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Packages that use Structure | |
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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 |
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Methods in org.biojava.bio.program.das.dasstructure that return Structure | |
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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 |
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Classes in org.biojava.bio.structure that implement Structure | |
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class |
StructureImpl
Implementation of a PDB Structure. |
Methods in org.biojava.bio.structure that return Structure | |
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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 | |
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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 | |
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AtomIterator(Structure struct)
Constructs an AtomIterator object. |
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GroupIterator(Structure struct)
Constructs a GroupIterator object. |
Uses of Structure in org.biojava.bio.structure.align |
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Methods in org.biojava.bio.structure.align with parameters of type Structure | |
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void |
StructurePairAligner.align(Structure s1,
Structure s2)
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void |
StructurePairAligner.align(Structure s1,
Structure s2,
StrucAligParameters params)
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Uses of Structure in org.biojava.bio.structure.align.pairwise |
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Methods in org.biojava.bio.structure.align.pairwise with parameters of type Structure | |
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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 |
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Methods in org.biojava.bio.structure.io that return Structure | |
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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 | |
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FileConvert(Structure struc)
Constructs a FileConvert object. |
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