org.biojava.nbio.structure.align.multiple

Class MultipleAlignmentScorer

java.lang.Object

org.biojava.nbio.structure.align.multiple.MultipleAlignmentScorer

public class MultipleAlignmentScorer
extends Object

Utility class for calculating common scores of MultipleAlignments.

Author:

Spencer Bliven, Aleix Lafita

Field Summary

Fields

Modifier and Type	Field and Description
static String	AVG_TMSCORE
static String	CE_SCORE
static String	CEMC_SCORE
static String	PROBABILITY
static String	REF_RMSD
static String	REF_TMSCORE
static String	RMSD

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentScorer()

Method Summary

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(MultipleAlignment alignment) Calculates the average TMScore all the possible pairwise structure comparisons of the given MultipleAlignment.
static double	getCEMCScore(MultipleAlignment alignment) Calculates the CEMC score, specific for the MultipleAlignment algorithm.
static double	getRefRMSD(MultipleAlignment alignment, int reference)
static double	getRefTMScore(MultipleAlignment alignment, int reference) Calculates the average TMScore from all structures to a reference structure, 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.
static List<Atom[]>	transformAtoms(MultipleAlignment alignment) Transforms atoms according to the superposition stored in the alignment.

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

AVG_TMSCORE

public static final String AVG_TMSCORE

See Also:

Constant Field Values

CEMC_SCORE

public static final String CEMC_SCORE

See Also:

Constant Field Values

REF_RMSD

public static final String REF_RMSD

See Also:

Constant Field Values

REF_TMSCORE

public static final String REF_TMSCORE

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)

transformAtoms

public static List<Atom[]> transformAtoms(MultipleAlignment alignment)

Transforms atoms according to the superposition stored in the alignment.

For each structure in the alignment, returns an atom for each representative atom in the aligned columns, omitting unaligned residues (i.e. an array of length alignment.length() ).

All blocks are concatenated together, so Atoms may not appear in the same order as in their parent structure. If the alignment blocks contain null residues (gaps), then the returned array will also contain null Atoms.

Parameters:

alignment - MultipleAlignment

Returns:

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

getRefRMSD

public static double getRefRMSD(MultipleAlignment alignment,
                int reference)

getAvgTMScore

public static double getAvgTMScore(MultipleAlignment alignment)
                            throws StructureException

Calculates the average TMScore all the possible pairwise structure comparisons of the given MultipleAlignment.

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

getRefTMScore

public static double getRefTMScore(MultipleAlignment alignment,
                   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), if n=number of structures and l=alignment length.

Parameters:

alignment -

reference - Index of the reference structure

Returns:

Throws:

StructureException

getCEMCScore

public static double getCEMCScore(MultipleAlignment alignment)
                           throws StructureException

Calculates the CEMC score, specific for the MultipleAlignment algorithm. The score function is modified from the original CEMC paper, making it continuous and differentiable.

Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment length.

Parameters:

alignment -

Returns:

Throws:

StructureException