Package org.biojava.nbio.structure.align.multiple.util

Class MultipleAlignmentScorer

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	Description
static final String	AVGTM_SCORE
static final String	CE_SCORE
static final String	MC_SCORE
static final String	PROBABILITY
static final String	REF_RMSD
static final String	REFTM_SCORE
static final String	RMSD

Constructor Summary

Constructors

Constructor	Description
MultipleAlignmentScorer()

Method Summary

Modifier and Type	Method	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 Details

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 Details

MultipleAlignmentScorer

public MultipleAlignmentScorer()

Method Details

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 -

ref - 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