SubunitClustererParameters (biojava 5.3.0 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()` Initialize with "local" metrics by default.
`SubunitClustererParameters(boolean useGlobalMetrics)` "Local" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a local alignment (normalised by the number of aligned residues) sequence coverage of the alignment (normalised by the length of the longer sequence) SubunitClustererMethod.STRUCTURE: RMSD of the aligned substructures and structure coverage of the alignment (normalised by the length of the larger structure) Two thresholds for each method are required.

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.
`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`	`getSequenceCoverageThreshold()` The minimum coverage of the sequence alignment between two subunits to be clustered together.
`double`	`getSequenceIdentityThreshold()` Sequence identity threshold to consider for the subunits clustering.
`double`	`getStructureCoverageThreshold()` The minimum coverage of the structure alignment between two subunits to be clustered together.
`String`	`getSuperpositionAlgorithm()` Method to superpose subunits (i.e., structural aligner).
`double`	`getTMThreshold()` Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
`boolean`	`isHighConfidenceScores(double sequenceIdentity, double sequenceCoverage)` Whether the subunits can be considered "identical" by sequence alignment.
`boolean`	`isInternalSymmetry()` The internal symmetry option divides each `Subunit` of each `SubunitCluster` into its internally symmetric repeats.
`boolean`	`isOptimizeAlignment()` Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
`boolean`	`isUseGlobalMetrics()` Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
`boolean`	`isUseRMSD()` Use RMSD for evaluating structure similarity
`boolean`	`isUseSequenceCoverage()` Use sequence coverage for evaluating sequence similarity
`boolean`	`isUseStructureCoverage()` Use structure coverage for evaluating sequence similarity
`boolean`	`isUseTMScore()` Use TMScore for evaluating structure similarity
`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`	`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`	`setOptimizeAlignment(boolean optimizeAlignment)` Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result.
`void`	`setRMSDThreshold(double rmsdThreshold)` Structure similarity threshold (measured with RMSD) to consider for the structural subunit clustering.
`void`	`setSequenceCoverageThreshold(double sequenceCoverageThreshold)` The minimum coverage of the sequence alignment between two subunits to be clustered together.
`void`	`setSequenceIdentityThreshold(double sequenceIdentityThreshold)` Sequence identity threshold to consider for the sequence subunit clustering.
`void`	`setStructureCoverageThreshold(double structureCoverageThreshold)` The minimum coverage of the structure alignment between two subunits to be clustered together.
`void`	`setSuperpositionAlgorithm(String superpositionAlgorithm)` Method to cluster subunits.
`void`	`setTMThreshold(double tmThreshold)` Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
`void`	`setUseGlobalMetrics(boolean useGlobalMetrics)` Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
`void`	`setUseRMSD(boolean useRMSD)` Use RMSD for evaluating structure similarity
`void`	`setUseSequenceCoverage(boolean useSequenceCoverage)` Use sequence coverage for evaluating sequence similarity
`void`	`setUseStructureCoverage(boolean useStructureCoverage)` Use structure coverage for evaluating sequence similarity
`void`	`setUseTMScore(boolean useTMScore)` Use TMScore for evaluating structure similarity
`String`	`toString()`

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

- Constructor Detail
  - SubunitClustererParameters
```
public SubunitClustererParameters(boolean useGlobalMetrics)
```
    "Local" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a local alignment (normalised by the number of aligned residues) sequence coverage of the alignment (normalised by the length of the longer sequence) SubunitClustererMethod.STRUCTURE: RMSD of the aligned substructures and structure coverage of the alignment (normalised by the length of the larger structure) Two thresholds for each method are required. "Global" metrics are scoring SubunitClustererMethod.SEQUENCE: sequence identity of a global alignment (normalised by the length of the alignment) SubunitClustererMethod.STRUCTURE: TMScore of the aligned structures (normalised by the length of the larger structure) One threshold for each method is required.
  - SubunitClustererParameters
```
public SubunitClustererParameters()
```
    Initialize with "local" metrics by default.
- 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 -
  - getSequenceCoverageThreshold
```
public double getSequenceCoverageThreshold()
```
    The minimum coverage of the sequence alignment between two subunits to be clustered together.
    
    Returns:
    
    sequenceCoverageThreshold
  - setSequenceCoverageThreshold
```
public void setSequenceCoverageThreshold(double sequenceCoverageThreshold)
```
    The minimum coverage of the sequence alignment between two subunits to be clustered together.
    
    Parameters:
    
    sequenceCoverageThreshold -
  - 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 -
  - getTMThreshold
```
public double getTMThreshold()
```
    Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
    
    Returns:
    
    tmThreshold
  - setTMThreshold
```
public void setTMThreshold(double tmThreshold)
```
    Structure similarity threshold (measured with TMScore) to consider for the structural subunit clustering.
    
    Parameters:
    
    tmThreshold -
  - getStructureCoverageThreshold
```
public double getStructureCoverageThreshold()
```
    The minimum coverage of the structure alignment between two subunits to be clustered together.
    
    Returns:
    
    structureCoverageThreshold
  - setStructureCoverageThreshold
```
public void setStructureCoverageThreshold(double structureCoverageThreshold)
```
    The minimum coverage of the structure alignment between two subunits to be clustered together.
    
    Parameters:
    
    structureCoverageThreshold -
  - getClustererMethod
```
public SubunitClustererMethod getClustererMethod()
```
    Method to cluster subunits.
    
    Returns:
    
    clustererMethod
  - setClustererMethod
```
public void setClustererMethod(SubunitClustererMethod method)
```
    Method to cluster subunits.
    
    Parameters:
    
    method -
  - 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
  - getSuperpositionAlgorithm
```
public String getSuperpositionAlgorithm()
```
    Method to superpose subunits (i.e., structural aligner).
    
    Returns:
    
    superpositionAlgorithm
  - setSuperpositionAlgorithm
```
public void setSuperpositionAlgorithm(String superpositionAlgorithm)
```
    Method to cluster subunits.
    
    Parameters:
    
    superpositionAlgorithm -
  - isOptimizeAlignment
```
public boolean isOptimizeAlignment()
```
    Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. Effect depends on implementation of the specific algorithm's method. *
    
    Returns:
    
    optimizeAlignment
  - setOptimizeAlignment
```
public void setOptimizeAlignment(boolean optimizeAlignment)
```
    Whether the alignment algorithm should try its best to optimize the alignment, or we are happy with a quick and dirty result. Effect depends on implementation of the specific algorithm's method. *
    
    Parameters:
    
    optimizeAlignment -
  - isUseRMSD
```
public boolean isUseRMSD()
```
    Use RMSD for evaluating structure similarity
    
    Returns:
    
    useRMSD
  - setUseRMSD
```
public void setUseRMSD(boolean useRMSD)
```
    Use RMSD for evaluating structure similarity
    
    Parameters:
    
    useRMSD -
  - isUseTMScore
```
public boolean isUseTMScore()
```
    Use TMScore for evaluating structure similarity
    
    Returns:
    
    useTMScore
  - setUseTMScore
```
public void setUseTMScore(boolean useTMScore)
```
    Use TMScore for evaluating structure similarity
    
    Parameters:
    
    useTMScore -
  - isUseSequenceCoverage
```
public boolean isUseSequenceCoverage()
```
    Use sequence coverage for evaluating sequence similarity
    
    Returns:
    
    useSequenceCoverage
  - setUseSequenceCoverage
```
public void setUseSequenceCoverage(boolean useSequenceCoverage)
```
    Use sequence coverage for evaluating sequence similarity
    
    Parameters:
    
    useSequenceCoverage -
  - isUseStructureCoverage
```
public boolean isUseStructureCoverage()
```
    Use structure coverage for evaluating sequence similarity
    
    Returns:
    
    useStructureCoverage
  - setUseStructureCoverage
```
public void setUseStructureCoverage(boolean useStructureCoverage)
```
    Use structure coverage for evaluating sequence similarity
    
    Parameters:
    
    useStructureCoverage -
  - isUseGlobalMetrics
```
public boolean isUseGlobalMetrics()
```
    Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
    
    Returns:
    
    useGlobalMetrics
  - setUseGlobalMetrics
```
public void setUseGlobalMetrics(boolean useGlobalMetrics)
```
    Use metrics calculated relative to the whole sequence or structure, rather than the aligned part only
    
    Parameters:
    
    useGlobalMetrics -
  - isHighConfidenceScores
```
public boolean isHighConfidenceScores(double sequenceIdentity,
                                      double sequenceCoverage)
```
    Whether the subunits can be considered "identical" by sequence alignment. For local sequence alignment (normalized by the number of aligned pairs) this means 0.95 or higher identity and 0.75 or higher coverage. For global sequence alignment (normalised by the alignment length) this means 0.85 or higher sequence identity.
    
    Parameters:
    
    sequenceIdentity -
    
    sequenceCoverage -
    
    Returns:
    
    true if the sequence alignment scores are equal to or better than the "high confidence" scores, false otherwise.

Class SubunitClustererParameters

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SubunitClustererParameters

SubunitClustererParameters

Method Detail

getMinimumSequenceLength

setMinimumSequenceLength

getAbsoluteMinimumSequenceLength

setAbsoluteMinimumSequenceLength

getMinimumSequenceLengthFraction

setMinimumSequenceLengthFraction

getSequenceIdentityThreshold

setSequenceIdentityThreshold

getSequenceCoverageThreshold

setSequenceCoverageThreshold

getRMSDThreshold

setRMSDThreshold

getTMThreshold

setTMThreshold

getStructureCoverageThreshold

setStructureCoverageThreshold

getClustererMethod

setClustererMethod

isInternalSymmetry

setInternalSymmetry

toString

getSuperpositionAlgorithm

setSuperpositionAlgorithm

isOptimizeAlignment

setOptimizeAlignment

isUseRMSD

setUseRMSD

isUseTMScore

setUseTMScore

isUseSequenceCoverage

setUseSequenceCoverage

isUseStructureCoverage

setUseStructureCoverage

isUseGlobalMetrics

setUseGlobalMetrics

isHighConfidenceScores