Uses of Interface
org.biojava.nbio.structure.Structure

Packages that use Structure

Package	Description
demo
org.biojava.nbio.protmod.structure
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.gui
org.biojava.nbio.structure.align.gui.jmol	Utility methods for better interaction with Jmol.
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.util
org.biojava.nbio.structure.asa
org.biojava.nbio.structure.basepairs
org.biojava.nbio.structure.cath
org.biojava.nbio.structure.cluster
org.biojava.nbio.structure.contact
org.biojava.nbio.structure.domain
org.biojava.nbio.structure.ecod
org.biojava.nbio.structure.gui	A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.nbio.structure.gui.events	Some event classes for the protein structure GUIs.
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.io.cif
org.biojava.nbio.structure.io.mmcif	Input and Output of mmcif files.
org.biojava.nbio.structure.io.mmtf
org.biojava.nbio.structure.quaternary
org.biojava.nbio.structure.scop	Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.nbio.structure.secstruc
org.biojava.nbio.structure.symmetry.core
org.biojava.nbio.structure.symmetry.gui
org.biojava.nbio.structure.symmetry.utils
org.biojava.nbio.structure.xtal

Uses of Structure in demo

Methods in demo that return Structure

Modifier and Type	Method and Description
static Structure	DemoShowLargeAssembly.readStructure(String pdbId, int bioAssemblyId) Load a specific biological assembly for a PDB entry

Methods in demo with parameters of type Structure

Modifier and Type	Method and Description
static void	DemoLoadSecStruc.printSecStruc(Structure s)

Uses of Structure in org.biojava.nbio.protmod.structure

Methods in org.biojava.nbio.protmod.structure with parameters of type Structure

Modifier and Type	Method and Description
void	ProteinModificationIdentifier.identify(Structure structure) Identify all registered modifications in a structure.
void	ProteinModificationIdentifier.identify(Structure structure, Set<ProteinModification> potentialModifications) Identify a set of modifications in a structure.

Uses of Structure in org.biojava.nbio.structure

Classes in org.biojava.nbio.structure that implement Structure

Modifier and Type	Class and Description
class	StructureImpl Implementation of a PDB Structure.

Methods in org.biojava.nbio.structure that return Structure

Modifier and Type	Method and Description
Structure	StructureImpl.clone() returns an identical copy of this structure .
Structure	Structure.clone() Return an identical copy of this Structure object
static Structure	StructureIO.getBiologicalAssembly(String pdbId) Returns the first biological assembly that is available for the given PDB id, using multiModel= For more documentation on quaternary structures see: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies
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=
static Structure	StructureIO.getBiologicalAssembly(String pdbId, int biolAssemblyNr, boolean multiModel) Returns the biological assembly for the given PDB id and bioassembly identifier.
Structure	Chain.getParent() Deprecated. use getStructure(Structure) instead.
Structure	DBRef.getParent() Get the structure object that this DBRef relates to.
Structure	ChainImpl.getParent() Deprecated. use getStructure instead.
static Structure	StructureTools.getReducedStructure(Structure s, String chainId) Deprecated. Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
Structure	Chain.getStructure() Returns the parent Structure of this chain.
Structure	ChainImpl.getStructure() Returns the parent Structure of this chain.
static Structure	StructureTools.getStructure(String name) Short version of StructureTools.getStructure(String, PDBFileParser, AtomCache) which creates new parsers when needed
static Structure	StructureIO.getStructure(String name) Loads a structure based on a name.
static Structure	StructureTools.getStructure(String name, PDBFileParser parser, AtomCache cache) Flexibly get a structure from an input String.
Structure	PassthroughIdentifier.loadStructure(AtomCache cache) Passthrough identifiers don't know how to load a structure
Structure	SubstructureIdentifier.loadStructure(AtomCache cache) Loads the complete structure based on SubstructureIdentifier.getPdbId().
Structure	StructureIdentifier.loadStructure(AtomCache cache) Loads a structure encompassing the structure identified.
Structure	URLIdentifier.loadStructure(AtomCache cache) Load the structure from the URL
Structure	BioAssemblyIdentifier.loadStructure(AtomCache cache)
Structure	Mutator.mutate(Structure struc, String chainId, String pdbResnum, String newType) creates a new structure which is identical with the original one.
Structure	PassthroughIdentifier.reduce(Structure input)
Structure	SubstructureIdentifier.reduce(Structure s) Takes a complete structure as input and reduces it to residues present in the specified ranges The returned structure will be a shallow copy of the input, with shared Chains, Residues, etc.
Structure	StructureIdentifier.reduce(Structure input) Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
Structure	URLIdentifier.reduce(Structure input)
Structure	BioAssemblyIdentifier.reduce(Structure input)
static Structure	StructureTools.removeModels(Structure s) Remove all models from a Structure and keep only the first

Methods in org.biojava.nbio.structure that return types with arguments of type Structure

Modifier and Type	Method and Description
static List<Structure>	StructureIO.getBiologicalAssemblies(String pdbId) Returns all biological assemblies for the given PDB id, using multiModel= If only one biological assembly is required use StructureIO.getBiologicalAssembly(String) or StructureIO.getBiologicalAssembly(String, int) instead.
static List<Structure>	StructureIO.getBiologicalAssemblies(String pdbId, boolean multiModel) Returns all biological assemblies for the given PDB id.

Methods in org.biojava.nbio.structure with parameters of type Structure

Modifier and Type	Method and Description
static void	StructureTools.addGroupsToStructure(Structure s, Collection<Group> groups, int model, boolean clone) Add a list of groups to a new structure.
static Chain	StructureTools.addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone) Adds a particular group to a structure.
static void	StructureTools.cleanUpAltLocs(Structure structure) Cleans up the structure's alternate location (altloc) groups.
protected static void	SubstructureIdentifier.copyLigandsByProximity(Structure full, Structure reduced) Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
protected static void	SubstructureIdentifier.copyLigandsByProximity(Structure full, Structure reduced, double cutoff, int fromModel, int toModel) Supplements the reduced structure with ligands from the full structure based on a distance cutoff.
static Atom[]	StructureTools.getAllAtomArray(Structure s) Convert all atoms of the structure (all models) into an Atom array
static Atom[]	StructureTools.getAllAtomArray(Structure s, int model) Convert all atoms of the structure (specified model) into an Atom array
static Atom[]	StructureTools.getAllNonHAtomArray(Structure s, boolean hetAtoms) Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.
static Atom[]	StructureTools.getAllNonHAtomArray(Structure s, boolean hetAtoms, int modelNr) Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.
static Atom[]	StructureTools.getAtomArray(Structure s, String[] atomNames) Returns an array of the requested Atoms from the Structure object.
static Atom[]	StructureTools.getAtomArrayAllModels(Structure s, String[] atomNames) Returns an array of the requested Atoms from the Structure object.
static Atom[]	StructureTools.getAtomCAArray(Structure s) Return an Atom array of the C-alpha atoms.
static Atom[]	StructureTools.getBackboneAtomArray(Structure s) Return an Atom array of the main chain atoms: CA, C, N, O Any group that contains those atoms will be included, be it a standard aminoacid or not
static Group	StructureTools.getGroupByPDBResidueNumber(Structure struc, ResidueNumber pdbResNum) Get a group represented by a ResidueNumber.
static Map<Group,Double>	StructureTools.getGroupDistancesWithinShell(Structure structure, Atom centroid, Set<ResidueNumber> excludeResidues, double radius, boolean includeWater, boolean useAverageDistance) Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
static Set<Group>	StructureTools.getGroupsWithinShell(Structure structure, Atom atom, Set<ResidueNumber> excludeResidues, double distance, boolean includeWater)
static Set<Group>	StructureTools.getGroupsWithinShell(Structure structure, Group group, double distance, boolean includeWater) Returns a Set of Groups in a structure within the distance specified of a given group.
static int	StructureTools.getNrAtoms(Structure s) Count how many Atoms are contained within a Structure object.
static int	StructureTools.getNrGroups(Structure s) Count how many groups are contained within a structure object.
static Structure	StructureTools.getReducedStructure(Structure s, String chainId) Deprecated. Use StructureIdentifier.reduce(Structure) instead (v. 4.2.0)
static Atom[]	StructureTools.getRepresentativeAtomArray(Structure s) Gets a representative atom for each group that is part of the chain backbone.
Structure	Mutator.mutate(Structure struc, String chainId, String pdbResnum, String newType) creates a new structure which is identical with the original one.
static void	Calc.plus(Structure s, Matrix matrix) calculate structure + Matrix coodinates ...
Structure	PassthroughIdentifier.reduce(Structure input)
Structure	SubstructureIdentifier.reduce(Structure s) Takes a complete structure as input and reduces it to residues present in the specified ranges The returned structure will be a shallow copy of the input, with shared Chains, Residues, etc.
Structure	StructureIdentifier.reduce(Structure input) Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
Structure	URLIdentifier.reduce(Structure input)
Structure	BioAssemblyIdentifier.reduce(Structure input)
static Structure	StructureTools.removeModels(Structure s) Remove all models from a Structure and keep only the first
static void	Calc.rotate(Structure structure, double[][] rotationmatrix) Rotate a structure.
static void	Calc.rotate(Structure structure, Matrix m) Rotate a structure object.
void	Chain.setParent(Structure parent) Deprecated. use setStructure instead
void	DBRef.setParent(Structure s) Set the structure object that this DBRef relates to.
void	ChainImpl.setParent(Structure parent) Deprecated.
void	Chain.setStructure(Structure parent) Sets the back-reference to its parent Structure.
void	ChainImpl.setStructure(Structure parent) Sets the back-reference to its parent Structure.
static void	Calc.shift(Structure structure, Atom a) shift a structure with a vector.
static void	Calc.transform(Structure structure, javax.vecmath.Matrix4d m) Transforms a structure object, given a Matrix4d (i.e. the vecmath library double-precision 4x4 rotation+translation matrix).
static void	Calc.translate(Structure structure, javax.vecmath.Vector3d v) Translates a Structure object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)

Constructors in org.biojava.nbio.structure with parameters of type Structure

Constructor and Description
AtomIterator(Structure struct) Constructs an AtomIterator object over all models
AtomIterator(Structure struct, int modelNr) Constructs an AtomIterator object over a single model
AtomPositionMap(Structure s) Creates a new AtomPositionMap containing representative atoms from a structure.
GroupIterator(Structure struct) Constructs a GroupIterator object over all models
GroupIterator(Structure struct, int modelNr) Constructs a GroupIterator object over a specific model

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

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

Modifier and Type	Method and Description
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
Atom[]	StructurePairAligner.getAlignmentAtoms(Structure s) Returns the atoms that are being used for the alignment.

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

Constructor and Description
MultiThreadedDBSearch(String name, Structure structure, String outFile, StructureAlignment algorithm, int nrCPUs, boolean domainSplit)

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

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

Modifier and Type	Method and Description
static Structure	GuiWrapper.getAlignedStructure(Atom[] ca1, Atom[] ca2)

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

Modifier and Type	Method and Description
static void	GuiWrapper.showStructure(Structure structure) Shows a structure in Jmol

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

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

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

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

Modifier and Type	Method and Description
Structure	StructureName.reduce(Structure input)

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

Methods in org.biojava.nbio.structure.align.gui that return Structure

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.
Structure	SelectPDBPanel.getStructure1()
Structure	SelectPDBPanel.getStructure2()

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

Constructor and Description
AlignmentCalc(AlignmentGui parent, Structure s1, Structure s2, String name1, String name2) requests an alignment of pdb1 vs pdb 2.
AlignmentCalcDB(AlignmentGui parent, Structure s1, String name1, UserConfiguration config, String outFile, Boolean domainSplit)

Constructor parameters in org.biojava.nbio.structure.align.gui with type arguments of type Structure

Constructor and Description
MultipleAlignmentCalc(MultipleAlignmentGUI parent, List<Structure> structures, List<StructureIdentifier> names) Requests an alignment of the pdbs.

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

Fields in org.biojava.nbio.structure.align.gui.jmol declared as Structure

Modifier and Type	Field and Description
protected Structure	AbstractAlignmentJmol.structure

Methods in org.biojava.nbio.structure.align.gui.jmol that return Structure

Modifier and Type	Method and Description
Structure	AbstractAlignmentJmol.getStructure() Return the current Structure in the AlignmentJmol instance.

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

Modifier and Type	Method and Description
void	AbstractAlignmentJmol.setStructure(Structure s) Set a new Structure to visualize in the AlignmentJmol window.
void	JmolPanel.setStructure(Structure s)
void	JmolPanel.setStructure(Structure s, boolean useMmtf)

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

Methods in org.biojava.nbio.structure.align.multiple.util that return Structure

Modifier and Type	Method and Description
static 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 Structure	MultipleAlignmentTools.toMultimodelStructure(MultipleAlignment multAln, List<Atom[]> transformedAtoms)

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

Methods in org.biojava.nbio.structure.align.pairwise that return Structure

Modifier and Type	Method and Description
Structure	AlternativeAlignment.getAlignedStructure(Structure s1, Structure s2) create an artifical Structure object that contains the two structures superimposed onto each other.

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

Modifier and Type	Method and Description
Structure	AlternativeAlignment.getAlignedStructure(Structure s1, Structure s2) create an artifical Structure object that contains the two structures superimposed onto each other.
String	AlternativeAlignment.toPDB(Structure s1, Structure s2) converts the alignment to a PDB file each of the structures will be represented as a model.

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

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

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

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

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

Modifier and Type	Method and Description
static Structure	AFPAlignmentDisplay.createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Structure	AlignmentTools.getAlignedStructure(Atom[] ca1, Atom[] ca2) Get an artifical Structure containing both chains.
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 getPDBHeader() Note, the number of available biological unit files varies.
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(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.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.getStructureForPdbId(String pdbId) Loads a structure directly by PDB ID
protected Structure	AtomCache.loadStructureFromCifByPdbId(String pdbId)
protected Structure	AtomCache.loadStructureFromPdbByPdbId(String pdbId)

Methods in org.biojava.nbio.structure.align.util that return types with arguments of type Structure

Modifier and Type	Method and Description
List<Structure>	AtomCache.getBiologicalAssemblies(String pdbId, boolean multiModel) Returns all biological assemblies for given PDB id.

Uses of Structure in org.biojava.nbio.structure.asa

Constructors in org.biojava.nbio.structure.asa with parameters of type Structure

Constructor and Description
AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) Constructs a new AsaCalculator.

Uses of Structure in org.biojava.nbio.structure.basepairs

Fields in org.biojava.nbio.structure.basepairs declared as Structure

Modifier and Type	Field and Description
protected Structure	BasePairParameters.structure

Constructors in org.biojava.nbio.structure.basepairs with parameters of type Structure

Constructor and Description
BasePairParameters(Structure structure) This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure for only canonical DNA pairs.
BasePairParameters(Structure structure, boolean useRNA) This constructor takes a Structure object, and whether to use the RNA standard bases.
BasePairParameters(Structure structure, boolean useRNA, boolean removeDups) This constructor takes a Structure object, whether to use RNA, and whether to remove duplicate sequences.
BasePairParameters(Structure structure, boolean useRNA, boolean removeDups, boolean canonical) This constructor takes a Structure object, finds base pair and base-pair step parameters for double-helical regions within the structure.
MismatchedBasePairParameters(Structure structure, boolean RNA, boolean removeDups, boolean canonical) This constructor is used to create the TertiaryBasePairParameters object.
TertiaryBasePairParameters(Structure structure, boolean RNA, boolean removeDups)

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

Methods in org.biojava.nbio.structure.cath that return Structure

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

Methods in org.biojava.nbio.structure.cath with parameters of type Structure

Modifier and Type	Method and Description
Structure	CathDomain.reduce(Structure input)

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

Methods in org.biojava.nbio.structure.cluster that return Structure

Modifier and Type	Method and Description
Structure	Subunit.getStructure() The parent Structure from which the Subunit atoms were obtained.

Methods in org.biojava.nbio.structure.cluster with parameters of type Structure

Modifier and Type	Method and Description
static Stoichiometry	SubunitClusterer.cluster(Structure structure, SubunitClustererParameters params)
static List<Subunit>	SubunitExtractor.extractSubunits(Structure structure, int absMinLen, double fraction, int minLen) Extract the information of each protein Chain in a Structure and converts them into a List of Subunit.

Constructors in org.biojava.nbio.structure.cluster with parameters of type Structure

Constructor and Description
Subunit(Atom[] reprAtoms, String name, StructureIdentifier identifier, Structure structure) A Subunit is solely defined by the coordinates of the representative Atoms of its residues.

Uses of Structure in org.biojava.nbio.structure.contact

Methods in org.biojava.nbio.structure.contact with parameters of type Structure

Modifier and Type	Method and Description
static StructureInterfaceList	StructureInterfaceList.calculateInterfaces(Structure struc) Calculates the interfaces for a structure using default parameters

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

Methods in org.biojava.nbio.structure.domain that return Structure

Modifier and Type	Method and Description
Structure	PDPProvider.getDomain(String pdpDomainName, AtomCache cache) Get the structure for a particular PDP domain
Structure	RemotePDPProvider.getDomain(String pdpDomainName, AtomCache cache) Get the structure for a particular PDP domain
Structure	PDPDomain.loadStructure(AtomCache cache)
Structure	PDPDomain.reduce(Structure input)

Methods in org.biojava.nbio.structure.domain with parameters of type Structure

Modifier and Type	Method and Description
Structure	PDPDomain.reduce(Structure input)
static List<Domain>	LocalProteinDomainParser.suggestDomains(Structure s) Suggest domains for a protein structure

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

Methods in org.biojava.nbio.structure.ecod that return Structure

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

Methods in org.biojava.nbio.structure.ecod with parameters of type Structure

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

Uses of Structure in org.biojava.nbio.structure.gui

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

Modifier and Type	Method and Description
void	BiojavaJmol.setStructure(Structure s)
void	StructureViewer.setStructure(Structure structure)
void	JmolViewerImpl.setStructure(Structure structure)
void	SequenceDisplay.setStructure1(Structure structure)
void	SequenceDisplay.setStructure2(Structure structure)

Uses of Structure in org.biojava.nbio.structure.gui.events

Methods in org.biojava.nbio.structure.gui.events with parameters of type Structure

Modifier and Type	Method and Description
void	JmolAlignedPositionListener.setStructure1(Structure structure1)
void	JmolAlignedPositionListener.setStructure2(Structure structure2)

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

Methods in org.biojava.nbio.structure.gui.util that return Structure

Modifier and Type	Method and Description
Structure	PDBUploadPanel.getStructure1()
Structure	PDBServerPanel.getStructure1()
Structure	PDBDirPanel.getStructure1()
Structure	ScopSelectPanel.getStructure1()
Structure	StructurePairSelector.getStructure1()
Structure	PDBUploadPanel.getStructure2()
Structure	PDBServerPanel.getStructure2()
Structure	PDBDirPanel.getStructure2()
Structure	ScopSelectPanel.getStructure2()
Structure	StructurePairSelector.getStructure2()

Methods in org.biojava.nbio.structure.gui.util that return types with arguments of type Structure

Modifier and Type	Method and Description
List<Structure>	SelectMultiplePanel.getStructures()

Constructors in org.biojava.nbio.structure.gui.util with parameters of type Structure

Constructor and Description
AlignmentCalc(AlignmentGui parent, Structure s1, Structure s2) requests an alignment of pdb1 vs pdb 2.
AlternativeAlignmentFrame(Structure s1, Structure s2)

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

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

Modifier and Type	Method and Description
Structure	LocalPDBDirectory.getStructure(File filename)
Structure	StructureIOFile.getStructure(File file) Read file from File and returns a Structure object.
abstract Structure	LocalPDBDirectory.getStructure(InputStream inStream) Handles the actual parsing of the file into a Structure object.
Structure	MMCIFFileReader.getStructure(InputStream inStream)
Structure	CifFileReader.getStructure(InputStream inStream)
Structure	BcifFileReader.getStructure(InputStream inStream)
Structure	MMTFFileReader.getStructure(InputStream inStream)
Structure	PDBFileReader.getStructure(InputStream inStream)
Structure	LocalPDBDirectory.getStructure(String filename)
Structure	StructureIOFile.getStructure(String filename) Open filename and return a Structure object.
Structure	LocalPDBDirectory.getStructure(URL u)
Structure	StructureProvider.getStructureById(String pdbId) Get the structure for a PDB ID
Structure	LocalPDBDirectory.getStructureById(String pdbId)
Structure	SandboxStyleStructureProvider.getStructureById(String pdbId)
Structure[]	FastaStructureParser.getStructures() Gets the protein structures mapped from the Fasta file.
static Structure	StructureSequenceMatcher.getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure) Get a substructure of wholeStructure containing only the Groups that are included in sequence.
Structure	PDBFileParser.parsePDBFile(BufferedReader buf) Parse a PDB file and return a datastructure implementing PDBStructure interface.
Structure	PDBFileParser.parsePDBFile(InputStream inStream) Parse a PDB file and return a datastructure implementing PDBStructure interface.

Methods in org.biojava.nbio.structure.io with parameters of type Structure

Modifier and Type	Method and Description
static void	ChargeAdder.addCharges(Structure structure) Function to add the charges to a given structure.
void	SeqRes2AtomAligner.align(Structure s, List<Chain> seqResList)
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
static ProteinSequence	StructureSequenceMatcher.getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition) Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.
static Structure	StructureSequenceMatcher.getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure) Get a substructure of wholeStructure containing only the Groups that are included in sequence.
static ResidueNumber[]	StructureSequenceMatcher.matchSequenceToStructure(ProteinSequence seq, Structure struct) Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.
static void	SeqRes2AtomAligner.storeUnAlignedSeqRes(Structure structure, List<Chain> seqResChains, boolean headerOnly) Storing unaligned SEQRES groups in a Structure.

Constructors in org.biojava.nbio.structure.io with parameters of type Structure

Constructor and Description
BondMaker(Structure structure, FileParsingParameters params)
FileConvert(Structure struc) Constructs a FileConvert object.

Uses of Structure in org.biojava.nbio.structure.io.cif

Methods in org.biojava.nbio.structure.io.cif that return Structure

Modifier and Type	Method and Description
static Structure	CifFileConverter.fromCifFile(org.rcsb.cif.model.CifFile cifFile) Convert CifFile to Structure without any FileParsingParameters.
static Structure	CifFileConverter.fromCifFile(org.rcsb.cif.model.CifFile cifFile, FileParsingParameters parameters) Convert CifFile to Structure.
static Structure	CifFileConverter.fromInputStream(InputStream inputStream) Convert InputStream to Structure without any FileParsingParameters.
static Structure	CifFileConverter.fromInputStream(InputStream inputStream, FileParsingParameters parameters) Convert InputStream to Structure.
static Structure	CifFileConverter.fromPath(Path path) Read data from a file and convert to Structure without any FileParsingParameters.
static Structure	CifFileConverter.fromPath(Path path, FileParsingParameters parameters) Read data from a file and convert to Structure.
static Structure	CifFileConverter.fromURL(URL url) Get data from a URL and convert to Structure without any FileParsingParameters.

Methods in org.biojava.nbio.structure.io.cif with parameters of type Structure

Modifier and Type	Method and Description
static byte[]	CifFileConverter.toBinary(Structure structure) Convert a structure to BCIF format.
static void	CifFileConverter.toBinaryFile(Structure structure, Path path) Write a structure to a BCIF file.
static org.rcsb.cif.model.CifFile	CifFileConverter.toCifFile(Structure structure) Convert Structure to CifFile.
static String	CifFileConverter.toText(Structure structure) Convert a structure to mmCIF format.
static void	CifFileConverter.toTextFile(Structure structure, Path path) Write a structure to a CIF file.

Uses of Structure in org.biojava.nbio.structure.io.mmcif

Methods in org.biojava.nbio.structure.io.mmcif that return Structure

Modifier and Type	Method and Description
Structure	SimpleMMcifConsumer.getStructure() This method will return the parsed protein structure, once the parsing has been finished

Methods in org.biojava.nbio.structure.io.mmcif with parameters of type Structure

Modifier and Type	Method and Description
static List<AtomSite>	MMCIFFileTools.convertStructureToAtomSites(Structure s) Converts a Structure into a List of AtomSite objects

Uses of Structure in org.biojava.nbio.structure.io.mmtf

Methods in org.biojava.nbio.structure.io.mmtf that return Structure

Modifier and Type	Method and Description
Structure	MmtfStructureReader.getStructure() Gets the structure.
static Structure	MmtfActions.readFromFile(Path filePath) Get a Structure object from a mmtf file.
static Structure	MmtfActions.readFromInputStream(InputStream inStream) Read a Biojava structure from an InputStream
static Structure	MmtfActions.readFromWeb(String pdbId) Get a Biojava structure from the mmtf REST service.

Methods in org.biojava.nbio.structure.io.mmtf with parameters of type Structure

Modifier and Type	Method and Description
static void	MmtfUtils.calculateDsspSecondaryStructure(Structure bioJavaStruct) Generate the secondary structure for a Biojava structure object.
static void	MmtfUtils.fixMicroheterogenity(Structure bioJavaStruct) This sets all microheterogeneous groups (previously alternate location groups) as separate groups.
static int	MmtfUtils.getNumGroups(Structure structure) Count the total number of groups in the structure
static MmtfSummaryDataBean	MmtfUtils.getStructureInfo(Structure structure) Get summary information for the structure.
static void	MmtfActions.writeToFile(Structure structure, Path path) Write a Structure object to a file.
static void	MmtfActions.writeToOutputStream(Structure structure, OutputStream outputStream) Write a Structure object to an OutputStream

Constructors in org.biojava.nbio.structure.io.mmtf with parameters of type Structure

Constructor and Description
MmtfStructureWriter(Structure structure, org.rcsb.mmtf.api.StructureAdapterInterface dataTransferInterface) Pass data from Biojava structure to another generic output type.

Uses of Structure in org.biojava.nbio.structure.quaternary

Methods in org.biojava.nbio.structure.quaternary that return Structure

Modifier and Type	Method and Description
static Structure	BioAssemblyTools.getReducedStructure(Structure orig) Reduce a structure to a single-atom representation (e.g.
Structure	BiologicalAssemblyBuilder.rebuildQuaternaryStructure(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations, boolean useAsymIds, boolean multiModel) Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models.

Methods in org.biojava.nbio.structure.quaternary with parameters of type Structure

Modifier and Type	Method and Description
static double[][]	BioAssemblyTools.getAtomCoordinateBounds(Structure s)
static double[][]	BioAssemblyTools.getBiologicalMoleculeBounds(Structure asymStructure, List<BiologicalAssemblyTransformation> transformations)
static double[]	BioAssemblyTools.getBiologicalMoleculeCentroid(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations) Returns the centroid of the biological molecule.
static double	BioAssemblyTools.getBiologicalMoleculeMaximumExtend(Structure structure, List<BiologicalAssemblyTransformation> transformations) Returns the maximum extend of the biological molecule in the x, y, or z direction.
static double	BioAssemblyTools.getMaximumExtend(Structure structure) Returns the maximum extend of the structure in the x, y, or z direction.
static Structure	BioAssemblyTools.getReducedStructure(Structure orig) Reduce a structure to a single-atom representation (e.g.
Structure	BiologicalAssemblyBuilder.rebuildQuaternaryStructure(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations, boolean useAsymIds, boolean multiModel) Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models.

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

Methods in org.biojava.nbio.structure.scop that return Structure

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

Methods in org.biojava.nbio.structure.scop with parameters of type Structure

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

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

Methods in org.biojava.nbio.structure.secstruc with parameters of type Structure

Modifier and Type	Method and Description
static void	SecStrucTools.assignSecStruc(Structure s, List<SecStrucInfo> listSSI)
List<SecStrucState>	SecStrucCalc.calculate(Structure s, boolean assign) Predicts the secondary structure of this Structure object, using a DSSP implementation.
static List<SecStrucState>	DSSPParser.fetch(String pdb, Structure structure, boolean assign) Fetch and parse the DSSP file of the specified pdb code from the PDB web server and return the secondary structure annotation as a List of SecStrucState objects.
static List<SecStrucElement>	SecStrucTools.getSecStrucElements(Structure s) Obtain the List of secondary structure elements (SecStrucElement) of a Structure.
static List<SecStrucInfo>	SecStrucTools.getSecStrucInfo(Structure s) Obtain the List of secondary structure information (SecStrucInfo) of a Structure.
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 Structure in org.biojava.nbio.structure.symmetry.core

Methods in org.biojava.nbio.structure.symmetry.core that return Structure

Modifier and Type	Method and Description
Structure	QuatSymmetryResults.getStructure()

Methods in org.biojava.nbio.structure.symmetry.core with parameters of type Structure

Modifier and Type	Method and Description
static QuatSymmetryResults	QuatSymmetryDetector.calcGlobalSymmetry(Structure structure, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams) Calculate GLOBAL symmetry results.
static List<QuatSymmetryResults>	QuatSymmetryDetector.calcLocalSymmetries(Structure structure, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams) Returns a List of LOCAL symmetry results.
void	QuatSymmetryResults.setStructure(Structure structure)

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

Constructors in org.biojava.nbio.structure.symmetry.gui with parameters of type Structure

Constructor and Description
SymmetryCalc(SymmetryGui p, Structure s) Requests for a structure to analyze.

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

Methods in org.biojava.nbio.structure.symmetry.utils that return types with arguments of type Structure

Modifier and Type	Method and Description
static List<Structure>	SymmetryTools.divideStructure(CeSymmResult symmetry) Method that converts the symmetric units of a structure into different structures, so that they can be individually visualized.

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

Modifier and Type	Method and Description
static Atom[]	SymmetryTools.getRepresentativeAtoms(Structure structure) Returns the representative Atom Array of the first model, if the structure is NMR, or the Array for each model, if it is a biological assembly with multiple models.

Uses of Structure in org.biojava.nbio.structure.xtal

Methods in org.biojava.nbio.structure.xtal with parameters of type Structure

Modifier and Type	Method and Description
static void	CrystalBuilder.expandNcsOps(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps) Apply the NCS operators in the given Structure adding new chains as needed.
void	UnitCellBoundingBox.setBbs(Structure structure, javax.vecmath.Matrix4d[] ops, boolean includeHetAtoms)

Constructors in org.biojava.nbio.structure.xtal with parameters of type Structure

Constructor and Description
CrystalBuilder(Structure structure)
CrystalBuilder(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps) Special constructor for NCS-aware CrystalBuilder.