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

Packages that use Structure

Package	Description
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

Modifier and Type	Method	Description
Structure	DASStructureXMLResponseParser.get_structure()	returns the Structure object.
Structure	DASStructureCall.getStructure(java.lang.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

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

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

Modifier and Type	Method	Description
Structure	Structure.clone()	returns an identical copy of this Structure object
Structure	StructureImpl.clone()	returns an identical copy of this structure .
Structure	Chain.getParent()	Returns the parent Structure of this chain.
Structure	ChainImpl.getParent()	Returns the parent Structure of this chain.
Structure	DBRef.getParent()	Get the structure object that this DBRef relates to.
Structure	Mutator.mutate(Structure struc, java.lang.String chainId, java.lang.String pdbResnum, java.lang.String newType)	creates a new structure which is identical with the original one.

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

Modifier and Type	Method	Description
static Atom[]	StructureTools.getAtomArray(Structure s, java.lang.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, java.lang.String chainId, java.lang.String pdbResnum, java.lang.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	Chain.setParent(Structure parent)	Set the back-reference to its parent Structure.
void	ChainImpl.setParent(Structure parent)	Set the back-reference to its parent Structure.
void	DBRef.setParent(Structure s)	Set the structure object that this DBRef relates to.
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

Constructor	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	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.bio.structure.align.pairwise with parameters of type Structure

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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

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

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

Constructor	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.bio.structure.io

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

Modifier and Type	Method	Description
Structure	MMCIFFileReader.getStructure(java.io.File filename)	Opens filename, parses it and returns a Structure object.
Structure	MMCIFFileReader.getStructure(java.lang.String filename)	Opens filename, parses it and returns a Structure object .
Structure	PDBFileReader.getStructure(java.io.File filename)	opens filename, parses it and returns a Structure object
Structure	PDBFileReader.getStructure(java.lang.String filename)	opens filename, parses it and returns aStructure object .
Structure	StructureIOFile.getStructure(java.io.File file)	read file from File and returns a Structure object.
Structure	StructureIOFile.getStructure(java.lang.String filename)	open filename and returns a Structure object.
Structure	DASStructureClient.getStructureById(java.lang.String pdb_code)	if pdb code is set (setId): connect to a DAS-structure service and retreive data.
Structure	MMCIFFileReader.getStructureById(java.lang.String pdbId)	Get a structure by PDB code.
Structure	PDBFileReader.getStructureById(java.lang.String pdbId)	load a structure from local file system and return a PDBStructure object
Structure	PDBMSDReader.getStructureById(java.lang.String pdbId)	Get a structure by providing a PDB code.
Structure	PDBSRSReader.getStructureById(java.lang.String pdbId)	load a structure from from SRS installation using wgetz returns null if no structure found
Structure	StructureIO.getStructureById(java.lang.String pdbId)	Get a structure by providing a PDB code.
Structure	PDBFileParser.parsePDBFile(java.io.BufferedReader buf)	parse a PDB file and return a datastructure implementing PDBStructure interface.
Structure	PDBFileParser.parsePDBFile(java.io.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

Modifier and Type	Method	Description
void	SeqRes2AtomAligner.align(Structure s, java.util.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

Constructor	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
Structure	FlatFileInstallation.getStructure(java.lang.String pdbId)
Structure	MMCIFFileInstallation.getStructure(java.lang.String pdbId)
Structure	PDBInstallation.getStructure(java.lang.String pdbId)	request a structure by its PDB identifier
Structure	StructureEvent.getStructure()
Structure	StructureEventImpl.getStructure()
Structure	FlatFileInstallation.next()
Structure	MMCIFFileInstallation.next()
Structure	PDBInstallation.next()	iterate over all structures in this Installation that pass the provided filters and return the next one in the list.

Constructors in org.biojava.bio.structure.server with parameters of type Structure

Constructor	Description
StructureEventImpl(Structure s)