MultipleAlignmentScorer (biojava 4.2.1 API)

java.lang.Object
- org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer

```
public class MultipleAlignmentScorer
extends Object
```
Utility class for calculating common scores of MultipleAlignments.

Since:

4.1.0

Author:

Spencer Bliven, Aleix Lafita

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`AVGTM_SCORE`
`static String`	`CE_SCORE`
`static String`	`MC_SCORE`
`static String`	`PROBABILITY`
`static String`	`REF_RMSD`
`static String`	`REFTM_SCORE`
`static String`	`RMSD`

Constructor Summary

Constructors
Constructor and Description

MultipleAlignmentScorer()

Constructors
Constructor and Description
`MultipleAlignmentScorer()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`calculateScores(MultipleAlignment alignment)` Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
`static double`	`getAvgTMScore(List<Atom[]> transformed, List<Integer> lengths)` Calculates the average TMScore all the possible pairwise structure comparisons of the given a set of superimposed Atoms and the original structure lengths.
`static double`	`getAvgTMScore(MultipleAlignment alignment)` Calculates the average TMScore of all the possible pairwise structure comparisons of the given alignment.
`static double`	`getMCScore(MultipleAlignment alignment, double gapOpen, double gapExtension, double dCutoff)` Calculates the MC score, specific for the MultipleAlignment algorithm.
`static double`	`getRefRMSD(List<Atom[]> transformed, int reference)` Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
`static double`	`getRefRMSD(MultipleAlignment alignment, int ref)` /** Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
`static double`	`getRefTMScore(List<Atom[]> transformed, List<Integer> lengths, int reference)` Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
`static double`	`getRefTMScore(MultipleAlignment alignment, int ref)` Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
`static double`	`getRMSD(List<Atom[]> transformed)` Calculates the RMSD of all-to-all structure comparisons (distances), given a set of superimposed atoms.
`static double`	`getRMSD(MultipleAlignment alignment)` Calculates the RMSD of all-to-all structure comparisons (distances) of the given MultipleAlignment.

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

- Field Detail
  - PROBABILITY
```
public static final String PROBABILITY
```
    See Also:
    
    Constant Field Values
  - CE_SCORE
```
public static final String CE_SCORE
```
    See Also:
    
    Constant Field Values
  - RMSD
```
public static final String RMSD
```
    See Also:
    
    Constant Field Values
  - AVGTM_SCORE
```
public static final String AVGTM_SCORE
```
    See Also:
    
    Constant Field Values
  - MC_SCORE
```
public static final String MC_SCORE
```
    See Also:
    
    Constant Field Values
  - REF_RMSD
```
public static final String REF_RMSD
```
    See Also:
    
    Constant Field Values
  - REFTM_SCORE
```
public static final String REFTM_SCORE
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MultipleAlignmentScorer
```
public MultipleAlignmentScorer()
```
- Method Detail
  - calculateScores
```
public static void calculateScores(MultipleAlignment alignment)
                            throws StructureException
```
    Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
    
    Parameters:
    
    alignment -
    
    Throws:
    
    StructureException
    
    See Also:
    
    getAvgTMScore(MultipleAlignment), getRMSD(MultipleAlignment)
  - getRMSD
```
public static double getRMSD(MultipleAlignment alignment)
```
    Calculates the RMSD of all-to-all structure comparisons (distances) of the given MultipleAlignment.
    Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.
    The formula used is just the sqroot of the average distance of all possible pairs of atoms. Thus, for R structures aligned over C columns without gaps, we have
```
 RMSD = \sqrt{1/(C*(R*(R-1)/2)) * \sum_{r1=1}^{R-1}
 \sum_{r2=r1+1}^{R-1} \sum_{j=0}^{C-1} (atom[r1][c]-atom[r2][c])^2}
 
```
    Parameters:
    
    alignment -
    
    Returns:
    
    double RMSD
  - getRMSD
```
public static double getRMSD(List<Atom[]> transformed)
```
    Calculates the RMSD of all-to-all structure comparisons (distances), given a set of superimposed atoms.
    
    Parameters:
    
    transformed -
    
    Returns:
    
    double RMSD
    
    See Also:
    
    getRMSD(MultipleAlignment)
  - getRefRMSD
```
public static double getRefRMSD(MultipleAlignment alignment,
                                int ref)
```
    /** Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
    Complexity: T(n,l) = O(l*n), if n=number of structures and l=alignment length.
    For ungapped alignments, this is just the sqroot of the average distance from an atom to the aligned atom from the reference. Thus, for R structures aligned over C columns (with structure 0 as the reference), we have:
```
 RefRMSD = \sqrt{ 1/(C*(R-1)) * \sum_{r=1}^{R-1} \sum_{j=0}^{C-1}
 (atom[1][c]-atom[r][c])^2 }
 
```
    For gapped alignments, null atoms are omitted from consideration, so that the RMSD is the average over all columns with non-null reference of the average RMSD within the non-null elements of the column.
    Parameters:
    
    alignment - MultipleAlignment
    
    ref - reference structure index
    
    Returns:
  - getRefRMSD
```
public static double getRefRMSD(List<Atom[]> transformed,
                                int reference)
```
    Calculates the average RMSD from all structures to a reference s tructure, given a set of superimposed atoms.
    Complexity: T(n,l) = O(l*n), if n=number of structures and l=alignment length.
    For ungapped alignments, this is just the sqroot of the average distance from an atom to the aligned atom from the reference. Thus, for R structures aligned over C columns (with structure 0 as the reference), we have:
```
 RefRMSD = \sqrt{ 1/(C*(R-1)) * \sum_{r=1}^{R-1} \sum_{j=0}^{C-1}
 (atom[1][c]-atom[r][c])^2 }
 
```
    For gapped alignments, null atoms are omitted from consideration, so that the RMSD is the average over all columns with non-null reference of the average RMSD within the non-null elements of the column.
    Parameters:
    
    transformed -
    
    reference -
    
    Returns:
  - getAvgTMScore
```
public static double getAvgTMScore(MultipleAlignment alignment)
                            throws StructureException
```
    Calculates the average TMScore of all the possible pairwise structure comparisons of the given alignment.
    Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.
    
    Parameters:
    
    alignment -
    
    Returns:
    
    double Average TMscore
    
    Throws:
    
    StructureException
  - getAvgTMScore
```
public static double getAvgTMScore(List<Atom[]> transformed,
                                   List<Integer> lengths)
                            throws StructureException
```
    Calculates the average TMScore all the possible pairwise structure comparisons of the given a set of superimposed Atoms and the original structure lengths.
    Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.
    
    Parameters:
    
    transformed - aligned Atoms transformed
    
    lengths - lengths of the structures in residue number
    
    Returns:
    
    double Average TMscore
    
    Throws:
    
    StructureException
  - getRefTMScore
```
public static double getRefTMScore(MultipleAlignment alignment,
                                   int ref)
                            throws StructureException
```
    Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
    Complexity: T(n,l) = O(l*n), if n=number of structures and l=alignment length.
    
    Parameters:
    
    alignment -
    
    reference - Index of the reference structure
    
    Returns:
    
    Throws:
    
    StructureException
  - getRefTMScore
```
public static double getRefTMScore(List<Atom[]> transformed,
                                   List<Integer> lengths,
                                   int reference)
                            throws StructureException
```
    Calculates the average TMScore from all structures to a reference structure, given a set of superimposed atoms.
    Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.
    
    Parameters:
    
    transformed - Arrays of aligned atoms, after superposition
    
    lengths - lengths of the full input structures
    
    reference - Index of the reference structure
    
    Returns:
    
    Throws:
    
    StructureException
  - getMCScore
```
public static double getMCScore(MultipleAlignment alignment,
                                double gapOpen,
                                double gapExtension,
                                double dCutoff)
                         throws StructureException
```
    Calculates the MC score, specific for the MultipleAlignment algorithm. The score function is modified from the original CEMC paper, making it continuous and differentiable.
    The maximum score of a match is 20, and the penalties for gaps are part of the input. The half-score distance, d0, is chosen as in the TM-score.
    Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.
    
    Parameters:
    
    alignment -
    
    gapOpen - penalty for gap opening (reasonable values are in the range (1.0-20.0)
    
    gapExtension - penalty for extending a gap (reasonable values are in the range (0.5-10.0)
    
    dCutoff - the distance cutoff
    
    Returns:
    
    the value of the score
    
    Throws:
    
    StructureException

Class MultipleAlignmentScorer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

PROBABILITY

CE_SCORE

RMSD

AVGTM_SCORE

MC_SCORE

REF_RMSD

REFTM_SCORE

Constructor Detail

MultipleAlignmentScorer

Method Detail

calculateScores

getRMSD

getRMSD

getRefRMSD

getRefRMSD

getAvgTMScore

getAvgTMScore

getRefTMScore

getRefTMScore

getMCScore