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

Packages that use Structure
org.biojava.bio.program.das.dasstructure   
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.io Input and Output of Structures 
 

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 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
 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
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)
           
 void StructurePairAligner.align(Structure s1, Structure s2, StrucAligParameters params)
           
 

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

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

Methods in org.biojava.bio.structure.io that return Structure
 Structure PDBFileReader.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 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 DASStructureClient.getStructureById(String pdb_code)
          if pdb code is set (setId): connect to a DAS-structure service and retreive data.
 Structure PDBFileReader.getStructureById(String pdbId)
          load a structure from local file system and return a PDBStructure object
 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.
 

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