Package | Description |
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org.biojava.nbio.structure.symmetry.gui | |
org.biojava.nbio.structure.symmetry.internal | |
org.biojava.nbio.structure.symmetry.utils |
Modifier and Type | Method and Description |
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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.printSymmetryAxes(CeSymmResult symm,
boolean allAxes)
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.
|
Constructor and Description |
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SymmetryListener(MultipleAlignmentJmol jmol,
CeSymmResult symm) |
Modifier and Type | Method and Description |
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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.
|
Constructor and Description |
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SymmOptimizer(CeSymmResult symmResult)
Constructor with a seed MultipleAligment storing a refined symmetry
alignment of the repeats.
|
Modifier and Type | Method and Description |
---|---|
static List<Structure> |
SymmetryTools.divideStructure(CeSymmResult symmetry)
Method that converts the symmetric units of a structure into different
structures, so that they can be individually visualized.
|
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.
|
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