Package org.biojava.nbio.structure.symmetry.utils

Class SymmetryTools

java.lang.Object
org.biojava.nbio.structure.symmetry.utils.SymmetryTools
public class SymmetryTools extends Object
Utility methods for the internal symmetry identification and manipulation.

Methods include: blank out regions of DP Matrix, build symmetry graphs, get rotation symmetry angles, split repeats in quaternary structure chains, convert between symmetry formats (full, repeats, rotations), determine if two symmetry axes are equivalent, get groups from representative Atoms.

Author:
Spencer Bliven, Aleix Lafita

  • Method Details

    • grayOutCEOrig

      public static Matrix grayOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff)
      Grays out the main diagonal of a duplicated distance matrix.
      Parameters:
      ca2 -
      rows - Number of rows
      cols - Number of original columns
      calculator - Used to get the matrix if origM is null
      origM - starting matrix. If null, uses CECalculator.getMatMatrix()
      blankWindowSize - Width of section to gray out
      gradientPolyCoeff -
      gradientExpCoeff -
      Returns:

    • grayOutPreviousAlignment

      public static Matrix grayOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff)

    • getDkMatrix

      public Matrix getDkMatrix(Atom[] ca1, Atom[] ca2, int fragmentLength, double[] dist1, double[] dist2, int rows, int cols)

    • blankOutPreviousAlignment

      public static Matrix blankOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize)

    • blankOutCEOrig

      public static Matrix blankOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize)

    • getDkMatrix

      public static Matrix getDkMatrix(Atom[] ca1, Atom[] ca2, int k, int fragmentLength)

    • blankOutBreakFlag

      public static boolean[][] blankOutBreakFlag(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, boolean[][] breakFlag, int blankWindowSize)

    • getAngle

      public static double getAngle(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
      Returns the magnitude of the angle between the first and second blocks of afpChain, measured in degrees. This is always a positive value (unsigned).
      Parameters:
      afpChain -
      ca1 -
      ca2 -
      Returns:

    • buildSymmetryGraph

      public static List<List<Integer>> buildSymmetryGraph(List<AFPChain> afps, Atom[] atoms, boolean undirected)
      Converts a set of AFP alignments into a Graph of aligned residues, where each vertex is a residue and each edge means the connection between the two residues in one of the alignments.
      Parameters:
      afps - List of AFPChains
      atoms - Atom array of the symmetric structure
      undirected - if true, the graph is undirected
      Returns:
      adjacency List of aligned residues

    • buildSymmetryGraph

      public static org.jgrapht.UndirectedGraph<Integer,org.jgrapht.graph.DefaultEdge> buildSymmetryGraph(AFPChain selfAlignment)
      Converts a self alignment into a directed jGraphT of aligned residues, where each vertex is a residue and each edge means the equivalence between the two residues in the self-alignment.
      Parameters:
      selfAlignment - AFPChain
      Returns:
      alignment Graph

    • divideStructure

      public static List<Structure> divideStructure(CeSymmResult symmetry) throws StructureException
      Method that converts the symmetric units of a structure into different structures, so that they can be individually visualized.
      Parameters:
      symmetry - CeSymmResult
      Throws:
      StructureException

    • toFullAlignment

      public static MultipleAlignment toFullAlignment(CeSymmResult symm)
      Method that converts a repeats symmetric alignment into an alignment of whole structures.

      Example: if the structure has repeats A,B and C, the original alignment is A-B-C, and the returned alignment is ABC-BCA-CAB.

      Parameters:
      symm - CeSymmResult
      Returns:
      MultipleAlignment of the full structure superpositions

    • toRepeatsAlignment

      public static MultipleAlignment toRepeatsAlignment(CeSymmResult result) throws StructureException
      Method that converts a symmetry alignment into an alignment of the repeats only, as new independent structures.

      This method changes the structure identifiers, the Atom arrays and re-scles the aligned residues in the Blocks corresponding to those changes.

      Application: display superimposed repeats in Jmol.

      Parameters:
      result - CeSymmResult of symmetry
      Returns:
      MultipleAlignment of the repeats
      Throws:
      StructureException

    • fromAFP

      public static MultipleAlignment fromAFP(AFPChain symm, Atom[] atoms) throws StructureException
      Converts a refined symmetry AFPChain alignment into the standard representation of symmetry in a MultipleAlignment, that contains the entire Atom array of the strcuture and the symmetric repeats are orgaized in different rows in a single Block.
      Parameters:
      symm - AFPChain created with a symmetry algorithm and refined
      atoms - Atom array of the entire structure
      Returns:
      MultipleAlignment format of the symmetry
      Throws:
      StructureException

    • equivalentAxes

      @Deprecated public static boolean equivalentAxes(javax.vecmath.Matrix4d axis1, javax.vecmath.Matrix4d axis2, double epsilon)
      Deprecated.
      Determines if two symmetry axis are equivalent inside the error threshold. It only takes into account the direction of the vector where the rotation is made: the angle and translation are not taken into account.
      Parameters:
      axis1 -
      axis2 -
      epsilon - error allowed in the axis comparison
      Returns:
      true if equivalent, false otherwise

    • getQuaternarySymmetry

      public static QuatSymmetryResults getQuaternarySymmetry(CeSymmResult result) throws StructureException
      Given a symmetry result, it calculates the overall global symmetry, factoring out the alignment and detection steps of QuatSymmetryDetector algorithm.
      Parameters:
      result - symmetry result
      Returns:
      global symmetry results
      Throws:
      StructureException

    • isRefined

      @Deprecated public static boolean isRefined(MultipleAlignment symm)
      Deprecated.
      Returns true a symmetry multiple alignment has been refined, false otherwise.

      For a refined alignment only one Block with no repeated residues is necessary. Sufficient condition is not tested (only known from the algorithm or CeSymmResult).

      Parameters:
      symm - the symmetry alignment
      Returns:
      true if the alignment is refined

    • isSignificant

      @Deprecated public static boolean isSignificant(MultipleAlignment msa, double symmetryThreshold) throws StructureException
      Deprecated.
      Returns true if the symmetry alignment is significant, false otherwise.

      For a symmetry alignment to be significant, the alignment has to be refined and the TM-score has to be higher than the threshold.

      It is recommended to use the CeSymmResult.isSignificant() method instead.

      Parameters:
      msa -
      symmetryThreshold -
      Returns:
      Throws:
      StructureException

    • getGroups

      public static List<Group> getGroups(Atom[] rAtoms)
      Returns the List of Groups of the corresponding representative Atom array. The representative Atom array needs to fulfill: no two Atoms are from the same Group and Groups are sequential (connected in the original Structure), except if they are from different Chains.
      Parameters:
      rAtoms - array of representative Atoms (CA, P, etc).
      Returns:
      List of Groups

    • updateSymmetryTransformation

      public static void updateSymmetryTransformation(SymmetryAxes axes, MultipleAlignment msa) throws StructureException
      Calculates the set of symmetry operation Matrices (transformations) of the new alignment, based on the symmetry relations in the SymmetryAxes object. It sets the transformations to the input MultipleAlignment and SymmetryAxes objects. If the SymmetryAxes object is null, the superposition of the repeats is done without symmetry constraints.

      This method also sets the scores (RMSD and TM-score) after the new superposition has been updated.

      Parameters:
      axes - SymmetryAxes object. It will be modified.
      msa - MultipleAlignment. It will be modified.
      Throws:
      StructureException

    • updateSymmetryScores

      public static void updateSymmetryScores(MultipleAlignment symm) throws StructureException
      Update the scores (TM-score and RMSD) of a symmetry multiple alignment. This method does not redo the superposition of the alignment.
      Parameters:
      symm - Symmetry Multiple Alignment of Repeats
      Throws:
      StructureException

    • getRepresentativeAtoms

      public static Atom[] getRepresentativeAtoms(Structure structure)
      Returns the representative Atom Array of the first model, if the structure is NMR, or the Array for each model, if it is a biological assembly with multiple models.
      Parameters:
      structure -
      Returns:
      representative Atom[]