| Package | Description |
|---|---|
| org.biojava.nbio.structure.align |
Classes for the alignment of structures.
|
| org.biojava.nbio.structure.align.gui | |
| org.biojava.nbio.structure.align.gui.aligpanel | |
| org.biojava.nbio.structure.align.gui.jmol |
Utility methods for better interaction with Jmol.
|
| org.biojava.nbio.structure.align.multiple | |
| org.biojava.nbio.structure.align.multiple.mc | |
| org.biojava.nbio.structure.align.multiple.util | |
| org.biojava.nbio.structure.align.quaternary | |
| org.biojava.nbio.structure.align.xml |
Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
|
| org.biojava.nbio.structure.cluster | |
| org.biojava.nbio.structure.symmetry.internal | |
| org.biojava.nbio.structure.symmetry.utils |
| Modifier and Type | Method and Description |
|---|---|
MultipleAlignment |
MultipleStructureAligner.align(List<Atom[]> atomArrays)
Run an alignment while specifying the atoms to be aligned.
|
MultipleAlignment |
MultipleStructureAligner.align(List<Atom[]> atomArrays,
Object params)
Run an alignment and also send a bean containing the parameters.
|
| Modifier and Type | Method and Description |
|---|---|
static MultipleAlignmentJmol |
MultipleAlignmentJmolDisplay.display(MultipleAlignment multAln)
Display a MultipleAlignment with a JmolPanel.
|
static JMenuBar |
MenuCreator.getAlignmentPanelMenu(JFrame frame,
ActionListener actionListener,
AFPChain afpChain,
MultipleAlignment msa)
Create the menu for the Alignment Panel representation of
Structural Alignments.
|
static JMenuBar |
MenuCreator.getAlignmentTextMenu(JFrame frame,
ActionListener actionListener,
AFPChain afpChain,
MultipleAlignment msa)
Create the menu for the Text representations of Structural Alignments.
|
static List<String> |
MultipleAlignmentJmolDisplay.getPDBresnum(int structNum,
MultipleAlignment multAln,
Atom[] ca)
Utility method used in the
MultipleAlignmentJmol Frame,
when the aligned residues of a structure in the alignment have
to be selected for formatting them (coloring and style). |
static JMenuItem |
MenuCreator.getSaveAlignmentMenuItem(AFPChain afpChain,
MultipleAlignment msa) |
static JMenuBar |
MenuCreator.initJmolMenu(JFrame frame,
AbstractAlignmentJmol parent,
AFPChain afpChain,
MultipleAlignment msa)
Provide a JMenuBar that can be added to a JFrame containing
a JmolPanel.
|
static void |
MultipleAlignmentJmolDisplay.showAlignmentImage(MultipleAlignment multAln,
String result)
Creates a new Frame with the String output representation of the
MultipleAlignment. |
static void |
MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(MultipleAlignment multAln,
AbstractAlignmentJmol jmol)
Creates a new Frame with the MultipleAlignment Sequence Panel.
|
| Constructor and Description |
|---|
MySaveFileListener(AFPChain afpChain,
MultipleAlignment msa)
Constructor to avoid checking which of the two is null before
instantiating this class.
|
MySaveFileListener(MultipleAlignment msa) |
| Modifier and Type | Method and Description |
|---|---|
MultipleAlignment |
MultipleAligPanel.getMultipleAlignment() |
| Constructor and Description |
|---|
MultipleAligPanel(MultipleAlignment msa,
AbstractAlignmentJmol jm)
Constructor using a MultipleAlignment.
|
| Modifier and Type | Method and Description |
|---|---|
MultipleAlignment |
MultipleAlignmentJmol.getMultipleAlignment() |
| Modifier and Type | Method and Description |
|---|---|
static String |
MultipleAlignmentJmol.getJmolString(MultipleAlignment multAln,
List<Atom[]> transformedAtoms,
org.jcolorbrewer.ColorBrewer colorPalette,
boolean colorByBlocks)
Generate a Jmol command String that colors the aligned residues of every
structure.
|
static String |
MultipleAlignmentJmol.getMultiBlockJmolString(MultipleAlignment multAln,
List<Atom[]> transformedAtoms,
org.jcolorbrewer.ColorBrewer colorPalette,
boolean colorByBlocks)
Colors every Block of the structures with a different color, following
the palette.
|
| Constructor and Description |
|---|
MultipleAlignmentJmol(MultipleAlignment msa,
List<Atom[]> rotatedAtoms)
The constructor displays the Mutltiple Alignment in a new JmolPanel
Frame.
|
| Modifier and Type | Class and Description |
|---|---|
class |
MultipleAlignmentImpl
A general implementation of a
MultipleAlignment. |
| Modifier and Type | Method and Description |
|---|---|
MultipleAlignment |
MultipleAlignment.clone()
Creates and returns an identical copy of this alignment, including a deep
copy of all constituent BlockSets.
|
MultipleAlignment |
BlockSetImpl.getMultipleAlignment() |
MultipleAlignment |
BlockSet.getMultipleAlignment()
Returns the parent MultipleAlignment of the BlockSet.
|
MultipleAlignment |
MultipleAlignmentEnsemble.getMultipleAlignment(int index)
Returns the MultipleAlignments at the specified index
in the ensemble.
|
MultipleAlignment |
MultipleAlignmentEnsembleImpl.getMultipleAlignment(int index) |
| Modifier and Type | Method and Description |
|---|---|
List<MultipleAlignment> |
MultipleAlignmentEnsemble.getMultipleAlignments()
Returns the List of MultipleAlignments in the ensemble.
|
List<MultipleAlignment> |
MultipleAlignmentEnsembleImpl.getMultipleAlignments() |
| Modifier and Type | Method and Description |
|---|---|
void |
MultipleAlignmentEnsemble.addMultipleAlignment(MultipleAlignment alignment)
Add a new MultipleAlignment to the end of the ensemble and set its
parent ensemble to this.
|
void |
MultipleAlignmentEnsembleImpl.addMultipleAlignment(MultipleAlignment alignment) |
void |
BlockSetImpl.setMultipleAlignment(MultipleAlignment parent) |
void |
BlockSet.setMultipleAlignment(MultipleAlignment parent)
Set the back-reference to its parent MultipleAlignment.
|
| Modifier and Type | Method and Description |
|---|---|
void |
MultipleAlignmentEnsemble.setMultipleAlignments(List<MultipleAlignment> alignments)
Set the List of MultipleAlignments in the ensemble.
|
void |
MultipleAlignmentEnsembleImpl.setMultipleAlignments(List<MultipleAlignment> alignments) |
| Constructor and Description |
|---|
BlockSetImpl(MultipleAlignment alignment)
Constructor.
|
| Modifier and Type | Method and Description |
|---|---|
MultipleAlignment |
MultipleMcMain.align(List<Atom[]> atomArrays) |
MultipleAlignment |
MultipleMcMain.align(List<Atom[]> atomArrays,
Object parameters) |
MultipleAlignment |
MultipleMcOptimizer.call() |
MultipleAlignment |
MultipleMcOptimizer.optimize()
Optimization method based in a Monte-Carlo approach.
|
| Constructor and Description |
|---|
MultipleMcOptimizer(MultipleAlignment seedAln,
MultipleMcParameters params,
int reference)
Constructor.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
MultipleAlignmentScorer.calculateScores(MultipleAlignment alignment)
Calculates and puts the RMSD and the average TM-Score of the
MultipleAlignment.
|
static Atom |
MultipleAlignmentTools.getAtomForSequencePosition(MultipleAlignment msa,
List<Integer> mapSeqToStruct,
int str,
int sequencePos)
Returns the Atom of the specified structure that is aligned in the
sequence alignment position specified.
|
static Matrix |
MultipleAlignmentTools.getAverageResidueDistances(MultipleAlignment msa)
The average residue distance Matrix contains the average distance from
each residue to all other residues aligned with it.
|
static double |
MultipleAlignmentScorer.getAvgTMScore(MultipleAlignment alignment)
Calculates the average TMScore of all the possible pairwise structure
comparisons of the given alignment.
|
static int |
MultipleAlignmentTools.getBlockForSequencePosition(MultipleAlignment multAln,
List<Integer> mapSeqToStruct,
int sequencePos)
Returns the block number of a specified position in the sequence
alignment, given the mapping from structure to function.
|
static List<String> |
MultipleAlignmentTools.getBlockSequenceAlignment(MultipleAlignment ma)
Calculate the sequence alignment Strings for the alignment Blocks in an
alignment.
|
static List<String> |
MultipleAlignmentTools.getBlockSequenceAlignment(MultipleAlignment alignment,
List<Integer> mapSeqToStruct)
Calculate the sequence alignment Strings for the alignment Blocks in an
alignment.
|
static org.forester.phylogeny.Phylogeny |
MultipleAlignmentTools.getHSDMTree(MultipleAlignment msta)
Calculate a phylogenetic tree of the MultipleAlignment using
dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for
distantly related proteins, structure-derived) and the Neighbor Joining
algorithm from forester.
|
static org.forester.phylogeny.Phylogeny |
MultipleAlignmentTools.getKimuraTree(MultipleAlignment msta)
Calculate a phylogenetic tree of the MultipleAlignment using Kimura
distances and the Neighbor Joining algorithm from forester.
|
static double |
MultipleAlignmentScorer.getMCScore(MultipleAlignment alignment,
double gapOpen,
double gapExtension,
double dCutoff)
Calculates the MC score, specific for the MultipleAlignment algorithm.
|
static double |
MultipleAlignmentScorer.getRefRMSD(MultipleAlignment alignment,
int ref)
/** Calculates the average RMSD from all structures to a reference s
tructure, given a set of superimposed atoms.
|
static double |
MultipleAlignmentScorer.getRefTMScore(MultipleAlignment alignment,
int ref)
Calculates the average TMScore from all structures to a reference
structure, given a set of superimposed atoms.
|
static double |
MultipleAlignmentScorer.getRMSD(MultipleAlignment alignment)
Calculates the RMSD of all-to-all structure comparisons (distances) of
the given MultipleAlignment.
|
static Matrix |
MultipleAlignmentTools.getRMSDMatrix(MultipleAlignment msa)
Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of
the matrix contains the RMSD between structures i and j.
|
static List<Atom[]> |
MultipleAlignmentDisplay.getRotatedAtoms(MultipleAlignment multAln)
New structures are downloaded if they were not cached in the alignment
and they are entirely transformed here with the superposition information
in the Multiple Alignment.
|
static List<String> |
MultipleAlignmentTools.getSequenceAlignment(MultipleAlignment msa)
Calculate the sequence alignment Strings for the whole alignment.
|
static List<String> |
MultipleAlignmentTools.getSequenceAlignment(MultipleAlignment alignment,
List<Integer> mapSeqToStruct)
Calculate the sequence alignment Strings for the whole alignment.
|
static org.forester.phylogeny.Phylogeny |
MultipleAlignmentTools.getStructuralTree(MultipleAlignment msta)
Calculate a phylogenetic tree of the MultipleAlignment using RMSD
distances and the Neighbor Joining algorithm from forester.
|
void |
MultipleSuperimposer.superimpose(MultipleAlignment alignment)
Superimpose all structures from a
MultipleAlignment. |
void |
ReferenceSuperimposer.superimpose(MultipleAlignment alignment) |
void |
CoreSuperimposer.superimpose(MultipleAlignment alignment) |
static String |
MultipleAlignmentWriter.to3DFormat(MultipleAlignment alignment,
int queryIndex,
int templateIndex)
Outputs a pairwise alignment in I-TASSER's 3D Format for target-template
alignment. http://zhanglab.ccmb.med.umich.edu/I-TASSER/option4.html
The format is closely related to a standard PDB file, but contains only
CA atoms and adds two columns for specifying the alignment:
ATOM 2001 CA MET 1 41.116 -30.727 6.866 129 THR
ATOM 2002 CA ALA 2 39.261 -27.408 6.496 130 ARG
ATOM 2003 CA ALA 3 35.665 -27.370 7.726 131 THR
ATOM 2004 CA ARG 4 32.662 -25.111 7.172 132 ARG
ATOM 2005 CA GLY 5 29.121 -25.194 8.602 133 ARG
Column 1 -30: Atom & Residue records of query sequence.
|
static String |
MultipleAlignmentWriter.toAlignedResidues(MultipleAlignment multAln)
Converts the alignment to its simplest form: a list of groups of aligned
residues.
|
static String |
MultipleAlignmentWriter.toFASTA(MultipleAlignment alignment)
Converts the
MultipleAlignment into a multiple sequence alignment
String in FASTA format. |
static String |
MultipleAlignmentWriter.toFatCat(MultipleAlignment alignment)
Converts the
MultipleAlignment into a FatCat String format. |
static Structure |
MultipleAlignmentTools.toMultimodelStructure(MultipleAlignment multAln,
List<Atom[]> transformedAtoms) |
static MultipleSequenceAlignment<ProteinSequence,AminoAcidCompound> |
MultipleAlignmentTools.toProteinMSA(MultipleAlignment msta)
Convert a MultipleAlignment into a MultipleSequenceAlignment of AminoAcid
residues.
|
static String |
MultipleAlignmentWriter.toTransformMatrices(MultipleAlignment alignment)
Converts the transformation Matrices of the alignment into a String
output.
|
static List<Atom[]> |
MultipleAlignmentTools.transformAtoms(MultipleAlignment alignment)
Transforms atoms according to the superposition stored in the alignment.
|
| Modifier and Type | Method and Description |
|---|---|
MultipleAlignment |
QsAlignResult.getAlignment()
The alignment that specifies the residue equivalencies of the equivalent
Subunits.
|
| Modifier and Type | Method and Description |
|---|---|
void |
QsAlignResult.setAlignment(MultipleAlignment alignment)
The alignment that specifies the residue equivalencies of the equivalent
Subunits.
|
| Modifier and Type | Method and Description |
|---|---|
static MultipleAlignment |
MultipleAlignmentXMLParser.parseMultipleAlignment(Node root,
MultipleAlignmentEnsemble ensemble) |
| Modifier and Type | Method and Description |
|---|---|
static BlockSet |
MultipleAlignmentXMLParser.parseBlockSet(Node root,
MultipleAlignment msa) |
static void |
MultipleAlignmentXMLConverter.printXMLalignment(PrettyXMLWriter xml,
MultipleAlignment msa) |
| Modifier and Type | Method and Description |
|---|---|
MultipleAlignment |
SubunitCluster.getMultipleAlignment()
The multiple alignment is calculated from the equivalent residues in the
SubunitCluster.
|
| Modifier and Type | Method and Description |
|---|---|
MultipleAlignment |
CeSymmResult.getMultipleAlignment() |
MultipleAlignment |
SymmOptimizer.optimize()
Optimization method based in a Monte-Carlo approach.
|
MultipleAlignment |
SequenceFunctionRefiner.refine(AFPChain selfAlignment,
Atom[] atoms,
int order) |
MultipleAlignment |
SymmetryRefiner.refine(AFPChain selfAlignment,
Atom[] atoms,
int order)
Returns a refined symmetry alignment, where the repeat residues are
aligned consistently in a MultipleAlignment.
|
MultipleAlignment |
GraphComponentRefiner.refine(AFPChain selfAlignment,
Atom[] atoms,
int order) |
| Modifier and Type | Method and Description |
|---|---|
void |
CeSymmResult.setMultipleAlignment(MultipleAlignment multipleAlignment) |
| Modifier and Type | Method and Description |
|---|---|
static MultipleAlignment |
SymmetryTools.fromAFP(AFPChain symm,
Atom[] atoms)
Converts a refined symmetry AFPChain alignment into the standard
representation of symmetry in a MultipleAlignment, that contains the
entire Atom array of the strcuture and the symmetric repeats are orgaized
in different rows in a single Block.
|
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.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
SymmetryTools.updateSymmetryScores(MultipleAlignment symm)
Update the scores (TM-score and RMSD) of a symmetry multiple alignment.
|
static void |
SymmetryTools.updateSymmetryTransformation(SymmetryAxes axes,
MultipleAlignment msa)
Calculates the set of symmetry operation Matrices (transformations) of
the new alignment, based on the symmetry relations in the SymmetryAxes
object.
|
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