Uses of Class
org.biojava.nbio.structure.align.util.AtomCache
-
Packages that use AtomCache Package Description org.biojava.nbio.structure 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 Structuresorg.biojava.nbio.structure.io.mmtf 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 that return AtomCache Modifier and Type Method Description static AtomCache
StructureIO. getAtomCache()
Methods in org.biojava.nbio.structure with parameters of type AtomCache Modifier and Type Method Description static Structure
StructureTools. getStructure(String name, PDBFileParser parser, AtomCache cache)
Flexibly get a structure from an input String.Structure
BioAssemblyIdentifier. loadStructure(AtomCache cache)
Structure
PassthroughIdentifier. loadStructure(AtomCache cache)
Passthrough identifiers don't know how to load a structureStructure
StructureIdentifier. loadStructure(AtomCache cache)
Loads a structure encompassing the structure identified.Structure
SubstructureIdentifier. loadStructure(AtomCache cache)
Loads the complete structure based onSubstructureIdentifier.getPdbId()
.Structure
URLIdentifier. loadStructure(AtomCache cache)
Load the structure from the URLstatic 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 Description AtomCache
MultiThreadedDBSearch. getAtomCache()
AtomCache
CallableStructureAlignment. getCache()
Methods in org.biojava.nbio.structure.align with parameters of type AtomCache Modifier and Type Method 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 Description protected AtomCache
FarmJobRunnable. cache
Methods in org.biojava.nbio.structure.align.client with parameters of type AtomCache Modifier and Type Method 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 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 Description Structure
PDPProvider. getDomain(String pdpDomainName, AtomCache cache)
Get the structure for a particular PDP domainStructure
RemotePDPProvider. getDomain(String pdpDomainName, AtomCache cache)
Get the structure for a particular PDP domainStructure
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 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 Description FastaStructureParser(File file, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(InputStream is, SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser, SequenceCreatorInterface<AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(FastaReader<ProteinSequence,AminoAcidCompound> reader, AtomCache cache)
-
Uses of AtomCache in org.biojava.nbio.structure.io.mmtf
Methods in org.biojava.nbio.structure.io.mmtf that return AtomCache Modifier and Type Method Description static AtomCache
MmtfUtils. setUpBioJava()
Set up the configuration parameters for BioJava.static AtomCache
MmtfUtils. setUpBioJava(String extraUrl)
Set up the configuration parameters for BioJava. -
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 Description Structure
ScopDomain. loadStructure(AtomCache cache)
-