Uses of Class
org.biojava.nbio.structure.align.util.AtomCache
Packages that use AtomCache
Package
Description
Classes for the alignment of structures.
This package deals with the server communication for auto-downloading pre-calculated alignments.
Input and Output of Structures
Parsers and API for SCOP, Structural Classification of Proteins.
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Uses of AtomCache in org.biojava.nbio.structure
Methods in org.biojava.nbio.structure that return AtomCacheMethods in org.biojava.nbio.structure with parameters of type AtomCacheModifier and TypeMethodDescriptionstatic Structure
StructureTools.getStructure
(String name, PDBFileParser parser, AtomCache cache) Flexibly get a structure from an input String.BioAssemblyIdentifier.loadStructure
(AtomCache cache) PassthroughIdentifier.loadStructure
(AtomCache cache) Passthrough identifiers don't know how to load a structureStructureIdentifier.loadStructure
(AtomCache cache) Loads a structure encompassing the structure identified.SubstructureIdentifier.loadStructure
(AtomCache cache) Loads the complete structure based onSubstructureIdentifier.getPdbId()
.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 AtomCacheMethods in org.biojava.nbio.structure.align with parameters of type AtomCache -
Uses of AtomCache in org.biojava.nbio.structure.align.client
Methods in org.biojava.nbio.structure.align.client with parameters of type AtomCache -
Uses of AtomCache in org.biojava.nbio.structure.cath
Methods in org.biojava.nbio.structure.cath with parameters of type AtomCache -
Uses of AtomCache in org.biojava.nbio.structure.ecod
Methods in org.biojava.nbio.structure.ecod with parameters of type AtomCache -
Uses of AtomCache in org.biojava.nbio.structure.io
Constructors in org.biojava.nbio.structure.io with parameters of type AtomCacheModifierConstructorDescriptionFastaStructureParser
(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.scop
Methods in org.biojava.nbio.structure.scop with parameters of type AtomCache