Modifier and Type | Method and Description |
---|---|
static Structure |
DemoShowLargeAssembly.readStructure(String pdbId,
int bioAssemblyId)
Load a specific biological assembly for a PDB entry
|
Modifier and Type | Method and Description |
---|---|
void |
ProteinModificationIdentifier.identify(Structure structure)
Identify all registered modifications in a structure.
|
void |
ProteinModificationIdentifier.identify(Structure structure,
Set<ProteinModification> potentialModifications)
Identify a set of modifications in a structure.
|
Modifier and Type | Class and Description |
---|---|
class |
StructureImpl
Implementation of a PDB Structure.
|
Modifier and Type | Method and Description |
---|---|
Structure |
StructureImpl.clone()
returns an identical copy of this structure .
|
Structure |
Structure.clone()
Return an identical copy of this Structure object
|
static Structure |
StructureIO.getBiologicalAssembly(String pdbId)
Returns the first biologicalAssembly that is available for a protein structure.
|
static Structure |
StructureIO.getBiologicalAssembly(String pdbId,
int biolAssemblyNr)
By default the getStructure method loads asym units.
|
static Structure |
StructureIO.getBiologicalAssembly(String pdbId,
int biolAssemblyNr,
AtomCache cache) |
static Structure |
StructureIO.getBiologicalAssembly(String pdbId,
int biolAssemblyNr,
AtomCache cache,
BioUnitDataProvider provider) |
Structure |
Chain.getParent()
Deprecated.
use getStructure(Structure) instead.
|
Structure |
DBRef.getParent()
Get the structure object that this DBRef relates to.
|
Structure |
ChainImpl.getParent()
Deprecated.
use getStructure instead.
|
static Structure |
StructureTools.getReducedStructure(Structure s,
int chainNr)
Deprecated.
Use
StructureIdentifier.reduce(Structure) instead (v. 4.2.0) |
static Structure |
StructureTools.getReducedStructure(Structure s,
String chainId)
Deprecated.
Use
StructureIdentifier.reduce(Structure) instead (v. 4.2.0) |
Structure |
Chain.getStructure()
Returns the parent Structure of this chain.
|
Structure |
ChainImpl.getStructure()
Returns the parent Structure of this chain.
|
static Structure |
StructureTools.getStructure(String name)
Short version of
StructureTools.getStructure(String, PDBFileParser, AtomCache)
which creates new parsers when needed |
static Structure |
StructureIO.getStructure(String name)
Loads a structure based on a name.
|
static Structure |
StructureTools.getStructure(String name,
PDBFileParser parser,
AtomCache cache)
Flexibly get a structure from an input String.
|
static Structure |
StructureTools.getSubRanges(Structure s,
String ranges)
Deprecated.
Use
StructureIdentifier instead (4.2.0) |
Structure |
PassthroughIdentifier.loadStructure(AtomCache cache)
Passthrough identifiers don't know how to load a structure
|
Structure |
SubstructureIdentifier.loadStructure(AtomCache cache)
Loads the complete structure based on
SubstructureIdentifier.getPdbId() . |
Structure |
StructureIdentifier.loadStructure(AtomCache cache)
Loads a structure encompassing the structure identified.
|
Structure |
URLIdentifier.loadStructure(AtomCache cache)
Load the structure from the URL
|
Structure |
BioAssemblyIdentifier.loadStructure(AtomCache cache) |
Structure |
Mutator.mutate(Structure struc,
String chainId,
String pdbResnum,
String newType)
creates a new structure which is identical with the original one.
|
Structure |
PassthroughIdentifier.reduce(Structure input) |
Structure |
SubstructureIdentifier.reduce(Structure s)
Takes a complete structure as input and reduces it to residues present in
the specified ranges
The returned structure will be a shallow copy of the input, with shared
Chains, Residues, etc.
|
Structure |
StructureIdentifier.reduce(Structure input)
Takes a complete structure as input and reduces it to the substructure
represented by this StructureIdentifier.
|
Structure |
URLIdentifier.reduce(Structure input) |
Structure |
BioAssemblyIdentifier.reduce(Structure input) |
static Structure |
StructureTools.removeModels(Structure s)
Remove all models from a Structure and keep only the first
|
Modifier and Type | Method and Description |
---|---|
static Atom[] |
StructureTools.getAllAtomArray(Structure s)
Convert all atoms of the structure (first model) into an Atom array
|
static Atom[] |
StructureTools.getAllNonHAtomArray(Structure s,
boolean hetAtoms)
Returns and array of all non-Hydrogen atoms in the given Structure,
optionally including HET atoms or not.
|
static Atom[] |
StructureTools.getAtomArray(Structure s,
String[] atomNames)
Returns an array of the requested Atoms from the Structure object.
|
static Atom[] |
StructureTools.getAtomArrayAllModels(Structure s,
String[] atomNames)
Returns an array of the requested Atoms from the Structure object.
|
static Atom[] |
StructureTools.getAtomCAArray(Structure s)
Return an Atom array of the C-alpha atoms.
|
static Atom[] |
StructureTools.getBackboneAtomArray(Structure s)
Return an Atom array of the main chain atoms: CA, C, N, O Any group that
contains those atoms will be included, be it a standard aminoacid or not
|
static Group |
StructureTools.getGroupByPDBResidueNumber(Structure struc,
ResidueNumber pdbResNum)
Get a group represented by a ResidueNumber.
|
static Map<Group,Double> |
StructureTools.getGroupDistancesWithinShell(Structure structure,
Atom centroid,
Set<ResidueNumber> excludeResidues,
double radius,
boolean includeWater,
boolean useAverageDistance)
Finds Groups in
structure that contain at least one Atom that is
within radius Angstroms of centroid . |
static Set<Group> |
StructureTools.getGroupsWithinShell(Structure structure,
Atom atom,
Set<ResidueNumber> excludeResidues,
double distance,
boolean includeWater) |
static Set<Group> |
StructureTools.getGroupsWithinShell(Structure structure,
Group group,
double distance,
boolean includeWater)
Returns a Set of Groups in a structure within the distance specified of a
given group.
|
static int |
StructureTools.getNrAtoms(Structure s)
Count how many Atoms are contained within a Structure object.
|
static int |
StructureTools.getNrGroups(Structure s)
Count how many groups are contained within a structure object.
|
static Structure |
StructureTools.getReducedStructure(Structure s,
int chainNr)
Deprecated.
Use
StructureIdentifier.reduce(Structure) instead (v. 4.2.0) |
static Structure |
StructureTools.getReducedStructure(Structure s,
String chainId)
Deprecated.
Use
StructureIdentifier.reduce(Structure) instead (v. 4.2.0) |
static Atom[] |
StructureTools.getRepresentativeAtomArray(Structure s)
Gets a representative atom for each group that is part of the chain
backbone.
|
static Structure |
StructureTools.getSubRanges(Structure s,
String ranges)
Deprecated.
Use
StructureIdentifier instead (4.2.0) |
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 ...
|
Structure |
PassthroughIdentifier.reduce(Structure input) |
Structure |
SubstructureIdentifier.reduce(Structure s)
Takes a complete structure as input and reduces it to residues present in
the specified ranges
The returned structure will be a shallow copy of the input, with shared
Chains, Residues, etc.
|
Structure |
StructureIdentifier.reduce(Structure input)
Takes a complete structure as input and reduces it to the substructure
represented by this StructureIdentifier.
|
Structure |
URLIdentifier.reduce(Structure input) |
Structure |
BioAssemblyIdentifier.reduce(Structure input) |
static Structure |
StructureTools.removeModels(Structure s)
Remove all models from a Structure and keep only the first
|
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)
Deprecated.
use setStructure instead
|
void |
DBRef.setParent(Structure s)
Set the structure object that this DBRef relates to.
|
void |
ChainImpl.setParent(Structure parent)
Deprecated.
|
void |
Chain.setStructure(Structure parent)
Sets the back-reference to its parent Structure.
|
void |
ChainImpl.setStructure(Structure parent)
Sets the back-reference to its parent Structure.
|
static void |
Calc.shift(Structure structure,
Atom a)
shift a structure with a vector.
|
static void |
Calc.transform(Structure structure,
javax.vecmath.Matrix4d m)
Transforms a structure object, given a Matrix4d (i.e. the vecmath library
double-precision 4x4 rotation+translation matrix).
|
static void |
Calc.translate(Structure structure,
javax.vecmath.Vector3d v)
Translates a Structure object, given a Vector3d (i.e. the vecmath library
double-precision 3-d vector)
|
Constructor and Description |
---|
AtomIterator(Structure struct)
Constructs an AtomIterator object.
|
AtomPositionMap(Structure s)
Creates a new AtomPositionMap containing representative atoms
from a structure.
|
GroupIterator(Structure struct)
Constructs a GroupIterator object.
|
Modifier and Type | Method and Description |
---|---|
void |
StructurePairAligner.align(Structure s1,
String chainId1,
Structure s2,
String chainId2)
Align two chains from the structures.
|
void |
StructurePairAligner.align(Structure s1,
String chainId1,
Structure s2,
String chainId2,
StrucAligParameters params)
Aligns two chains from the structures using user provided parameters.
|
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)
Returns the atoms that are being used for the alignment.
|
Constructor and Description |
---|
MultiThreadedDBSearch(String name,
Structure structure,
String outFile,
StructureAlignment algorithm,
int nrCPUs,
boolean domainSplit) |
Modifier and Type | Method and Description |
---|---|
static Structure |
GuiWrapper.getAlignedStructure(Atom[] ca1,
Atom[] ca2) |
Modifier and Type | Method and Description |
---|---|
static void |
GuiWrapper.showStructure(Structure structure)
Shows a structure in Jmol
|
Modifier and Type | Method and Description |
---|---|
Structure |
StructureName.loadStructure(AtomCache cache) |
Structure |
StructureName.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
Structure |
StructureName.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
static Structure |
DisplayAFP.createArtificalStructure(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2)
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.
|
static Structure |
DisplayAFP.getAlignedStructure(Atom[] ca1,
Atom[] ca2)
Get an artifical Structure containing both chains.
|
static Structure |
MultipleAlignmentJmolDisplay.getAlignedStructure(List<Atom[]> atomArrays)
Get an artifical Structure containing a different model for every
input structure, so that the alignment result can be viewed in Jmol.
|
Structure |
SelectPDBPanel.getStructure1() |
Structure |
SelectPDBPanel.getStructure2() |
Constructor and Description |
---|
AlignmentCalc(AlignmentGui parent,
Structure s1,
Structure s2,
String name1,
String name2)
requests an alignment of pdb1 vs pdb 2.
|
AlignmentCalcDB(AlignmentGui parent,
Structure s1,
String name1,
UserConfiguration config,
String outFile,
Boolean domainSplit) |
Constructor and Description |
---|
MultipleAlignmentCalc(MultipleAlignmentGUI parent,
List<Structure> structures,
List<StructureIdentifier> names)
Requests an alignment of the pdbs.
|
Modifier and Type | Field and Description |
---|---|
protected Structure |
AbstractAlignmentJmol.structure |
Modifier and Type | Method and Description |
---|---|
Structure |
AbstractAlignmentJmol.getStructure()
Return the current Structure in the AlignmentJmol instance.
|
Modifier and Type | Method and Description |
---|---|
void |
AbstractAlignmentJmol.setStructure(Structure s)
Set a new Structure to visualize in the AlignmentJmol window.
|
void |
JmolPanel.setStructure(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.
|
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 |
---|---|
static Structure |
AFPAlignmentDisplay.createArtificalStructure(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2) |
Structure |
AtomCache.getBiologicalAssembly(String pdbId)
Loads the default biological unit (e.g. *.pdb1.gz).
|
Structure |
AtomCache.getBiologicalAssembly(String pdbId,
int bioAssemblyId)
Loads the default biological unit (e.g. *.pdb1.gz).
|
Structure |
AtomCache.getBiologicalAssembly(String pdbId,
int bioAssemblyId,
boolean bioAssemblyFallback)
Loads the biological assembly for a given PDB ID and bioAssemblyId.
|
Structure |
AtomCache.getBiologicalUnit(String pdbId)
Deprecated.
Renamed to
AtomCache.getBiologicalAssembly(String) in 4.2 |
Structure |
AtomCache.getStructure(String name)
Request a Structure based on a name.
|
Structure |
AtomCache.getStructure(StructureIdentifier strucId)
Get the structure corresponding to the given
StructureIdentifier . |
Structure |
AtomCache.getStructureForCathDomain(StructureName structureName)
Returns a
Structure corresponding to the CATH identifier supplied in structureName , using the the CathDatabase
at CathFactory.getCathDatabase() . |
Structure |
AtomCache.getStructureForCathDomain(StructureName structureName,
CathDatabase cathInstall)
Returns a
Structure corresponding to the CATH identifier supplied in structureName , using the specified CathDatabase . |
Structure |
AtomCache.getStructureForDomain(ScopDomain domain)
Returns the representation of a
ScopDomain as a BioJava Structure object. |
Structure |
AtomCache.getStructureForDomain(ScopDomain domain,
ScopDatabase scopDatabase)
Returns the representation of a
ScopDomain as a BioJava Structure object. |
Structure |
AtomCache.getStructureForDomain(ScopDomain domain,
ScopDatabase scopDatabase,
boolean strictLigandHandling)
Returns the representation of a
ScopDomain as a BioJava Structure object. |
Structure |
AtomCache.getStructureForDomain(String scopId)
Returns the representation of a
ScopDomain as a BioJava Structure object. |
Structure |
AtomCache.getStructureForDomain(String scopId,
ScopDatabase scopDatabase)
Returns the representation of a
ScopDomain as a BioJava Structure object. |
Structure |
AtomCache.getStructureForPdbId(String pdbId)
Loads a structure directly by PDB ID
|
protected Structure |
AtomCache.loadStructureFromCifByPdbId(String pdbId) |
protected Structure |
AtomCache.loadStructureFromPdbByPdbId(String pdbId) |
Constructor and Description |
---|
AsaCalculator(Structure structure,
double probe,
int nSpherePoints,
int nThreads,
boolean hetAtoms)
Constructs a new AsaCalculator.
|
Modifier and Type | Method and Description |
---|---|
Structure |
CathDomain.loadStructure(AtomCache cache) |
Structure |
CathDomain.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
Structure |
CathDomain.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
static StructureInterfaceList |
StructureInterfaceList.calculateInterfaces(Structure struc)
Calculates the interfaces for a structure using default parameters
|
Modifier and Type | Method and Description |
---|---|
Structure |
PDPProvider.getDomain(String pdpDomainName,
AtomCache cache)
Get the structure for a particular PDP domain
|
Structure |
RemotePDPProvider.getDomain(String pdpDomainName,
AtomCache cache)
Get the structure for a particular PDP domain
|
Structure |
PDPDomain.loadStructure(AtomCache cache) |
Structure |
PDPDomain.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
Structure |
PDPDomain.reduce(Structure input) |
static List<Domain> |
LocalProteinDomainParser.suggestDomains(Structure s)
Suggest domains for a protein structure
|
Modifier and Type | Method and Description |
---|---|
Structure |
EcodDomain.loadStructure(AtomCache cache) |
Structure |
EcodDomain.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
Structure |
EcodDomain.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
void |
BiojavaJmol.setStructure(Structure s) |
void |
StructureViewer.setStructure(Structure structure) |
void |
JmolViewerImpl.setStructure(Structure structure) |
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 |
PDBUploadPanel.getStructure1() |
Structure |
PDBServerPanel.getStructure1() |
Structure |
PDBDirPanel.getStructure1() |
Structure |
ScopSelectPanel.getStructure1() |
Structure |
StructurePairSelector.getStructure1() |
Structure |
PDBUploadPanel.getStructure2() |
Structure |
PDBServerPanel.getStructure2() |
Structure |
PDBDirPanel.getStructure2() |
Structure |
ScopSelectPanel.getStructure2() |
Structure |
StructurePairSelector.getStructure2() |
Modifier and Type | Method and Description |
---|---|
List<Structure> |
SelectMultiplePanel.getStructures() |
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 |
LocalPDBDirectory.getStructure(File filename) |
Structure |
StructureIOFile.getStructure(File file)
Read file from File and returns
a Structure object.
|
abstract Structure |
LocalPDBDirectory.getStructure(InputStream inStream)
Handles the actual parsing of the file into a Structure object.
|
Structure |
MMCIFFileReader.getStructure(InputStream inStream) |
Structure |
PDBFileReader.getStructure(InputStream inStream) |
Structure |
LocalPDBDirectory.getStructure(String filename) |
Structure |
StructureIOFile.getStructure(String filename)
Open filename and return a Structure object.
|
Structure |
LocalPDBDirectory.getStructure(URL u) |
Structure |
StructureProvider.getStructureById(String pdbId)
get the structure for a PDB ID
|
Structure |
LocalPDBDirectory.getStructureById(String pdbId) |
Structure |
SandboxStyleStructureProvider.getStructureById(String pdbId) |
Structure[] |
FastaStructureParser.getStructures()
Gets the protein structures mapped from the Fasta file.
|
static Structure |
StructureSequenceMatcher.getSubstructureMatchingProteinSequence(ProteinSequence sequence,
Structure wholeStructure)
|
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.
|
Modifier and Type | Method and Description |
---|---|
static void |
ChargeAdder.addCharges(Structure structure)
Function to add the charges to a given structure.
|
void |
SeqRes2AtomAligner.align(Structure s,
List<Chain> seqResList) |
static AFPChain |
FastaAFPChainConverter.cpFastaToAfpChain(File fastaFile,
Structure structure,
int cpSite)
Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
cpSite residues to the right. |
static AFPChain |
FastaAFPChainConverter.cpFastaToAfpChain(ProteinSequence first,
ProteinSequence second,
Structure structure,
int cpSite)
Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
cpSite residues to the right. |
static AFPChain |
FastaAFPChainConverter.cpFastaToAfpChain(String first,
String second,
Structure structure,
int cpSite) |
static AFPChain |
FastaAFPChainConverter.fastaFileToAfpChain(File fastaFile,
Structure structure1,
Structure structure2)
Reads the file
fastaFile , expecting exactly two sequences which give a pairwise alignment. |
static AFPChain |
FastaAFPChainConverter.fastaStringToAfpChain(String sequence1,
String sequence2,
Structure structure1,
Structure structure2)
Returns an AFPChain corresponding to the alignment between
structure1 and structure2 , which is given by the gapped protein sequences sequence1 and sequence2 . |
static AFPChain |
FastaAFPChainConverter.fastaToAfpChain(Map<String,ProteinSequence> sequences,
Structure structure1,
Structure structure2)
Uses two sequences each with a corresponding structure to create an AFPChain corresponding to the alignment.
|
static AFPChain |
FastaAFPChainConverter.fastaToAfpChain(ProteinSequence sequence1,
ProteinSequence sequence2,
Structure structure1,
Structure structure2)
Returns an AFPChain corresponding to the alignment between
structure1 and structure2 , which is given by the gapped protein sequences sequence1 and sequence2 . |
static AFPChain |
FastaAFPChainConverter.fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment,
Structure structure1,
Structure structure2)
Provided only for convenience.
|
static AFPChain |
FastaAFPChainConverter.fastaToAfpChain(String sequence1,
String sequence2,
Structure structure1,
Structure structure2)
TODO Write comment
|
static ProteinSequence |
StructureSequenceMatcher.getProteinSequenceForStructure(Structure struct,
Map<Integer,Group> groupIndexPosition)
Generates a ProteinSequence corresponding to the sequence of struct,
and maintains a mapping from the sequence back to the original groups.
|
static Structure |
StructureSequenceMatcher.getSubstructureMatchingProteinSequence(ProteinSequence sequence,
Structure wholeStructure)
|
void |
PDBFileParser.linkChains2Compound(Structure s)
|
static ResidueNumber[] |
StructureSequenceMatcher.matchSequenceToStructure(ProteinSequence seq,
Structure struct)
Given a sequence and the corresponding Structure, get the ResidueNumber
for each residue in the sequence.
|
static void |
SeqRes2AtomAligner.storeUnAlignedSeqRes(Structure structure,
List<Chain> seqResChains,
boolean headerOnly)
Storing unaligned SEQRES groups in a Structure.
|
Constructor and Description |
---|
BondMaker(Structure structure,
FileParsingParameters params) |
CompoundFinder(Structure s) |
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 |
---|---|
static List<AtomSite> |
MMCIFFileTools.convertStructureToAtomSites(Structure s)
Converts a Structure into a List of
AtomSite objects |
Modifier and Type | Method and Description |
---|---|
static Structure |
BioAssemblyTools.getReducedCAStructure(Structure orig)
Deprecated.
Use the more generic
BioAssemblyTools.getReducedStructure(Structure) |
static Structure |
BioAssemblyTools.getReducedStructure(Structure orig)
reduce a structure to a single-atom representation (e.g.
|
Structure |
BiologicalAssemblyBuilder.rebuildQuaternaryStructure(Structure asymUnit,
List<BiologicalAssemblyTransformation> transformations) |
Modifier and Type | Method and Description |
---|---|
static double[][] |
BioAssemblyTools.getAtomCoordinateBounds(Structure s) |
static double[][] |
BioAssemblyTools.getBiologicalMoleculeBounds(Structure asymStructure,
List<BiologicalAssemblyTransformation> transformations) |
static double[] |
BioAssemblyTools.getBiologicalMoleculeCentroid(Structure asymUnit,
List<BiologicalAssemblyTransformation> transformations)
Returns the centroid of the biological molecule.
|
static double |
BioAssemblyTools.getBiologicalMoleculeMaximumExtend(Structure structure,
List<BiologicalAssemblyTransformation> transformations)
Returns the maximum extend of the biological molecule in the x, y, or z direction.
|
static double |
BioAssemblyTools.getMaximumExtend(Structure structure)
Returns the maximum extend of the structure in the x, y, or z direction.
|
static Structure |
BioAssemblyTools.getReducedCAStructure(Structure orig)
Deprecated.
Use the more generic
BioAssemblyTools.getReducedStructure(Structure) |
static Structure |
BioAssemblyTools.getReducedStructure(Structure orig)
reduce a structure to a single-atom representation (e.g.
|
Structure |
BiologicalAssemblyBuilder.rebuildQuaternaryStructure(Structure asymUnit,
List<BiologicalAssemblyTransformation> transformations) |
Modifier and Type | Method and Description |
---|---|
Structure |
MmCifPDBBiolAssemblyProvider.getAsymUnit()
get the asym unit for this PDB ID
|
Structure |
MmCifBiolAssemblyProvider.getAsymUnit(String pdbId) |
Structure |
PDBBioUnitDataProvider.getAsymUnit(String pdbId) |
Structure |
RemoteBioUnitDataProvider.getAsymUnit(String pdbId) |
Structure |
BioUnitDataProvider.getAsymUnit(String pdbId)
load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object
|
Structure |
MmCifBiolAssemblyProvider.getBiolAssembly(String pdbId,
int biolAssemblyNr) |
Modifier and Type | Method and Description |
---|---|
void |
MmCifBiolAssemblyProvider.setAsymUnit(Structure s) |
void |
MmCifPDBBiolAssemblyProvider.setAsymUnit(Structure s) |
void |
PDBBioUnitDataProvider.setAsymUnit(Structure s) |
void |
RemoteBioUnitDataProvider.setAsymUnit(Structure s) |
void |
BioUnitDataProvider.setAsymUnit(Structure asymUnit) |
Modifier and Type | Method and Description |
---|---|
Structure |
ScopDomain.loadStructure(AtomCache cache) |
Structure |
ScopDomain.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
Structure |
ScopDomain.reduce(Structure input) |
Modifier and Type | Method and Description |
---|---|
List<SecStrucState> |
SecStrucCalc.calculate(Structure s,
boolean assign)
Predicts the secondary structure of this Structure object,
using a DSSP implementation.
|
static List<SecStrucState> |
DSSPParser.fetch(String pdb,
Structure structure,
boolean assign)
Fetch and parse the DSSP file of the specified pdb code
from the PDB web server and return the secondary structure
annotation as a List of
SecStrucState objects. |
static List<SecStrucElement> |
SecStrucTools.getSecStrucElements(Structure s)
Obtain the List of secondary structure elements (SecStrucElement) of a
Structure.
|
static List<SecStrucInfo> |
SecStrucTools.getSecStrucInfo(Structure s)
Obtain the List of secondary structure information (SecStrucInfo) of a
Structure.
|
static List<SecStrucState> |
DSSPParser.parseFile(String dsspPath,
Structure structure,
boolean assign)
Parse a DSSP output file and return the secondary structure
annotation as a List of
SecStrucState objects. |
static List<SecStrucState> |
DSSPParser.parseString(String dsspOut,
Structure structure,
boolean assign)
Parse a DSSP format String and return the secondary structure
annotation as a List of
SecStrucState objects. |
Constructor and Description |
---|
CalcBioAssemblySymmetry(Structure bioAssembly,
QuatSymmetryParameters parameters) |
Constructor and Description |
---|
ClusterProteinChains(Structure structure,
QuatSymmetryParameters parameters) |
ClusterProteinChains(Structure structure1,
Structure structure2,
QuatSymmetryParameters parameters) |
ProteinChainExtractor(Structure structure,
QuatSymmetryParameters parameters) |
ProteinSequenceClusterer(Structure structure,
QuatSymmetryParameters parameters) |
ProteinSequenceClusterer(Structure structure1,
Structure structure2,
QuatSymmetryParameters parameters) |
QuatSymmetryDetector(Structure structure,
QuatSymmetryParameters parameters) |
Constructor and Description |
---|
SymmetryCalc(SymmetryGui p,
Structure s)
Requests for a structure to analyze.
|
Modifier and Type | Method and Description |
---|---|
static List<Structure> |
SymmetryTools.divideStructure(CeSymmResult symmetry)
Method that converts the symmetric units of a structure into different
structures, so that they can be individually visualized.
|
Modifier and Type | Method and Description |
---|---|
static Atom[] |
SymmetryTools.getRepresentativeAtoms(Structure structure)
Returns the representative Atom Array of the first model, if the
structure is NMR, or the Array for each model, if it is a biological
assembly with multiple models.
|
Modifier and Type | Method and Description |
---|---|
void |
UnitCellBoundingBox.setBbs(Structure structure,
javax.vecmath.Matrix4d[] ops,
boolean includeHetAtoms) |
Constructor and Description |
---|
CrystalBuilder(Structure structure) |
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