Uses of Class
org.biojava.nbio.structure.symmetry.internal.CeSymmResult

Packages that use CeSymmResult

Package	Description
org.biojava.nbio.structure.symmetry.gui
org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.utils

Uses of CeSymmResult in org.biojava.nbio.structure.symmetry.gui

Methods in org.biojava.nbio.structure.symmetry.gui with parameters of type CeSymmResult

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

Constructors in org.biojava.nbio.structure.symmetry.gui with parameters of type CeSymmResult

Constructor and Description
SymmetryListener(MultipleAlignmentJmol jmol, CeSymmResult symm)

Uses of CeSymmResult in org.biojava.nbio.structure.symmetry.internal

Methods in org.biojava.nbio.structure.symmetry.internal that return CeSymmResult

Modifier and Type	Method and Description
protected static CeSymmResult	CeSymm.align(Atom[] atoms, CESymmParameters params)
static CeSymmResult	CeSymm.analyze(Atom[] atoms) Analyze the symmetries of the input Atom array using the DEFAULT parameters.
static CeSymmResult	CeSymm.analyze(Atom[] atoms, CESymmParameters params) Analyze the symmetries of the input Atom array using the provided parameters.
static CeSymmResult	CeSymm.analyzeLevel(Atom[] atoms, CESymmParameters params) Analyze a single level of symmetry.
CeSymmResult	CeSymmIterative.execute(Atom[] atoms) This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.

Constructors in org.biojava.nbio.structure.symmetry.internal with parameters of type CeSymmResult

Constructor and Description
SymmOptimizer(CeSymmResult symmResult) Constructor with a seed MultipleAligment storing a refined symmetry alignment of the repeats.

Uses of CeSymmResult in org.biojava.nbio.structure.symmetry.utils

Methods in org.biojava.nbio.structure.symmetry.utils with parameters of type CeSymmResult

Modifier and Type	Method and Description
static Structure	SymmetryTools.getQuaternaryStructure(CeSymmResult symmetry) Method that converts the symmetric units of a structure into different chains, so that internal symmetry can be translated into quaternary.
static QuatSymmetryResults	SymmetryTools.getQuaternarySymmetry(CeSymmResult result) Given a symmetry result, it calculates the overall global symmetry, factoring out the alignment and detection steps of QuatSymmetryDetector algorithm.
static MultipleAlignment	SymmetryTools.toFullAlignment(CeSymmResult symm) Method that converts a repeats symmetric alignment into an alignment of whole structures.
static MultipleAlignment	SymmetryTools.toRepeatsAlignment(CeSymmResult result) Method that converts a symmetry alignment into an alignment of the repeats only, as new independent structures.