Package | Description |
---|---|
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.
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org.biojava.bio.structure.gui.util |
Some utility classes for the protein structure GUIs.
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org.biojava.bio.structure.io |
Input and Output of Structures
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org.biojava.bio.structure.io.mmcif |
Input and Output of mmcif files
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org.biojava.bio.structure.server |
classes for easier management of PDB installations
|
Modifier and Type | Method and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
StructureImpl
Implementation of a PDB Structure.
|
Modifier and Type | Method and Description |
---|---|
Structure |
Structure.clone()
returns an identical copy of this Structure object
|
Structure |
StructureImpl.clone()
returns an identical copy of this structure .
|
Structure |
DBRef.getParent()
Get the structure object that this DBRef relates to.
|
Structure |
Chain.getParent()
Returns the parent Structure of this chain.
|
Structure |
ChainImpl.getParent()
Returns the parent Structure of this chain.
|
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.
|
Modifier and Type | Method and 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 |
DBRef.setParent(Structure s)
Set the structure object that this DBRef relates to.
|
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.
|
static void |
Calc.shift(Structure structure,
Atom a)
shift a structure with a vector.
|
Constructor and Description |
---|
AtomIterator(Structure struct)
Constructs an AtomIterator object.
|
GroupIterator(Structure struct)
Constructs a GroupIterator object.
|
Modifier and Type | Method and Description |
---|---|
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) |
Modifier and Type | Method and Description |
---|---|
Structure |
AlternativeAlignment.getAlignedStructure(Structure s1,
Structure s2)
create an artifical Structure object that contains the two
structures superimposed onto each other.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
void |
BiojavaJmol.setStructure(Structure s) |
void |
SequenceDisplay.setStructure1(Structure structure) |
void |
SequenceDisplay.setStructure2(Structure structure) |
Modifier and Type | Method and Description |
---|---|
void |
JmolAlignedPositionListener.setStructure1(Structure structure1) |
void |
JmolAlignedPositionListener.setStructure2(Structure structure2) |
Modifier and Type | Method and Description |
---|---|
Structure |
PDBServerPanel.getStructure1() |
Structure |
PDBDirPanel.getStructure1() |
Structure |
StructurePairSelector.getStructure1() |
Structure |
PDBUploadPanel.getStructure1() |
Structure |
PDBServerPanel.getStructure2() |
Structure |
PDBDirPanel.getStructure2() |
Structure |
StructurePairSelector.getStructure2() |
Structure |
PDBUploadPanel.getStructure2() |
Constructor and Description |
---|
AlignmentCalc(AlignmentGui parent,
Structure s1,
Structure s2)
requests an alignment of pdb1 vs pdb 2.
|
AlternativeAlignmentFrame(Structure s1,
Structure s2) |
Modifier and Type | Method and Description |
---|---|
Structure |
PDBFileReader.getStructure(java.io.File filename)
opens filename, parses it and returns a Structure object
|
Structure |
StructureIOFile.getStructure(java.io.File file)
read file from File and returns
a Structure object.
|
Structure |
MMCIFFileReader.getStructure(java.io.File filename)
Opens filename, parses it and returns a Structure object.
|
Structure |
PDBFileReader.getStructure(java.lang.String filename)
opens filename, parses it and returns
aStructure object .
|
Structure |
StructureIOFile.getStructure(java.lang.String filename)
open filename and returns
a Structure object.
|
Structure |
MMCIFFileReader.getStructure(java.lang.String filename)
Opens filename, parses it and returns
a Structure object .
|
Structure |
PDBFileReader.getStructureById(java.lang.String pdbId)
load a structure from local file system and return a PDBStructure 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 |
StructureIO.getStructureById(java.lang.String pdbId)
Get a structure by providing a PDB code.
|
Structure |
PDBMSDReader.getStructureById(java.lang.String pdbId)
Get a structure by providing a PDB code.
|
Structure |
MMCIFFileReader.getStructureById(java.lang.String pdbId)
Get a structure by PDB code.
|
Structure |
PDBSRSReader.getStructureById(java.lang.String pdbId)
load a structure from from SRS installation using wgetz
returns null if no structure found
|
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.
|
Modifier and Type | Method and Description |
---|---|
void |
SeqRes2AtomAligner.align(Structure s,
java.util.List<Chain> seqResList) |
void |
PDBFileParser.linkChains2Compound(Structure s)
|
Constructor and Description |
---|
FileConvert(Structure struc)
Constructs a FileConvert object.
|
Modifier and Type | Method and Description |
---|---|
Structure |
SimpleMMcifConsumer.getStructure()
This method will return the parsed protein structure, once the parsing has been finished
|
Modifier and Type | Method and Description |
---|---|
Structure |
StructureEvent.getStructure() |
Structure |
StructureEventImpl.getStructure() |
Structure |
MMCIFFileInstallation.getStructure(java.lang.String pdbId) |
Structure |
PDBInstallation.getStructure(java.lang.String pdbId)
request a structure by its PDB identifier
|
Structure |
FlatFileInstallation.getStructure(java.lang.String pdbId) |
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.
|
Structure |
FlatFileInstallation.next() |
Constructor and Description |
---|
StructureEventImpl(Structure s) |