## Uses of Interface
org.biojava.bio.structure.Structure

Packages that use Structure
org.biojava.bio.program.das.dasstructure: request a protein structure via DAS
org.biojava.bio.structure: Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align: Classes for the super-imposition of structures.
org.biojava.bio.structure.align.pairwise: Classes for the pairwise alignment of structures.
org.biojava.bio.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.bio.structure.gui.events: Some event classes for the protein structure GUIs.
org.biojava.bio.structure.gui.util: Some utility classes for the protein structure GUIs.
org.biojava.bio.structure.io: Input and Output of Structures
org.biojava.bio.structure.io.mmcif: Input and Output of mmcif files
org.biojava.bio.structure.server: classes for easier management of PDB installations

Uses of Structure in org.biojava.bio.program.das.dasstructure

Methods in org.biojava.bio.program.das.dasstructure that return Structure
`Structure` `DASStructureXMLResponseParser.get_structure()` returns the Structure object.
`Structure` `DASStructureCall.getStructure(String pdb_code)` connect to a DAS structure service and retreive 3D data.

Uses of Structure in org.biojava.bio.structure

Classes in org.biojava.bio.structure that implement Structure
`class` `StructureImpl` Implementation of a PDB Structure.

Methods in org.biojava.bio.structure that return Structure
`Structure` `StructureImpl.clone()` returns an identical copy of this structure .
`Structure` `Structure.clone()` returns an identical copy of this Structure object
`Structure` `DBRef.getParent()` Get the structure object that this DBRef relates to.
`Structure` `ChainImpl.getParent()` Returns the parent Structure of this chain.
`Structure` `Chain.getParent()` Returns the parent Structure of this chain.
`Structure` `Mutator.mutate(Structure struc, String chainId, String pdbResnum, String newType)` creates a new structure which is identical with the original one.

Methods in org.biojava.bio.structure with parameters of type Structure
`static Atom[]` `StructureTools.getAtomArray(Structure s, String[] atomNames)` Returns an array of the requested Atoms from the Structure object.
`static Atom[]` `StructureTools.getAtomCAArray(Structure s)` Returns an Atom array of the CA atoms.
`static Atom[]` `StructureTools.getBackboneAtomArray(Structure s)` Returns an Atom array of the MainChain atoms.
`static int` `StructureTools.getNrAtoms(Structure s)` Count how many number of Atoms are contained within a Structure object.
`static int` `StructureTools.getNrGroups(Structure s)` Count how many groups are contained within a structure object.
`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 ...
`static void` `Calc.rotate(Structure structure, double[][] rotationmatrix)` Rotate a structure.
`static void` `Calc.rotate(Structure structure, Matrix m)` Rotate a structure object.
`void` `DBRef.setParent(Structure s)` Set the structure object that this DBRef relates to.
`void` `ChainImpl.setParent(Structure parent)` Set the back-reference to its parent Structure.
`void` `Chain.setParent(Structure parent)` Set the back-reference to its parent Structure.
`static void` `Calc.shift(Structure structure, Atom a)` shift a structure with a vector.

Constructors in org.biojava.bio.structure with parameters of type Structure
`AtomIterator(Structure struct)` Constructs an AtomIterator object.
`GroupIterator(Structure struct)` Constructs a GroupIterator object.

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

Methods in org.biojava.bio.structure.align with parameters of type Structure
`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)`

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

Methods in org.biojava.bio.structure.align.pairwise that return Structure
`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.bio.structure.align.pairwise with parameters of type Structure
`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.bio.structure.gui

Methods in org.biojava.bio.structure.gui with parameters of type Structure
`void` `BiojavaJmol.setStructure(Structure s)`
`void` `SequenceDisplay.setStructure1(Structure structure)`
`void` `SequenceDisplay.setStructure2(Structure structure)`

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

Methods in org.biojava.bio.structure.gui.events with parameters of type Structure
`void` `JmolAlignedPositionListener.setStructure1(Structure structure1)`
`void` `JmolAlignedPositionListener.setStructure2(Structure structure2)`

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

Methods in org.biojava.bio.structure.gui.util that return Structure
`Structure` `StructurePairSelector.getStructure1()`
`Structure` `PDBUploadPanel.getStructure1()`
`Structure` `PDBServerPanel.getStructure1()`
`Structure` `PDBDirPanel.getStructure1()`
`Structure` `StructurePairSelector.getStructure2()`
`Structure` `PDBUploadPanel.getStructure2()`
`Structure` `PDBServerPanel.getStructure2()`
`Structure` `PDBDirPanel.getStructure2()`

Constructors in org.biojava.bio.structure.gui.util with parameters of type Structure
`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.bio.structure.io

Methods in org.biojava.bio.structure.io that return Structure
`Structure` `StructureIOFile.getStructure(File file)` read file from File and returns a Structure object.
`Structure` `PDBFileReader.getStructure(File filename)` opens filename, parses it and returns a Structure object
`Structure` `MMCIFFileReader.getStructure(File filename)` Opens filename, parses it and returns a Structure object.
`Structure` `StructureIOFile.getStructure(String filename)` open filename and returns a Structure object.
`Structure` `PDBFileReader.getStructure(String filename)` opens filename, parses it and returns aStructure object .
`Structure` `MMCIFFileReader.getStructure(String filename)` Opens filename, parses it and returns a Structure object .
`Structure` `StructureIO.getStructureById(String pdbId)` Get a structure by providing a PDB code.
`Structure` `PDBSRSReader.getStructureById(String pdbId)` load a structure from from SRS installation using wgetz returns null if no structure found
`Structure` `PDBMSDReader.getStructureById(String pdbId)` Get a structure by providing a PDB code.
`Structure` `PDBFileReader.getStructureById(String pdbId)` load a structure from local file system and return a PDBStructure object
`Structure` `MMCIFFileReader.getStructureById(String pdbId)` Get a structure by PDB code.
`Structure` `DASStructureClient.getStructureById(String pdb_code)` if pdb code is set (setId): connect to a DAS-structure service and retreive data.
`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.bio.structure.io with parameters of type Structure
`void` `SeqRes2AtomAligner.align(Structure s, List<Chain> seqResList)`
`void` `PDBFileParser.linkChains2Compound(Structure s)` After the parsing of a PDB file the `Chain` and `Compound` objects need to be linked to each other.

Constructors in org.biojava.bio.structure.io with parameters of type Structure
`FileConvert(Structure struc)` Constructs a FileConvert object.

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

Methods in org.biojava.bio.structure.io.mmcif that return Structure
`Structure` `SimpleMMcifConsumer.getStructure()` This method will return the parsed protein structure, once the parsing has been finished

Uses of Structure in org.biojava.bio.structure.server

Methods in org.biojava.bio.structure.server that return Structure
`Structure` `StructureEventImpl.getStructure()`
`Structure` `StructureEvent.getStructure()`
`Structure` `PDBInstallation.getStructure(String pdbId)` request a structure by its PDB identifier
`Structure` `MMCIFFileInstallation.getStructure(String pdbId)`
`Structure` `FlatFileInstallation.getStructure(String pdbId)`
`Structure` `PDBInstallation.next()` iterate over all structures in this Installation that pass the provided filters and return the next one in the list.
`Structure` `MMCIFFileInstallation.next()`
`Structure` `FlatFileInstallation.next()`

Constructors in org.biojava.bio.structure.server with parameters of type Structure
`StructureEventImpl(Structure s)`