Class RemotePDPProvider
java.lang.Object
org.biojava.nbio.structure.domain.SerializableCache<String,SortedSet<String>>
org.biojava.nbio.structure.domain.RemotePDPProvider
- All Implemented Interfaces:
PDPProvider
public class RemotePDPProvider
extends SerializableCache<String,SortedSet<String>>
implements PDPProvider
A class that provided PDP assignments that are loaded from a remote web server
- Author:
- Andreas Prlic
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Field Summary
FieldsFields inherited from class org.biojava.nbio.structure.domain.SerializableCache
cacheFileName, serializedCache -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionGet the structure for a particular PDP domaingetPDPDomain(String pdpDomainName) Get a StructureIdentifier representing the specified PDP domain.getPDPDomainNamesForPDB(String pdbId) Get a list of all PDP domains for a given PDB entrystatic voidvoidMethods inherited from class org.biojava.nbio.structure.domain.SerializableCache
cache, disableCache, enableCache, flushCache, get, isCacheEnabled, reloadFromFile
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Field Details
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DEFAULT_SERVER
- See Also:
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Constructor Details
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RemotePDPProvider
public RemotePDPProvider() -
RemotePDPProvider
- Parameters:
useCache-- Throws:
IOException
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Method Details
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main
- Throws:
IOExceptionStructureException
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getServer
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setServer
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getDomain
public Structure getDomain(String pdpDomainName, AtomCache cache) throws IOException, StructureException Get the structure for a particular PDP domain- Specified by:
getDomainin interfacePDPProvider- Parameters:
pdpDomainName- PDP identifier, e.g. "PDP:4HHBAa"cache- AtomCache, responsible for fetching and storing the coordinates- Returns:
- Structure representing the PDP domain
- Throws:
IOException- if the server cannot be reachedStructureException- For errors parsing the structure
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getPDPDomain
Get a StructureIdentifier representing the specified PDP domain.- Specified by:
getPDPDomainin interfacePDPProvider- Parameters:
pdpDomainName- PDP domain name- Returns:
- a PDPDomain representing this domain name
- Throws:
IOException- if the server cannot be reached
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getPDPDomainNamesForPDB
Get a list of all PDP domains for a given PDB entry- Specified by:
getPDPDomainNamesForPDBin interfacePDPProvider- Parameters:
pdbId- PDB ID- Returns:
- Set of domain names, e.g. "PDP:4HHBAa"
- Throws:
IOException- if the server cannot be reached
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