Class 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 -

  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