Uses of Class
org.biojava.nbio.structure.StructureException

Packages that use StructureException

Package	Description
demo
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
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.multiple
org.biojava.nbio.structure.align.multiple.mc
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.align.pairwise	Classes for the pairwise alignment of structures.
org.biojava.nbio.structure.align.quaternary
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.cath
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.domain
org.biojava.nbio.structure.domain.pdp
org.biojava.nbio.structure.ecod
org.biojava.nbio.structure.gui.util	Some utility classes for the protein structure GUIs.
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.scop	Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.nbio.structure.secstruc
org.biojava.nbio.structure.symmetry.gui
org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.utils

Uses of StructureException in demo

Methods in demo that throw StructureException

Modifier and Type	Method	Description
static void	DemoAlignmentFromFasta.getAlignmentFromFasta()
static void	DemoAlignmentFromFasta.main(String[] args)
static void	DemoAsa.main(String[] args)
static void	DemoCeSymm.main(String[] args)
static void	DemoContacts.main(String[] args)
static void	DemoLoadSecStruc.main(String[] args)
static void	DemoMmtfWriter.main(String[] args)
static void	DemoMultipleMC.main(String[] args)
static void	DemoQsAlign.main(String[] args)
static void	DemoQuatSymmetryJmol.main(String[] args)
static void	DemoSecStrucCalc.main(String[] args)

Uses of StructureException in org.biojava.nbio.structure

Methods in org.biojava.nbio.structure that throw StructureException

Modifier and Type	Method	Description
static final Atom[]	Calc.centerAtoms(Atom[] atomSet)	Center the atoms at the Centroid.
static final Atom[]	Calc.centerAtoms(Atom[] atomSet, Atom centroid)	Center the atoms at the Centroid, if the centroid is already know.
static final Atom	Calc.createVirtualCBAtom(AminoAcid amino)	creates a virtual C-beta atom. this might be needed when working with GLY thanks to Peter Lackner for a python template of this method.
Group	Structure.findGroup(String authId, String pdbResnum)	Request a particular group from a structure.
Group	Structure.findGroup(String authId, String pdbResnum, int modelnr)	Request a particular group from a structure.
Group	StructureImpl.findGroup(String chainName, String pdbResnum)	Request a particular group from a structure.
Group	StructureImpl.findGroup(String chainName, String pdbResnum, int modelnr)	Request a particular group from a structure.
static List<Structure>	StructureIO.getBiologicalAssemblies(String pdbId)	Returns all biological assemblies for the given PDB id, using multiModel=false
static List<Structure>	StructureIO.getBiologicalAssemblies(String pdbId, boolean multiModel)	Returns all biological assemblies for the given PDB id.
static Structure	StructureIO.getBiologicalAssembly(String pdbId)	Returns the first biological assembly that is available for the given PDB id, using multiModel=false
static Structure	StructureIO.getBiologicalAssembly(String pdbId, boolean multiModel)	Returns the first biological assembly that is available for the given PDB id.
static Structure	StructureIO.getBiologicalAssembly(String pdbId, int biolAssemblyNr)	Returns the biological assembly for the given PDB id and bioassembly identifier, using multiModel=false
static Structure	StructureIO.getBiologicalAssembly(String pdbId, int biolAssemblyNr, boolean multiModel)	Returns the biological assembly for the given PDB id and bioassembly identifier.
Group	Chain.getGroupByPDB(ResidueNumber resNum)	Get a group by its PDB residue numbering.
Group	ChainImpl.getGroupByPDB(ResidueNumber resNum)
static Group	StructureTools.getGroupByPDBResidueNumber(Structure struc, ResidueNumber pdbResNum)	Get a group represented by a ResidueNumber.
Group[]	Chain.getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd)	Get all groups that are located between two PDB residue numbers.
Group[]	Chain.getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd, boolean ignoreMissing)	Get all groups that are located between two PDB residue numbers.
Group[]	ChainImpl.getGroupsByPDB(ResidueNumber start, ResidueNumber end)
Group[]	ChainImpl.getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ignoreMissing)
static final double	Calc.getPhi(AminoAcid a, AminoAcid b)	Calculate the phi angle.
static final double	Calc.getPsi(AminoAcid a, AminoAcid b)	Calculate the psi angle.
String	PdbId.getShortId()	Get the PDB Id in the short format.
static Structure	StructureIO.getStructure(String name)	Loads a structure based on a name.
static Structure	StructureTools.getStructure(String name)	Short version of StructureTools.getStructure(String, PDBFileParser, AtomCache) which creates new parsers when needed
static Structure	StructureTools.getStructure(String name, PDBFileParser parser, AtomCache cache)	Flexibly get a structure from an input String.
static double	Calc.getTMScore(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2)	Calculate the TM-Score for the superposition.
static double	Calc.getTMScore(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2, boolean normalizeMin)	Calculate the TM-Score for the superposition.
Structure	BioAssemblyIdentifier.loadStructure(AtomCache cache)
Structure	PassthroughIdentifier.loadStructure(AtomCache cache)	Passthrough identifiers don't know how to load a structure
Structure	StructureIdentifier.loadStructure(AtomCache cache)	Loads a structure encompassing the structure identified.
Structure	SubstructureIdentifier.loadStructure(AtomCache cache)	Loads the complete structure based on SubstructureIdentifier.getPdbId().
Structure	URLIdentifier.loadStructure(AtomCache cache)	Load the structure from the URL
Structure	BioAssemblyIdentifier.reduce(Structure input)
Structure	PassthroughIdentifier.reduce(Structure input)
Structure	StructureIdentifier.reduce(Structure input)	Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
Structure	SubstructureIdentifier.reduce(Structure s)	Takes a complete structure as input and reduces it to residues present in the specified ranges
Structure	URLIdentifier.reduce(Structure input)
static final void	Calc.rotate(Group group, double[][] rotationmatrix)	Rotate a Group.
static final void	Calc.rotate(Structure structure, double[][] rotationmatrix)	Rotate a structure.
SubstructureIdentifier	BioAssemblyIdentifier.toCanonical()
SubstructureIdentifier	StructureIdentifier.toCanonical()	Convert to a canonical SubstructureIdentifier.
SubstructureIdentifier	URLIdentifier.toCanonical()
static String	PdbId.toExtendedId(String shortId)	Converts shortId to the PDB ID extended format.
static String	PdbId.toShortId(String extendedId)	Converts extendedId to the PDB ID short format.

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

Methods in org.biojava.nbio.structure.align that throw StructureException

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)
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.
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.
void	StructurePairAligner.align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)	Calculate the protein structure superimposition, between two sets of atoms.
void	StructurePairAligner.align(Structure s1, String chainId1, Structure s2, String chainId2)	Align two chains from the structures.
void	StructurePairAligner.align(Structure s1, String chainId1, Structure s2, String chainId2, StrucAligParameters params)	Aligns two chains from the structures using user provided parameters.
void	StructurePairAligner.align(Structure s1, Structure s2)	Calculate the alignment between the two full structures with default parameters
void	StructurePairAligner.align(Structure s1, Structure s2, StrucAligParameters params)	Calculate the alignment between the two full structures with user provided parameters
static StructureAlignment	StructureAlignmentFactory.getAlgorithm(String name)
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 StructureException in org.biojava.nbio.structure.align.ce

Methods in org.biojava.nbio.structure.align.ce that throw StructureException

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.
double	CECalculator.calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform)	superimpose and get rmsd
double	CeCalculatorEnhanced.calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show)	superimpose and get rmsd
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)
void	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 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

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

Methods in org.biojava.nbio.structure.align.client that throw StructureException

Modifier and Type	Method	Description
StructureIdentifier	StructureName.getBaseIdentifier()	StructureName wraps another StructureIdentifier.
String	PdbPair.getPDBCode1()	Deprecated. use PdbPair.getPDBCode1() instead
String	PdbPair.getPDBCode2()	Deprecated. use PdbPair.getPDBCode2() instead
PdbId	StructureName.getPdbId()	Get the PDB ID for this name, if any.
PdbId	PdbPair.getPdbId1()
PdbId	PdbPair.getPdbId2()
Structure	StructureName.loadStructure(AtomCache cache)
Structure	StructureName.reduce(Structure input)
SubstructureIdentifier	StructureName.toCanonical()

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

Methods in org.biojava.nbio.structure.align.fatcat that throw StructureException

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 StructureException in org.biojava.nbio.structure.align.fatcat.calc

Methods in org.biojava.nbio.structure.align.fatcat.calc that throw StructureException

Modifier and Type	Method	Description
void	FatCatAligner.align(Atom[] ca1, Atom[] ca2, boolean doRigid, FatCatParameters params)
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
void	StructureAlignmentOptimizer.runOptimization(int maxi)	run the optimization

Constructors in org.biojava.nbio.structure.align.fatcat.calc that throw StructureException

Modifier	Constructor	Description
	StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2, Atom[] c2, int iniLen, int[][] iniSet)	optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues

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

Methods in org.biojava.nbio.structure.align.gui that throw StructureException

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 final 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 MultipleAlignmentJmol	MultipleAlignmentJmolDisplay.display(MultipleAlignment multAln)	Display a MultipleAlignment with a JmolPanel.
static StructureAlignmentJmol	StructureAlignmentDisplay.display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)	Display an AFPChain alignment
static final Atom[]	DisplayAFP.getAtomArray(Atom[] ca, List<Group> hetatms)	Returns the first atom for each group
static final 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
Structure	SelectPDBPanel.getStructure1()
Structure	SelectPDBPanel.getStructure2()
static void	DisplayAFP.showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)
static void	MultipleAlignmentJmolDisplay.showMultipleAligmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol)	Deprecated. Replace with
static void	MultipleAlignmentJmolDisplay.showMultipleAlignmentPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol)	Creates a new Frame with the MultipleAlignment Sequence Panel.

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

Constructors in org.biojava.nbio.structure.align.gui.aligpanel that throw StructureException

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

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

Methods in org.biojava.nbio.structure.align.multiple that throw StructureException

Modifier and Type	Method	Description
void	MultipleAlignmentEnsembleImpl.updateAtomArrays()	Force the atom arrays to regenerate based on MultipleAlignmentEnsembleImpl.getStructureIdentifiers().

Uses of StructureException in org.biojava.nbio.structure.align.multiple.mc

Methods in org.biojava.nbio.structure.align.multiple.mc that throw StructureException

Modifier and Type	Method	Description
MultipleAlignment	MultipleMcMain.align(List<Atom[]> atomArrays)
MultipleAlignment	MultipleMcMain.align(List<Atom[]> atomArrays, Object parameters)
MultipleAlignment	MultipleMcOptimizer.optimize()	Optimization method based in a Monte-Carlo approach.

Uses of StructureException in org.biojava.nbio.structure.align.multiple.util

Methods in org.biojava.nbio.structure.align.multiple.util that throw StructureException

Modifier and Type	Method	Description
static void	MultipleAlignmentScorer.calculateScores(MultipleAlignment alignment)	Calculates and puts the RMSD and the average TM-Score of the MultipleAlignment.
static final Structure	MultipleAlignmentTools.getAlignedStructure(List<Atom[]> atomArrays)	Get an artificial Structure containing a different model for every input structure, so that the alignment result can be viewed in Jmol.
static double	MultipleAlignmentScorer.getAvgTMScore(List<Atom[]> transformed, List<Integer> lengths)	Calculates the average TMScore all the possible pairwise structure comparisons of the given a set of superimposed Atoms and the original structure lengths.
static double	MultipleAlignmentScorer.getAvgTMScore(MultipleAlignment alignment)	Calculates the average TMScore of all the possible pairwise structure comparisons of the given alignment.
static double	MultipleAlignmentScorer.getMCScore(MultipleAlignment alignment, double gapOpen, double gapExtension, double dCutoff)	Calculates the MC score, specific for the MultipleAlignment algorithm.
static double	MultipleAlignmentScorer.getRefTMScore(List<Atom[]> transformed, List<Integer> lengths, int reference)	Calculates the average TMScore from all structures to a reference structure, 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 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.
void	CoreSuperimposer.superimpose(MultipleAlignment alignment)
void	MultipleSuperimposer.superimpose(MultipleAlignment alignment)	Superimpose all structures from a MultipleAlignment.
void	ReferenceSuperimposer.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
static Structure	MultipleAlignmentTools.toMultimodelStructure(MultipleAlignment multAln, List<Atom[]> transformedAtoms)

Uses of StructureException in org.biojava.nbio.structure.align.pairwise

Methods in org.biojava.nbio.structure.align.pairwise that throw StructureException

Modifier and Type	Method	Description
JointFragments[]	FragmentJoiner.approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
void	AlternativeAlignment.calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)
void	FragmentJoiner.extendFragments(Atom[] ca1, Atom[] ca2, JointFragments[] fragments, StrucAligParameters params)
void	FragmentJoiner.extendFragments(Atom[] ca1, Atom[] ca2, JointFragments fragments, StrucAligParameters params)
void	AlternativeAlignment.finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
static double	FragmentJoiner.getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)	Get the RMS of the JointFragments pair frag
void	AlternativeAlignment.refine(StrucAligParameters params, Atom[] ca1, Atom[] ca2)	Refinement procedure based on superposition and dynamic programming.

Uses of StructureException in org.biojava.nbio.structure.align.quaternary

Methods in org.biojava.nbio.structure.align.quaternary that throw StructureException

Modifier and Type	Method	Description
static QsAlignResult	QsAlign.align(List<Subunit> s1, List<Subunit> s2, SubunitClustererParameters cParams, QsAlignParameters aParams)
static QsAlignResult	QsAlign.align(Structure s1, Structure s2, SubunitClustererParameters cParams, QsAlignParameters aParams)

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

Methods in org.biojava.nbio.structure.align.seq that throw StructureException

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

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

Methods in org.biojava.nbio.structure.align.util that throw StructureException

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 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 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 final Structure	AlignmentTools.getAlignedStructure(Atom[] ca1, Atom[] ca2)	Get an artifical Structure containing both chains.
static double	RotationAxis.getAngle(AFPChain afpChain)	Calculate the rotation angle for a structure
Atom[]	AtomCache.getAtoms(String name)	Returns the CA atoms for the provided name.
Atom[]	AtomCache.getAtoms(StructureIdentifier name)
List<Structure>	AtomCache.getBiologicalAssemblies(String pdbId, boolean multiModel)	Returns all biological assemblies for given PDB id.
Structure	AtomCache.getBiologicalAssembly(String pdbId, boolean multiModel)	Returns the default biological unit (bioassemblyId=1, known in PDB as pdb1.gz).
Structure	AtomCache.getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean multiModel)	Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()
Structure	AtomCache.getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean multiModel)	Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()
Atom[]	AtomCache.getRepresentativeAtoms(String name)	Returns the representative atoms for the provided name.
Atom[]	AtomCache.getRepresentativeAtoms(StructureIdentifier name)
static Matrix	AFPAlignmentDisplay.getRotMax(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Structure	AtomCache.getStructure(String name)	Request a Structure based on a name.
Structure	AtomCache.getStructure(StructureIdentifier strucId)	Get the structure corresponding to the given StructureIdentifier.
Structure	AtomCache.getStructureForCathDomain(StructureName structureName)	Returns a Structure corresponding to the CATH identifier supplied in structureName, using the the CathDatabase at CathFactory.getCathDatabase().
Structure	AtomCache.getStructureForCathDomain(StructureName structureName, CathDatabase cathInstall)	Returns a Structure corresponding to the CATH identifier supplied in structureName, using the specified CathDatabase.
Structure	AtomCache.getStructureForDomain(String scopId)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	AtomCache.getStructureForDomain(String scopId, ScopDatabase scopDatabase)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	AtomCache.getStructureForDomain(ScopDomain domain)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	AtomCache.getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	AtomCache.getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	AtomCache.getStructureForPdbId(String id)	Loads a structure directly by PDB ID
static int	AlignmentTools.getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float minimumMetricChange)	Guesses the order of symmetry in an alignment
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 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(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 map
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 that throw StructureException

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

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

Methods in org.biojava.nbio.structure.align.xml that throw StructureException

Modifier and Type	Method	Description
static String	AFPChainXMLParser.flipAlignment(String xml)	Takes an XML representation of the alignment and flips the positions of name1 and name2
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 needed

Uses of StructureException in org.biojava.nbio.structure.cath

Methods in org.biojava.nbio.structure.cath that throw StructureException

Modifier and Type	Method	Description
Set<String>	CathDomain.getChains()	Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
Structure	CathDomain.loadStructure(AtomCache cache)
Structure	CathDomain.reduce(Structure input)
SubstructureIdentifier	CathDomain.toCanonical()

Uses of StructureException in org.biojava.nbio.structure.cluster

Methods in org.biojava.nbio.structure.cluster that throw StructureException

Modifier and Type	Method	Description
boolean	SubunitCluster.divideInternally(SubunitClustererParameters clusterParams)	Analyze the internal symmetry of the SubunitCluster and divide its Subunit into the internal repeats (domains) if they are internally symmetric.
MultipleAlignment	SubunitCluster.getMultipleAlignment()	The multiple alignment is calculated from the equivalent residues in the SubunitCluster.
boolean	SubunitCluster.mergeStructure(SubunitCluster other, SubunitClustererParameters params)	Merges the other SubunitCluster into this one if their representative Atoms are structurally similar (according to the criteria in params).

Uses of StructureException in org.biojava.nbio.structure.domain

Methods in org.biojava.nbio.structure.domain that throw StructureException

Modifier and Type	Method	Description
SortedSet<String>	DomainProvider.getDomainNames(String name)	Get a list of constituent domain identifiers
static List<Domain>	LocalProteinDomainParser.suggestDomains(Atom[] ca)	Suggest domains for a set of Calpha atoms
static List<Domain>	LocalProteinDomainParser.suggestDomains(Structure s)	Suggest domains for a protein structure

Uses of StructureException in org.biojava.nbio.structure.domain.pdp

Methods in org.biojava.nbio.structure.domain.pdp that throw StructureException

Modifier and Type	Method	Description
PDPDistanceMatrix	GetDistanceMatrix.getDistanceMatrix(Atom[] protein)	A set of Calpha atoms that are representing the protein

Uses of StructureException in org.biojava.nbio.structure.ecod

Methods in org.biojava.nbio.structure.ecod that throw StructureException

Modifier and Type	Method	Description
Structure	EcodDomain.loadStructure(AtomCache cache)
Structure	EcodDomain.reduce(Structure input)

Uses of StructureException in org.biojava.nbio.structure.gui.util

Methods in org.biojava.nbio.structure.gui.util that throw StructureException

Modifier and Type	Method	Description
Structure	PDBDirPanel.getStructure1()
Structure	PDBServerPanel.getStructure1()
Structure	PDBUploadPanel.getStructure1()
Structure	ScopSelectPanel.getStructure1()
Structure	StructurePairSelector.getStructure1()
Structure	PDBDirPanel.getStructure2()
Structure	PDBServerPanel.getStructure2()
Structure	PDBUploadPanel.getStructure2()
Structure	ScopSelectPanel.getStructure2()
Structure	StructurePairSelector.getStructure2()
List<Structure>	SelectMultiplePanel.getStructures()

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

Methods in org.biojava.nbio.structure.io that throw StructureException

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 site cpSite 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 site cpSite residues to the right.
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(String sequence1, String sequence2, Structure structure1, Structure structure2)	TODO Write comment
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(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 between structure1 and structure2, which is given by the gapped protein sequences sequence1 and sequence2.
Structure	StructureProvider.getStructureById(String pdbId)	Get the structure for a PDB ID
Structure	StructureProvider.getStructureById(PdbId pdbId)	Get the structure for a PDB ID
static void	FastaAFPChainConverter.main(String[] args)	Prints out the XML representation of an AFPChain from a file containing exactly two FASTA sequences.
void	FastaStructureParser.process()	Parses the fasta file and loads it into memory.

Uses of StructureException in org.biojava.nbio.structure.scop

Methods in org.biojava.nbio.structure.scop that throw StructureException

Modifier and Type	Method	Description
Structure	ScopDomain.loadStructure(AtomCache cache)
Structure	ScopDomain.reduce(Structure input)

Uses of StructureException in org.biojava.nbio.structure.secstruc

Methods in org.biojava.nbio.structure.secstruc that throw StructureException

Modifier and Type	Method	Description
List<SecStrucState>	SecStrucCalc.calculate(Structure s, boolean assign)	Predicts the secondary structure of this Structure object, using a DSSP implementation.
static List<SecStrucState>	DSSPParser.parseFile(String dsspPath, Structure structure, boolean assign)	Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
static List<SecStrucState>	DSSPParser.parseInputStream(InputStream dsspIs, Structure structure, boolean assign)	Parse a DSSP output file and return the secondary structure annotation as a List of SecStrucState objects.
static List<SecStrucState>	DSSPParser.parseString(String dsspOut, Structure structure, boolean assign)	Parse a DSSP format String and return the secondary structure annotation as a List of SecStrucState objects.

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

Methods in org.biojava.nbio.structure.symmetry.gui that throw StructureException

Modifier and Type	Method	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.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.

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

Methods in org.biojava.nbio.structure.symmetry.internal that throw StructureException

Modifier and Type	Method	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.
List<StructureIdentifier>	CeSymmResult.getRepeatsID()	Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.
MultipleAlignment	SymmOptimizer.optimize()	Optimization method based in a Monte-Carlo approach.
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 Map<Integer,Integer>	SequenceFunctionRefiner.refineSymmetry(Map<Integer,Integer> alignment, int k)	Refines a CE-Symm alignment so that it is perfectly symmetric.
static AFPChain	SequenceFunctionRefiner.refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k)	Refines a CE-Symm alignment so that it is perfectly symmetric.

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

Methods in org.biojava.nbio.structure.symmetry.utils that throw StructureException

Modifier and Type	Method	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 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 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.toRepeatsAlignment(CeSymmResult result)	Method that converts a symmetry alignment into an alignment of the repeats only, as new independent structures.
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.