Uses of Interface org.biojava.bio.structure.Structure (BioJava-1.5-beta API)

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## 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 |
org.biojava.bio.structure.align.pairwise |
org.biojava.bio.structure.io |

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 th 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.

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