Uses of Class
org.biojava.nbio.structure.align.util.AtomCache

Packages that use AtomCache

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

Uses of AtomCache in org.biojava.nbio.structure

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

Modifier and Type	Method and Description
static Structure	StructureIO.getBiologicalAssembly(String pdbId, int biolAssemblyNr, AtomCache cache)
static Structure	StructureIO.getBiologicalAssembly(String pdbId, int biolAssemblyNr, AtomCache cache, BioUnitDataProvider provider)
static Structure	StructureTools.getStructure(String name, PDBFileParser parser, AtomCache cache) Flexibly get a structure from an input String.
static StructureIdentifier	Identifier.loadIdentifier(String id, AtomCache cache) Deprecated. Create a new StructureName instead.
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)
static void	StructureIO.setAtomCache(AtomCache c)

Uses of AtomCache in org.biojava.nbio.structure.align

Methods in org.biojava.nbio.structure.align that return AtomCache

Modifier and Type	Method and Description
AtomCache	MultiThreadedDBSearch.getAtomCache()
AtomCache	CallableStructureAlignment.getCache()

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

Modifier and Type	Method and Description
void	MultiThreadedDBSearch.setAtomCache(AtomCache cache)
void	CallableStructureAlignment.setCache(AtomCache cache)

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

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

Modifier and Type	Field and Description
protected AtomCache	FarmJobRunnable.cache

Methods in org.biojava.nbio.structure.align.client with parameters of type AtomCache

Modifier and Type	Method and Description
Structure	StructureName.loadStructure(AtomCache cache)

Uses of AtomCache in org.biojava.nbio.structure.cath

Methods in org.biojava.nbio.structure.cath with parameters of type AtomCache

Modifier and Type	Method and Description
Structure	CathDomain.loadStructure(AtomCache cache)

Uses of AtomCache in org.biojava.nbio.structure.domain

Methods in org.biojava.nbio.structure.domain with parameters of type AtomCache

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)

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

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

Modifier and Type	Method and Description
Structure	EcodDomain.loadStructure(AtomCache cache)

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

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

Constructor and Description
FastaStructureParser(FastaReader<ProteinSequence,AminoAcidCompound> reader, AtomCache cache)
FastaStructureParser(File file, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(InputStream is, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)

Uses of AtomCache in org.biojava.nbio.structure.quaternary.io

Methods in org.biojava.nbio.structure.quaternary.io that return AtomCache

Modifier and Type	Method and Description
AtomCache	MmCifBiolAssemblyProvider.getAtomCache()
AtomCache	MmCifPDBBiolAssemblyProvider.getAtomCache()
AtomCache	PDBBioUnitDataProvider.getAtomCache()
AtomCache	RemoteBioUnitDataProvider.getAtomCache()
AtomCache	BioUnitDataProvider.getAtomCache()

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

Modifier and Type	Method and Description
void	MmCifBiolAssemblyProvider.setAtomCache(AtomCache cache)
void	MmCifPDBBiolAssemblyProvider.setAtomCache(AtomCache cache)
void	PDBBioUnitDataProvider.setAtomCache(AtomCache cache)
void	RemoteBioUnitDataProvider.setAtomCache(AtomCache cache)
void	BioUnitDataProvider.setAtomCache(AtomCache cache) Set an AtomCache to use when fetching asymmetric units.

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

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

Modifier and Type	Method and Description
Structure	ScopDomain.loadStructure(AtomCache cache)