Uses of Class
org.biojava.nbio.structure.align.model.AFPChain

Packages that use AFPChain

Package	Description
org.biojava.nbio.structure.align	Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.client	This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.fatcat	Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.fatcat.calc
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.model
org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.seq
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.align.xml	Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.utils

Uses of AFPChain in org.biojava.nbio.structure.align

Methods in org.biojava.nbio.structure.align that return AFPChain

Modifier and Type	Method and Description
AFPChain	BioJavaStructureAlignment.align(Atom[] ca1, Atom[] ca2)
AFPChain	StructureAlignment.align(Atom[] ca1, Atom[] ca2) Run an alignment while specifying the atoms to be aligned.
abstract AFPChain	AbstractStructureAlignment.align(Atom[] ca1, Atom[] ca2)
AFPChain	BioJavaStructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params)
AFPChain	StructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params) run an alignment and also send a bean containing the parameters.
abstract AFPChain	AbstractStructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params)
AFPChain	CallableStructureAlignment.call()

Methods in org.biojava.nbio.structure.align with parameters of type AFPChain

Modifier and Type	Method and Description
static int	AFPTwister.afp2Res(AFPChain afpChain, int afpn, int[] afpPositions, int listStart) Set the list of equivalent residues in the two proteins given a list of AFPs WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
static Group[]	AFPTwister.twistOptimized(AFPChain afpChain, Atom[] ca1, Atom[] ca2) superimposing according to the optimized alignment
static Group[]	AFPTwister.twistPDB(AFPChain afpChain, Atom[] ca1, Atom[] ca2) calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B

Uses of AFPChain in org.biojava.nbio.structure.align.ce

Methods in org.biojava.nbio.structure.align.ce that return AFPChain

Modifier and Type	Method and Description
AFPChain	CeMain.align(Atom[] ca1, Atom[] ca2)
AFPChain	OptimalCECPMain.align(Atom[] ca1, Atom[] ca2, Object param) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AFPChain	CeMain.align(Atom[] ca1, Atom[] ca2, Object param) Align ca2 onto ca1.
AFPChain	CeCPMain.align(Atom[] ca1, Atom[] ca2, Object param) Aligns ca1 and ca2 using a heuristic to check for CPs.
AFPChain	OptimalCECPMain.alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AFPChain	OptimalCECPMain.alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp) Aligns ca1 with ca2 permuted by cp residues.
AFPChain	CeCalculatorEnhanced.extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain	CECalculator.extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated) Takes as input an AFPChain where ca2 has been artificially duplicated.
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated, CECPParameters params)
AFPChain	CeCPMain.invertAlignment(AFPChain a) Swaps the order of structures in an AFPChain
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator) Circular permutation specific code to be run after the standard CE alignment
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param) Circular permutation specific code to be run after the standard CE alignment

Methods in org.biojava.nbio.structure.align.ce with parameters of type AFPChain

Modifier and Type	Method and Description
AFPChain	OptimalCECPMain.alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
void	CeCalculatorEnhanced.convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) copy data from this class into AFPChain container object.
void	CECalculator.convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) copy data from this class into AFPChain container object.
static Object	GuiWrapper.display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain	CeCalculatorEnhanced.extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain	CECalculator.extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated) Takes as input an AFPChain where ca2 has been artificially duplicated.
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated, CECPParameters params)
String	AbstractUserArgumentProcessor.getDbSearchResult(AFPChain afpChain)
AFPChain	CeCPMain.invertAlignment(AFPChain a) Swaps the order of structures in an AFPChain
void	CeCalculatorEnhanced.nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	CECalculator.nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator) Circular permutation specific code to be run after the standard CE alignment
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param) Circular permutation specific code to be run after the standard CE alignment
static void	GuiWrapper.showAlignmentImage(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Object jmol)
void	CeCalculatorEnhanced.traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	CECalculator.traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Uses of AFPChain in org.biojava.nbio.structure.align.client

Methods in org.biojava.nbio.structure.align.client that return AFPChain

Modifier and Type	Method and Description
static AFPChain	JFatCatClient.getAFPChainFromServer(String serverLocation, String name1, String name2, Atom[] ca1, Atom[] ca2)
static AFPChain	JFatCatClient.getAFPChainFromServer(String serverLocation, String method, String name1, String name2, Atom[] ca1, Atom[] ca2, int timeout)

Methods in org.biojava.nbio.structure.align.client with parameters of type AFPChain

Modifier and Type	Method and Description
static void	JFatCatClient.sendAFPChainToServer(String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Uses of AFPChain in org.biojava.nbio.structure.align.fatcat

Methods in org.biojava.nbio.structure.align.fatcat that return AFPChain

Modifier and Type	Method and Description
AFPChain	FatCatRigid.align(Atom[] ca1, Atom[] ca2)
AFPChain	FatCatFlexible.align(Atom[] ca1, Atom[] ca2)
protected AFPChain	FatCat.align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)
AFPChain	FatCatRigid.align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain	FatCatFlexible.align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain	FatCat.alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params)
AFPChain	FatCat.alignRigid(Atom[] ca1, Atom[] ca2)
AFPChain	FatCat.alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params)

Uses of AFPChain in org.biojava.nbio.structure.align.fatcat.calc

Methods in org.biojava.nbio.structure.align.fatcat.calc that return AFPChain

Modifier and Type	Method and Description
AFPChain	FatCatAligner.getAfpChain()

Methods in org.biojava.nbio.structure.align.fatcat.calc with parameters of type AFPChain

Modifier and Type	Method and Description
static boolean	AFPChainer.afpPairConn(int afp1, int afp2, FatCatParameters params, AFPChain afpChain) //Key function: calculate the connectivity of AFP pairs //no compatibility criteria is executed //note: afp1 is previous to afp2 in terms of the position //this module must be optimized
static void	AFPOptimizer.blockInfo(AFPChain afpChain) get the afp list and residue list for each block
protected static double	AFPChainer.calAfpRmsd(int afpn, int[] afpPositions, int listStart, AFPChain afpChain, Atom[] ca1, Atom[] ca2) //return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
double	SigEva.calNS(FatCatParameters params, AFPChain afpChain)
double	SigEva.calSigAll(FatCatParameters params, AFPChain afpChain)
static void	AFPChainer.doChainAfp(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2) // Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
static void	AFPCalculator.extractAFPChains(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPOptimizer.optimizeAln(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2) optimize the alignment by dynamic programming
static void	AFPPostProcessor.postProcess(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPCalculator.sortAfps(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPOptimizer.updateScore(FatCatParameters params, AFPChain afpChain) to update the chaining score after block delete and merge processed the blockScore value is important for significance evaluation

Uses of AFPChain in org.biojava.nbio.structure.align.gui

Methods in org.biojava.nbio.structure.align.gui with parameters of type AFPChain

Modifier and Type	Method and Description
static Structure	DisplayAFP.createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
static StructureAlignmentJmol	StructureAlignmentDisplay.display(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Display an AFPChain alignment
static StructureAlignmentJmol	DisplayAFP.display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms1, List<Group> hetatms2) Note: ca2, hetatoms2 and nucleotides2 should not be rotated.
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 Atom	DisplayAFP.getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious) Return the atom at alignment position aligPos. at the present only works with block 0
static List<Integer>	DisplayAFP.getEQRAlignmentPos(AFPChain afpChain)
static List<String>	DisplayAFP.getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca) Return a list of pdb Strings corresponding to the aligned positions of the molecule.
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	DisplayAFP.showAlignmentImage(AFPChain afpChain, String result)
static void	DisplayAFP.showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)

Constructors in org.biojava.nbio.structure.align.gui with parameters of type AFPChain

Constructor and Description
DotPlotListener(AFPChain afpChain)
DotPlotPanel(AFPChain alignment)
MySaveFileListener(AFPChain afpChain)
MySaveFileListener(AFPChain afpChain, MultipleAlignment msa) Constructor to avoid checking which of the two is null before instantiating this class.

Uses of AFPChain in org.biojava.nbio.structure.align.gui.aligpanel

Methods in org.biojava.nbio.structure.align.gui.aligpanel that return AFPChain

Modifier and Type	Method and Description
AFPChain	StatusDisplay.getAfpChain()
AFPChain	AligPanel.getAFPChain()

Methods in org.biojava.nbio.structure.align.gui.aligpanel with parameters of type AFPChain

Modifier and Type	Method and Description
void	StatusDisplay.setAfpChain(AFPChain afpChain)
void	AFPChainCoordManager.setAFPChain(AFPChain afpChain)
void	AligPanel.setAFPChain(AFPChain afpChain)

Constructors in org.biojava.nbio.structure.align.gui.aligpanel with parameters of type AFPChain

Constructor and Description
MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol) Constructor using an afpChain and the atom arrays for pairwise alignments.

Uses of AFPChain in org.biojava.nbio.structure.align.gui.jmol

Methods in org.biojava.nbio.structure.align.gui.jmol with parameters of type AFPChain

Modifier and Type	Method and Description
static String	StructureAlignmentJmol.getJmolScript4Block(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNr)
static String	StructureAlignmentJmol.getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Constructors in org.biojava.nbio.structure.align.gui.jmol with parameters of type AFPChain

Constructor and Description
StructureAlignmentJmol(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Uses of AFPChain in org.biojava.nbio.structure.align.model

Methods in org.biojava.nbio.structure.align.model with parameters of type AFPChain

Modifier and Type	Method and Description
static void	AfpChainWriter.printScoresInLines(AFPChain afpChain, int blockNum, int optLength, double totalRmsdOpt, double alignScore, int alnLength, int gapLen, double identity, double similarity, StringBuffer txt)
static String	AfpChainWriter.toAlignedPairs(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Prints the alignment in the simplest form: a list of aligned residues.
static String	AfpChainWriter.toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static String	AfpChainWriter.toDBSearchResult(AFPChain afpChain)
static String	AfpChainWriter.toFatCat(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static String	AfpChainWriter.toFatCatCore(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean printLegend, boolean longHeader, boolean showHTML, boolean showAlignmentBlock) Output in FatCatCore format Note that if a circular permutation has occured the residue numbers may be innaccurate.
static String	AfpChainWriter.toPrettyAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showHTML, boolean showAlignmentBlock)
static String	AfpChainWriter.toRotMat(AFPChain afpChain)
static String	AfpChainWriter.toScoresList(AFPChain afpChain)
static String	AfpChainWriter.toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
static String	AfpChainWriter.toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showAlignmentBlock) Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.

Constructors in org.biojava.nbio.structure.align.model with parameters of type AFPChain

Constructor and Description
AFPChain(AFPChain o) Copy constructor

Uses of AFPChain in org.biojava.nbio.structure.align.multiple

Constructors in org.biojava.nbio.structure.align.multiple with parameters of type AFPChain

Constructor and Description
MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2, boolean flexible) Constructor from an AFPChain instance.

Uses of AFPChain in org.biojava.nbio.structure.align.seq

Methods in org.biojava.nbio.structure.align.seq that return AFPChain

Modifier and Type	Method and Description
AFPChain	SmithWaterman3Daligner.align(Atom[] ca1, Atom[] ca2)
AFPChain	SmithWaterman3Daligner.align(Atom[] ca1, Atom[] ca2, Object parameters)

Uses of AFPChain in org.biojava.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util that return AFPChain

Modifier and Type	Method and Description
static AFPChain	AlignmentTools.createAFPChain(Atom[] ca1, Atom[] ca2, ResidueNumber[] aligned1, ResidueNumber[] aligned2) Fundamentally, an alignment is just a list of aligned residues in each protein.
static AFPChain	AlignmentTools.deleteColumn(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int block, int pos) Delete an alignment position from the original alignment object.
static AFPChain	AlignmentTools.deleteHighestDistanceColumn(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Find the alignment position with the highest atomic distance between the equivalent atomic positions of the arrays and remove it from the alignment.
static AFPChain	AlignmentTools.replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNum, int[] optLens, int[][][] optAln)
static AFPChain	AlignmentTools.replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Map<Integer,Integer> alignment) Takes an AFPChain and replaces the optimal alignment based on an alignment map Parameters are filled with defaults (often null) or sometimes calculated.
static AFPChain	AlignmentTools.replaceOptAln(int[][][] newAlgn, AFPChain afpChain, Atom[] ca1, Atom[] ca2) It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and variables.
static AFPChain	AlignmentTools.splitBlocksByTopology(AFPChain a, Atom[] ca1, Atom[] ca2)

Methods in org.biojava.nbio.structure.align.util with parameters of type AFPChain

Modifier and Type	Method and Description
static Map<Integer,Integer>	AlignmentTools.alignmentAsMap(AFPChain afpChain) Creates a Map specifying the alignment as a mapping between residue indices of protein 1 and residue indices of protein 2.
static void	AlignmentTools.alignmentToSIF(Writer out, AFPChain afpChain, Atom[] ca1, Atom[] ca2, String backboneInteraction, String alignmentInteraction) Creates a simple interaction format (SIF) file for an alignment.
static Structure	AFPAlignmentDisplay.createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static AFPChain	AlignmentTools.deleteColumn(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int block, int pos) Delete an alignment position from the original alignment object.
static AFPChain	AlignmentTools.deleteHighestDistanceColumn(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Find the alignment position with the highest atomic distance between the equivalent atomic positions of the arrays and remove it from the alignment.
static void	AlignmentTools.fillAlignedAtomArrays(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Atom[] ca1aligned, Atom[] ca2aligned) Fill the aligned Atom arrays with the equivalent residues in the afpChain.
static void	AFPAlignmentDisplay.getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Extract the alignment output eg STWNTWACTWHLKQP--WSTILILA 111111111111 22222222 SQNNTYACSWKLKSWNNNSTILILG Those position pairs labeled by 1 and 2 are equivalent positions, belongs to two blocks 1 and 2.
static void	AFPAlignmentDisplay.getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showSeq) Sets the following properties: The alignment strings alnseq1, alnseq2, and alnsymb alnbeg1 and 2 alnLength and gapLen Expects the following properties to be previously computed: getOptAln() and lengths Known Bugs Expects the alignment to have linear topology.
static Atom[]	AFPAlignmentDisplay.getAlignedAtoms1(AFPChain afpChain, Atom[] ca1)
static Atom[]	AFPAlignmentDisplay.getAlignedAtoms2(AFPChain afpChain, Atom[] ca2)
static double	RotationAxis.getAngle(AFPChain afpChain) Calculate the rotation angle for a structure
static int	AFPAlignmentDisplay.getBlockNrForAlignPos(AFPChain afpChain, int aligPos) get the block number for an aligned position
static List<List<List<Integer>>>	AlignmentTools.getOptAlnAsList(AFPChain afpChain) Retrieves the optimum alignment from an AFPChain and returns it as a java collection.
static Matrix	AFPAlignmentDisplay.getRotMax(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static int	AlignmentTools.getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float minimumMetricChange) Guesses the order of symmetry in an alignment Uses AlignmentTools.getSymmetryOrder(Map alignment, Map identity, int, float) to determine the the symmetry order.
static double	AFPChainScorer.getTMScore(AFPChain align, Atom[] ca1, Atom[] ca2)
static double	AFPChainScorer.getTMScore(AFPChain align, Atom[] ca1, Atom[] ca2, boolean normalizeMin)
static Atom	AFPAlignmentDisplay.getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static boolean	AlignmentTools.isSequentialAlignment(AFPChain afpChain, boolean checkWithinBlocks) Checks that the alignment given by afpChain is sequential.
static Group[]	AlignmentTools.prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Rotate the Atoms/Groups so they are aligned for the 3D visualisation
static AFPChain	AlignmentTools.replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNum, int[] optLens, int[][][] optAln)
static AFPChain	AlignmentTools.replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Map<Integer,Integer> alignment) Takes an AFPChain and replaces the optimal alignment based on an alignment map Parameters are filled with defaults (often null) or sometimes calculated.
static AFPChain	AlignmentTools.replaceOptAln(int[][][] newAlgn, AFPChain afpChain, Atom[] ca1, Atom[] ca2) It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and variables.
static void	AlignmentTools.shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift, Group[] twistedGroups) only shift CA positions.
static AFPChain	AlignmentTools.splitBlocksByTopology(AFPChain a, Atom[] ca1, Atom[] ca2)
static void	AlignmentTools.updateSuperposition(AFPChain afpChain, Atom[] ca1, Atom[] ca2) After the alignment changes (optAln, optLen, blockNum, at a minimum), many other properties which depend on the superposition will be invalid.

Constructors in org.biojava.nbio.structure.align.util with parameters of type AFPChain

Constructor and Description
RotationAxis(AFPChain afpChain) Calculate the rotation axis for the first block of an AFPChain

Uses of AFPChain in org.biojava.nbio.structure.align.xml

Methods in org.biojava.nbio.structure.align.xml that return AFPChain

Modifier and Type	Method and Description
static AFPChain	AFPChainFlipper.flipChain(AFPChain o) Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
static AFPChain	AFPChainXMLParser.fromXML(String xml, Atom[] ca1, Atom[] ca2)
static AFPChain	AFPChainXMLParser.fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
static AFPChain[]	AFPChainXMLParser.parseMultiXML(String xml)

Methods in org.biojava.nbio.structure.align.xml with parameters of type AFPChain

Modifier and Type	Method and Description
static AFPChain	AFPChainFlipper.flipChain(AFPChain o) Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
static void	AFPChainXMLConverter.printXMLEQRInferPositions(PrettyXMLWriter xml, AFPChain afpChain, int bk, Atom[] ca1, Atom[] ca2)
static void	AFPChainXMLConverter.printXMLHeader(PrettyXMLWriter xml, AFPChain afpChain)
static void	AFPChainXMLParser.rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) replace the PDB res nums with atom positions:
static String	AFPChainXMLConverter.toXML(AFPChain afpChain)
static String	AFPChainXMLConverter.toXML(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Convert an afpChain to a simple XML representation
static void	AFPChainXMLConverter.toXML(AFPChain afpChain, StringWriter swriter, Atom[] ca1, Atom[] ca2) Write the XML representation to a StringWriter

Uses of AFPChain in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io that return AFPChain

Modifier and Type	Method and Description
static AFPChain	FastaAFPChainConverter.cpFastaToAfpChain(File fastaFile, Structure structure, int cpSite) Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
static AFPChain	FastaAFPChainConverter.cpFastaToAfpChain(ProteinSequence first, ProteinSequence second, Structure structure, int cpSite) Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site cpSite residues to the right.
static AFPChain	FastaAFPChainConverter.cpFastaToAfpChain(String first, String second, Structure structure, int cpSite)
static AFPChain	FastaAFPChainConverter.fastaFileToAfpChain(File fastaFile, Structure structure1, Structure structure2) Reads the file fastaFile, expecting exactly two sequences which give a pairwise alignment.
static AFPChain	FastaAFPChainConverter.fastaStringToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2) Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(Map<String,ProteinSequence> sequences, Structure structure1, Structure structure2) Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(ProteinSequence sequence1, ProteinSequence sequence2, Structure structure1, Structure structure2) Returns an AFPChain corresponding to the alignment between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment, Structure structure1, Structure structure2) Provided only for convenience.
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2) TODO Write comment

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

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

Modifier and Type	Method and Description
AFPChain	CeSymmResult.getSelfAlignment()
static AFPChain	SequenceFunctionRefiner.refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k) Refines a CE-Symm alignment so that it is perfectly symmetric.

Methods in org.biojava.nbio.structure.symmetry.internal with parameters of type AFPChain

Modifier and Type	Method and Description
int	AngleOrderDetectorPlus.calculateOrder(AFPChain afpChain, Atom[] ca)
int	GraphComponentOrderDetector.calculateOrder(AFPChain selfAlignment, Atom[] ca)
int	SequenceFunctionOrderDetector.calculateOrder(AFPChain afpChain, Atom[] ca)
int	OrderDetector.calculateOrder(AFPChain afpChain, Atom[] ca)
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)
static AFPChain	SequenceFunctionRefiner.refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k) Refines a CE-Symm alignment so that it is perfectly symmetric.
void	CeSymmResult.setSelfAlignment(AFPChain selfAlignment)

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

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

Modifier and Type	Method and Description
static boolean[][]	SymmetryTools.blankOutBreakFlag(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, boolean[][] breakFlag, int blankWindowSize)
static Matrix	SymmetryTools.blankOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize)
static org.jgrapht.Graph<Integer,org.jgrapht.graph.DefaultEdge>	SymmetryTools.buildSymmetryGraph(AFPChain selfAlignment) Converts a self alignment into a directed jGraphT of aligned residues, where each vertex is a residue and each edge means the equivalence between the two residues in the self-alignment.
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 double	SymmetryTools.getAngle(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Returns the magnitude of the angle between the first and second blocks of afpChain, measured in degrees.
static Matrix	SymmetryTools.grayOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff)

Method parameters in org.biojava.nbio.structure.symmetry.utils with type arguments of type AFPChain

Modifier and Type	Method and Description
static List<List<Integer>>	SymmetryTools.buildSymmetryGraph(List<AFPChain> afps, Atom[] atoms, boolean undirected) Converts a set of AFP alignments into a Graph of aligned residues, where each vertex is a residue and each edge means the connection between the two residues in one of the alignments.