Class RemoteDomainProvider
java.lang.Object
org.biojava.nbio.structure.domain.SerializableCache<String,SortedSet<String>>
org.biojava.nbio.structure.domain.RemoteDomainProvider
- All Implemented Interfaces:
DomainProvider
public class RemoteDomainProvider
extends SerializableCache<String,SortedSet<String>>
implements DomainProvider
A DomainProvider that uses a mixture of SCOP and PDP domains.
SCOP domains are preferred, with PDP providing a backup for structures where
SCOP has not been assigned.
As of 2015, this class is equivalent to the method used by RCSB to define
representatives for structural similarity comparisons.
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Field Summary
FieldsFields inherited from class org.biojava.nbio.structure.domain.SerializableCache
cacheFileName, serializedCache -
Constructor Summary
ConstructorsConstructorDescriptionRemoteDomainProvider(boolean cache) initialize this provider with caching enabled -
Method Summary
Modifier and TypeMethodDescriptionvoidgetDomainNames(String name) Get a list of constituent domain identifiersGet the full list of representative domains for the PDB.static voidMethods inherited from class org.biojava.nbio.structure.domain.SerializableCache
cache, disableCache, enableCache, get, isCacheEnabled, reloadFromFile
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Field Details
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url
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Constructor Details
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RemoteDomainProvider
public RemoteDomainProvider() -
RemoteDomainProvider
initialize this provider with caching enabled- Parameters:
cache-- Throws:
IOException
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Method Details
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getDomainNames
Description copied from interface:DomainProviderGet a list of constituent domain identifiers- Specified by:
getDomainNamesin interfaceDomainProvider- Parameters:
name- a structure identifier- Returns:
- A list of domain names
- Throws:
IOException- For IO errors getting the domainsStructureException- For errors converting name to a valid identifier
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main
- Throws:
IOExceptionStructureException
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flushCache
public void flushCache()- Overrides:
flushCachein classSerializableCache<String,SortedSet<String>>
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getRepresentativeDomains
Description copied from interface:DomainProviderGet the full list of representative domains for the PDB. The exact definition representatives is implementation-specific, but should cover as many structures as possible.- Specified by:
getRepresentativeDomainsin interfaceDomainProvider- Returns:
- A full list of all representative domains recognized by this provider
- Throws:
IOException- For IO errors getting the representatives
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