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 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, 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 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
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 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
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 MMCIFFileReader.getStructure(File filename)
          Opens filename, parses it and returns a Structure object.
 Structure PDBFileReader.getStructure(File filename)
          opens filename, parses it and returns a Structure object
 Structure StructureIOFile.getStructure(File file)
          read file from File and returns a Structure object.
 Structure MMCIFFileReader.getStructure(String filename)
          Opens filename, parses it and returns a Structure object .
 Structure PDBFileReader.getStructure(String filename)
          opens filename, parses it and returns aStructure object .
 Structure StructureIOFile.getStructure(String filename)
          open filename and returns a Structure object.
 Structure DASStructureClient.getStructureById(String pdb_code)
          if pdb code is set (setId): connect to a DAS-structure service and retreive data.
 Structure MMCIFFileReader.getStructureById(String pdbId)
          Get a structure by PDB code.
 Structure PDBFileReader.getStructureById(String pdbId)
          load a structure from local file system and return a PDBStructure object
 Structure PDBMSDReader.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 StructureIO.getStructureById(String pdbId)
          Get a structure by providing a PDB code.
 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 StructureEvent.getStructure()
           
 Structure StructureEventImpl.getStructure()
           
 Structure FlatFileInstallation.getStructure(String pdbId)
           
 Structure MMCIFFileInstallation.getStructure(String pdbId)
           
 Structure PDBInstallation.getStructure(String pdbId)
          request a structure by its PDB identifier
 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
StructureEventImpl(Structure s)