Uses of Interface
org.biojava.bio.structure.Structure
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Packages that use Structure Package Description org.biojava.bio.program.das.dasstructure request a protein structure via DASorg.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 Structuresorg.biojava.bio.structure.io.mmcif Input and Output of mmcif filesorg.biojava.bio.structure.server classes for easier management of PDB installations -
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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 objectStructure
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 parametersvoid
StructurePairAligner. align(Structure s1, Structure s2, StrucAligParameters params)
calculate the alignment between the two full structures with user provided parametersAtom[]
StructurePairAligner. getAlignmentAtoms(Structure s)
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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)
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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)
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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)
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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 objectStructure
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 objectStructure
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 foundStructure
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)
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 identifierStructure
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)
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