Package org.biojava.nbio.structure.symmetry.gui

Class SymmetryDisplay

  • public class SymmetryDisplay
extends Object
    Class that provides visualizations methods for symmetry alignments. Call the display() method for the default visualization of symmetry.
    Since:
    4.2.0
    Author:
    Aleix Lafita

    • Constructor Summary

      Constructors 
      Constructor Description
      SymmetryDisplay()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static AbstractAlignmentJmol display​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symmResult)
      Displays a single structure in a cartoon representation with each symmetric repeat colored differently.
      static MultipleAlignmentJmol displayFull​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm)
      Displays a multiple alignment of the whole structure transformations colored by blocks, corresponding to the symmetric protodomains.
      static MultipleAlignmentJmol displayRepeats​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm)
      Displays a multiple alignment of the symmetry repeats.
      static String getSymmTitle​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult result)
      Create a symmetry title for a display frame (Jmol, alignment, etc).
      static String printSymmetryAxes​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm)
      Generates a String that displays the symmetry axes of a structure.
      static String printSymmetryAxes​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm, boolean allAxes)
      Generates a String that displays the symmetry axes of a structure.
      static String printSymmetryGroup​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm)
      Given a symmetry alignment, it draws the symmetry group axes and the polyhedron box around the structure.

    • Constructor Detail

      • SymmetryDisplay

        public SymmetryDisplay()

    • Method Detail

      • displayRepeats

        public static MultipleAlignmentJmol displayRepeats​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm)
                                            throws org.biojava.nbio.structure.StructureException
        Displays a multiple alignment of the symmetry repeats. * @param symm CeSymmResult
        Throws:
        org.biojava.nbio.structure.StructureException

      • displayFull

        public static MultipleAlignmentJmol displayFull​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm)
                                         throws org.biojava.nbio.structure.StructureException
        Displays a multiple alignment of the whole structure transformations colored by blocks, corresponding to the symmetric protodomains.
        Parameters:
        symm - CeSymmResult
        Throws:
        org.biojava.nbio.structure.StructureException

      • display

        public static AbstractAlignmentJmol display​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symmResult)
                                     throws org.biojava.nbio.structure.StructureException
        Displays a single structure in a cartoon representation with each symmetric repeat colored differently.
        Parameters:
        msa - the symmetry multiple alignment obtained from CeSymm
        Throws:
        org.biojava.nbio.structure.StructureException

      • printSymmetryAxes

        public static String printSymmetryAxes​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm)
                                throws org.biojava.nbio.structure.StructureException
        Generates a String that displays the symmetry axes of a structure.
        Parameters:
        symm - CeSymmResult
        Returns:
        Throws:
        org.biojava.nbio.structure.StructureException

      • printSymmetryAxes

        public static String printSymmetryAxes​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm,
                                       boolean allAxes)
                                throws org.biojava.nbio.structure.StructureException
        Generates a String that displays the symmetry axes of a structure.
        Parameters:
        symm - CeSymmResult
        allAxes - Indicates whether all axes should be displayed or just the elemenatary ones
        Returns:
        Throws:
        org.biojava.nbio.structure.StructureException

      • printSymmetryGroup

        public static String printSymmetryGroup​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult symm)
                                 throws org.biojava.nbio.structure.StructureException
        Given a symmetry alignment, it draws the symmetry group axes and the polyhedron box around the structure. It uses the quaternary symmetry detection code, but tries to factor out the alignment and detection steps.
        Parameters:
        symm - CeSymmResult
        Returns:
        Throws:
        org.biojava.nbio.structure.StructureException

      • getSymmTitle

        public static String getSymmTitle​(org.biojava.nbio.structure.symmetry.internal.CeSymmResult result)
        Create a symmetry title for a display frame (Jmol, alignment, etc). The title contains information about the algorithm, structure id and parameters used.
        Parameters:
        result -
        Returns:
        title String