererMethod -
  - isInternalSymmetry
```
public boolean isInternalSymmetry()
```
    The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.
    The SubunitClustererMethod.STRUCTURE must be chosen to consider internal symmetry, otherwise this parameter will be ignored.
    
    Returns:
    
    true if internal symmetry is considered, false otherwise
  - setInternalSymmetry
```
public void setInternalSymmetry(boolean internalSymmetry)
```
    The internal symmetry option divides each Subunit of each SubunitCluster into its internally symmetric repeats.
    The SubunitClustererMethod.STRUCTURE must be chosen to consider internal symmetry, otherwise this parameter will be ignored.
    
    Parameters:
    
    internalSymmetry - true if internal symmetry is considered, false otherwise
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class SubunitClustererParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SubunitClustererParameters

Method Detail

getMinimumSequenceLength

setMinimumSequenceLength

getAbsoluteMinimumSequenceLength

setAbsoluteMinimumSequenceLength

getMinimumSequenceLengthFraction

setMinimumSequenceLengthFraction

getSequenceIdentityThreshold

setSequenceIdentityThreshold

getRmsdThreshold

setRmsdThreshold

getCoverageThreshold

setCoverageThreshold

getClustererMethod

setClustererMethod

isInternalSymmetry

setInternalSymmetry

toString