Uses of Class
org.biojava.nbio.structure.PdbId

Packages that use PdbId

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align.client	This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.ecod
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.io.density
org.biojava.nbio.structure.scop	Parsers and API for SCOP, Structural Classification of Proteins.

Uses of PdbId in org.biojava.nbio.structure

Methods in org.biojava.nbio.structure that return PdbId

Modifier and Type	Method	Description
PdbId	PDBHeader.getPdbId()	Gets the PDB identifier for this protein structure.
PdbId	Structure.getPdbId()	Returns the PDB identifier associated with this StructureIdentifier.
PdbId	StructureImpl.getPdbId()	Returns the PDB identifier associated with this StructureIdentifier.
PdbId	SubstructureIdentifier.getPdbId()	Get the PDB identifier part of the SubstructureIdentifier

Methods in org.biojava.nbio.structure with parameters of type PdbId

Modifier and Type	Method	Description
int	PdbId.compareTo(PdbId o)
void	PDBHeader.setPdbId(PdbId pdbId)	Sets the PDB identifier code for this protein structure.
void	Structure.setPdbId(PdbId pdbId)	Sets the PdbId identifier associated with this structure.
void	StructureImpl.setPdbId(PdbId pdbId)	Sets the PdbId identifier associated with this structure.

Constructors in org.biojava.nbio.structure with parameters of type PdbId

Modifier	Constructor	Description
	BioAssemblyIdentifier(PdbId pdbId, int biolNr)
	SubstructureIdentifier(PdbId pdbId, List<ResidueRange> ranges)	Create a new identifier based on a set of ranges.

Uses of PdbId in org.biojava.nbio.structure.align.client

Fields in org.biojava.nbio.structure.align.client declared as PdbId

Modifier and Type	Field	Description
protected PdbId	StructureName.pdbId

Methods in org.biojava.nbio.structure.align.client that return PdbId

Modifier and Type	Method	Description
PdbId	StructureName.getPdbId()	Get the PDB ID for this name, if any.
PdbId	PdbPair.getPdbId1()
PdbId	PdbPair.getPdbId2()

Uses of PdbId in org.biojava.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util with parameters of type PdbId

Modifier and Type	Method	Description
protected void	AtomCache.flagLoading(PdbId pdbId)
protected void	AtomCache.flagLoadingFinished(PdbId pdbId)
Structure	AtomCache.getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean multiModel)	Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()
Structure	AtomCache.getStructureForPdbId(PdbId pdbId)	Loads a structure directly by PDB ID
protected Structure	AtomCache.loadStructureFromBcifByPdbId(PdbId pdbId)
protected Structure	AtomCache.loadStructureFromCifByPdbId(PdbId pdbId)
protected Structure	AtomCache.loadStructureFromPdbByPdbId(PdbId pdbId)

Uses of PdbId in org.biojava.nbio.structure.ecod

Methods in org.biojava.nbio.structure.ecod that return PdbId

Modifier and Type	Method	Description
PdbId	EcodDomain.getPdbId()	Gets the PdbId object. Before 6.0.0, this method used to return a String.

Methods in org.biojava.nbio.structure.ecod with parameters of type PdbId

Modifier and Type	Method	Description
void	EcodDomain.setPdbId(PdbId pdbId)

Uses of PdbId in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io with parameters of type PdbId

Modifier and Type	Method	Description
protected boolean	LocalPDBDirectory.checkFileExists(PdbId pdbId)
boolean	LocalPDBDirectory.deleteStructure(PdbId pdbId)	Attempts to delete all versions of a structure from the local directory.
protected File	LocalPDBDirectory.downloadStructure(PdbId pdbId)	Downloads an MMCIF file from the PDB to the local path
protected InputStream	LocalPDBDirectory.getInputStream(PdbId pdbId)	Load or download the specified structure and return it as an InputStream for direct parsing.
File	LocalPDBDirectory.getLocalFile(PdbId pdbId)	Searches for previously downloaded files
Structure	LocalPDBDirectory.getStructureById(PdbId pdbId)	Get the structure for a PDB ID
Structure	StructureProvider.getStructureById(PdbId pdbId)	Get the structure for a PDB ID

Uses of PdbId in org.biojava.nbio.structure.io.density

Methods in org.biojava.nbio.structure.io.density that return PdbId

Modifier and Type	Method	Description
PdbId	DensityMapRequest.getPdbId()
PdbId	DensityMapResult.getPdbId()
PdbId	NoDensityMapException.getPdbId()

Methods in org.biojava.nbio.structure.io.density with parameters of type PdbId

Modifier and Type	Method	Description
static DensityMapRequest.Builder	DensityMapRequest.builder(PdbId pdbId)	Starts a request for a PDB entry.
String	PdbeCcp4MapProvider.buildUrl(PdbId pdbId, DensityMapKind kind)	Builds the URL for a map without fetching it.
String	WwpdbMapCoefficientsProvider.buildUrl(PdbId pdbId, DensityMapKind kind)	Builds the URL for a set of coefficients without fetching them.
int	DensityMapCache.deleteDensityMaps(PdbId pdbId)	Removes every cached density file for an entry, including the sidecars.
static File	DensityCacheLayout.emdbMappingFile(File cacheRoot, PdbId pdbId)	The file caching the EMDB identifiers and author contour level associated with a PDB entry.
Optional<DensityMapResult>	DensityMapCache.findDensityMap(PdbId pdbId, DensityMapKind kind)	As DensityMapCache.getDensityMap(PdbId, DensityMapKind) but returning an empty Optional rather than throwing when nothing is available.
DensityMapResult	DensityMapCache.getCached(PdbId pdbId, DensityMapKind kind, DensityMapSource source)	Looks a map up in the cache without contacting any server.
Double	EmdbEntryResolver.getContourLevelFor(PdbId pdbId)	The contour level the depositors recommend for the map a PDB entry was fitted into, as reported by the EMDB search.
DensityMapResult	DensityMapCache.getDensityMap(PdbId pdbId, DensityMapKind kind)	Fetches a density map, using the cache where possible.
List<DensityMapResult>	DensityMapCache.getDifferenceMapPair(PdbId pdbId)	Fetches both halves of the conventional X-ray pair: the 2mFo-DFc map and the mFo-DFc difference map.
List<String>	EmdbEntryResolver.getEmdbIds(PdbId pdbId)	The EMDB entries a PDB entry was fitted into.
static File	DensityCacheLayout.pdbMapFile(File cacheRoot, PdbId pdbId, String kindToken, DensityMapSource source, DensityFileFormat format, String qualifier)	The cache file for a PDB-keyed map, naming the kind explicitly.
static File	DensityCacheLayout.pdbMapFile(File cacheRoot, PdbId pdbId, DensityMapKind kind, DensityMapSource source, DensityFileFormat format, String qualifier)	The cache file for a PDB-keyed map.
static String	DensityCacheLayout.shortIdOrFull(PdbId pdbId)	The short four-character spelling of an identifier where one exists.
protected String	AbstractDensityMapProvider.urlId(PdbId pdbId)	The identifier spelling to put into a URL: four characters and lower case where the entry has a short form.

Constructors in org.biojava.nbio.structure.io.density with parameters of type PdbId

Modifier	Constructor	Description
	DensityMapResult(File file, DensityMapSource source, DensityFileFormat format, DensityMapKind kind, PdbId pdbId, String emdbId, String sourceUrl, boolean fromCache, Double recommendedContourLevel, Double sigma)
	NoDensityMapException(PdbId pdbId, DensityMapKind kind, Map<DensityMapSource,String> attempts)

Uses of PdbId in org.biojava.nbio.structure.scop

Methods in org.biojava.nbio.structure.scop that return PdbId

Modifier and Type	Method	Description
PdbId	ScopDomain.getPdbId()	Gets the PDB identifier for this protein structure.

Methods in org.biojava.nbio.structure.scop with parameters of type PdbId

Modifier and Type	Method	Description
void	ScopDomain.setPdbId(PdbId pdbId)