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.domain
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.quaternary.io

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	StructureTools.getStructure(String name, PDBFileParser parser, AtomCache cache) Flexibly get a structure from an input String.
static StructureIdentifier	Identifier.loadIdentifier(String id, AtomCache cache) Loads a StructureIdentifier from the specified string.
static void	StructureIO.setAtomCache(AtomCache c)

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

Constructor and Description
SubstructureIdentifier(String id, AtomCache cache)

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

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	RemotePDPProvider.getDomain(String pdpDomainName, AtomCache cache)
Structure	PDPProvider.getDomain(String pdbDomainName, 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	RemoteBioUnitDataProvider.getAtomCache()
AtomCache	PDBBioUnitDataProvider.getAtomCache()
AtomCache	MmCifPDBBiolAssemblyProvider.getAtomCache()
AtomCache	BioUnitDataProvider.getAtomCache()
AtomCache	MmCifBiolAssemblyProvider.getAtomCache()

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

Modifier and Type	Method and Description
void	RemoteBioUnitDataProvider.setAtomCache(AtomCache cache)
void	PDBBioUnitDataProvider.setAtomCache(AtomCache cache)
void	MmCifPDBBiolAssemblyProvider.setAtomCache(AtomCache cache)
void	BioUnitDataProvider.setAtomCache(AtomCache cache)
void	MmCifBiolAssemblyProvider.setAtomCache(AtomCache cache)