Uses of Class
org.biojava.nbio.structure.align.model.AFPChain
-
-
Uses of AFPChain in org.biojava.nbio.structure.align
Methods in org.biojava.nbio.structure.align that return AFPChain Modifier and Type Method Description abstract AFPChain
AbstractStructureAlignment. align(Atom[] ca1, Atom[] ca2)
abstract AFPChain
AbstractStructureAlignment. align(Atom[] ca1, Atom[] ca2, Object params)
AFPChain
BioJavaStructureAlignment. align(Atom[] ca1, Atom[] ca2)
AFPChain
BioJavaStructureAlignment. align(Atom[] ca1, Atom[] ca2, Object params)
AFPChain
StructureAlignment. align(Atom[] ca1, Atom[] ca2)
Run an alignment while specifying the atoms to be aligned.AFPChain
StructureAlignment. align(Atom[] ca1, Atom[] ca2, Object params)
run an alignment and also send a bean containing the parameters.AFPChain
CallableStructureAlignment. call()
Methods in org.biojava.nbio.structure.align with parameters of type AFPChain Modifier and Type Method 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 alignmentstatic 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 Description AFPChain
CeCPMain. align(Atom[] ca1, Atom[] ca2, Object param)
Aligns ca1 and ca2 using a heuristic to check for CPs.AFPChain
CeMain. align(Atom[] ca1, Atom[] ca2)
AFPChain
CeMain. align(Atom[] ca1, Atom[] ca2, Object param)
Align ca2 onto ca1.AFPChain
OptimalCECPMain. align(Atom[] ca1, Atom[] ca2, Object param)
Finds the optimal alignment between two proteins allowing for a circular permutation (CP).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
CECalculator. extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain
CeCalculatorEnhanced. 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 AFPChainstatic AFPChain
CeCPMain. postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator)
Circular permutation specific code to be run after the standard CE alignmentstatic AFPChain
CeCPMain. postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param)
Circular permutation specific code to be run after the standard CE alignmentMethods in org.biojava.nbio.structure.align.ce with parameters of type AFPChain Modifier and Type Method 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
CECalculator. convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
copy data from this class into AFPChain container object.void
CeCalculatorEnhanced. 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
CECalculator. extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain
CeCalculatorEnhanced. 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 AFPChainvoid
CECalculator. nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void
CeCalculatorEnhanced. 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 alignmentstatic AFPChain
CeCPMain. postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param)
Circular permutation specific code to be run after the standard CE alignmentstatic void
GuiWrapper. showAlignmentImage(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Object jmol)
void
CECalculator. traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void
CeCalculatorEnhanced. 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 Description static AFPChain
JFatCatClient. getAFPChainFromServer(String serverLocation, String method, String name1, String name2, Atom[] ca1, Atom[] ca2, int timeout)
static AFPChain
JFatCatClient. getAFPChainFromServer(String serverLocation, String name1, String name2, Atom[] ca1, Atom[] ca2)
Methods in org.biojava.nbio.structure.align.client with parameters of type AFPChain Modifier and Type Method 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 Description protected AFPChain
FatCat. align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)
AFPChain
FatCatFlexible. align(Atom[] ca1, Atom[] ca2)
AFPChain
FatCatFlexible. align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain
FatCatRigid. align(Atom[] ca1, Atom[] ca2)
AFPChain
FatCatRigid. 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 Description AFPChain
FatCatAligner. getAfpChain()
Methods in org.biojava.nbio.structure.align.fatcat.calc with parameters of type AFPChain Modifier and Type Method 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 optimizedstatic void
AFPOptimizer. blockInfo(AFPChain afpChain)
get the afp list and residue list for each blockprotected 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 AFPsdouble
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 programmingstatic 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 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
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 StructureAlignmentJmol
StructureAlignmentDisplay. display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Display an AFPChain alignmentstatic 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 0static 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 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 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 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 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 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 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 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 formatstatic 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 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 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 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 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(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. 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 mapstatic 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 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 outputstatic void
AFPAlignmentDisplay. getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showSeq)
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 structurestatic int
AFPAlignmentDisplay. getBlockNrForAlignPos(AFPChain afpChain, int aligPos)
get the block number for an aligned positionstatic 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 alignmentstatic 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 visualisationstatic 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. 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 mapstatic 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 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 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, 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 neededstatic AFPChain
AFPChainXMLParser. fromXML(String xml, Atom[] ca1, Atom[] ca2)
static AFPChain[]
AFPChainXMLParser. parseMultiXML(String xml)
Methods in org.biojava.nbio.structure.align.xml with parameters of type AFPChain Modifier and Type Method 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 void
AFPChainXMLConverter. toXML(AFPChain afpChain, StringWriter swriter, Atom[] ca1, Atom[] ca2)
Write the XML representation to a StringWriterstatic String
AFPChainXMLConverter. toXML(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Convert an afpChain to a simple XML representation -
Uses of AFPChain in org.biojava.nbio.structure.io
Methods in org.biojava.nbio.structure.io that return AFPChain Modifier and Type Method 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 sitecpSite
residues to the right.static AFPChain
FastaAFPChainConverter. cpFastaToAfpChain(String first, String second, Structure structure, int cpSite)
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 sitecpSite
residues to the right.static AFPChain
FastaAFPChainConverter. fastaFileToAfpChain(File fastaFile, Structure structure1, Structure structure2)
Reads the filefastaFile
, 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 betweenstructure1
andstructure2
, which is given by the gapped protein sequencessequence1
andsequence2
.static AFPChain
FastaAFPChainConverter. fastaToAfpChain(String sequence1, String sequence2, Structure structure1, Structure structure2)
TODO Write commentstatic 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(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment, Structure structure1, Structure structure2)
Provided only for convenience.static AFPChain
FastaAFPChainConverter. fastaToAfpChain(ProteinSequence sequence1, ProteinSequence sequence2, Structure structure1, Structure structure2)
Returns an AFPChain corresponding to the alignment betweenstructure1
andstructure2
, which is given by the gapped protein sequencessequence1
andsequence2
. -
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 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 Description int
AngleOrderDetectorPlus. calculateOrder(AFPChain afpChain, Atom[] ca)
int
GraphComponentOrderDetector. calculateOrder(AFPChain selfAlignment, Atom[] ca)
int
OrderDetector. calculateOrder(AFPChain afpChain, Atom[] ca)
int
SequenceFunctionOrderDetector. calculateOrder(AFPChain afpChain, Atom[] ca)
MultipleAlignment
GraphComponentRefiner. refine(AFPChain selfAlignment, Atom[] atoms, int order)
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.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 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 ofafpChain
, 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 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.
-