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Packages that use Structure | |
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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 |
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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 |
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 | |
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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. |
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 | |
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AtomIterator(Structure struct)
Constructs an AtomIterator object. |
|
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)
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 |
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Methods in org.biojava.bio.structure.align.pairwise that return Structure | |
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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 | |
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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 |
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Methods in org.biojava.bio.structure.gui with parameters of type Structure | |
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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 |
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Methods in org.biojava.bio.structure.gui.events with parameters of type Structure | |
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void |
JmolAlignedPositionListener.setStructure1(Structure structure1)
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void |
JmolAlignedPositionListener.setStructure2(Structure structure2)
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Uses of Structure in org.biojava.bio.structure.gui.util |
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Methods in org.biojava.bio.structure.gui.util that return Structure | |
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Structure |
PDBDirPanel.getStructure1()
|
Structure |
PDBUploadPanel.getStructure1()
|
Structure |
StructurePairSelector.getStructure1()
|
Structure |
PDBServerPanel.getStructure1()
|
Structure |
PDBDirPanel.getStructure2()
|
Structure |
PDBUploadPanel.getStructure2()
|
Structure |
StructurePairSelector.getStructure2()
|
Structure |
PDBServerPanel.getStructure2()
|
Constructors in org.biojava.bio.structure.gui.util with parameters of type Structure | |
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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 |
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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 |
MMCIFFileReader.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 |
PDBFileReader.getStructure(String filename)
opens filename, parses it and returns aStructure object . |
Structure |
MMCIFFileReader.getStructure(String filename)
Opens filename, parses it and returns a Structure 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 |
StructureIO.getStructureById(String pdbId)
Get a structure by providing a PDB code. |
Structure |
PDBFileReader.getStructureById(String pdbId)
load a structure from local file system and return a PDBStructure object |
Structure |
MMCIFFileReader.getStructureById(String pdbId)
Get a structure by PDB code. |
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 |
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 | |
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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 | |
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FileConvert(Structure struc)
Constructs a FileConvert object. |
Uses of Structure in org.biojava.bio.structure.io.mmcif |
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Methods in org.biojava.bio.structure.io.mmcif that return Structure | |
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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 |
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Methods in org.biojava.bio.structure.server that return Structure | |
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Structure |
StructureEvent.getStructure()
|
Structure |
StructureEventImpl.getStructure()
|
Structure |
MMCIFFileInstallation.getStructure(String pdbId)
|
Structure |
FlatFileInstallation.getStructure(String pdbId)
|
Structure |
PDBInstallation.getStructure(String pdbId)
request a structure by its PDB identifier |
Structure |
MMCIFFileInstallation.next()
|
Structure |
FlatFileInstallation.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 | |
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StructureEventImpl(Structure s)
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