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

Class SymmetryDisplay

java.lang.Object
org.biojava.nbio.structure.symmetry.gui.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 Details

    • SymmetryDisplay

      public SymmetryDisplay()

  • Method Details

    • displayRepeats

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

    • displayFull

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

    • display

      public static AbstractAlignmentJmol display(CeSymmResult symmResult) throws 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:
      StructureException

    • printSymmetryAxes

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

    • printSymmetryAxes

      public static String printSymmetryAxes(CeSymmResult symm, boolean allAxes) throws 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:
      StructureException

    • printSymmetryGroup

      public static String printSymmetryGroup(CeSymmResult symm) throws 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:
      StructureException

    • getSymmTitle

      public static String getSymmTitle(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