Uses of Class org.biojava.nbio.structure.PdbId (biojava 6.1.0 API)

Packages that use PdbId
Package	Description
org.biojava.nbio.structure
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.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
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.`loadStructureFromMmtfByPdbId(PdbId pdbId)`	Load a `Structure` from MMTF either from the local file system.
`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.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)