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 Summary

Constructors

Constructor	Description
SymmetryDisplay()

Method Summary

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SymmetryDisplay

public SymmetryDisplay()

Method Detail

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