org.biojava.bio.structure.scop

Class ScopFactory

java.lang.Object

org.biojava.bio.structure.scop.ScopFactory

public class ScopFactory
extends java.lang.Object

Controls the global ScopDatabase being used.

Defaults to a RemoteScopInstallation, which is fast for small numbers of queries. For many queries, a ScopInstallation instance may be faster, since it makes only one network request.

Example: Fetch the structure corresponding to an old version of scop

 ScopInstallation scop = new ScopInstallation();
 scop.setScopVersion("1.69");
 ScopFactory.setScopDatabase(scop);
 AtomCache cache = new AtomCache();
 cache.setFetchFileEvenIfObsolete(true); //fetch older PDBs
 cache.setStrictSCOP(false); // correct simple errors in domain names
 Structure s = cache.getStructure("d3hbia_");

Author:

sbliven

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	VERSION_1_75
static java.lang.String	VERSION_1_75A
static java.lang.String	VERSION_1_75B

Constructor Summary

Constructors

Constructor and Description
ScopFactory()

Method Summary

Methods

Modifier and Type	Method and Description
static ScopDatabase	getSCOP()
static ScopDatabase	getSCOP(java.lang.String version) requests a particular version of SCOP
static ScopDatabase	getSCOP(java.lang.String version, boolean useLocalData)
static void	setScopDatabase(ScopDatabase s)
static void	setScopDatabase(java.lang.String s)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

VERSION_1_75A

public static final java.lang.String VERSION_1_75A

See Also:

Constant Field Values

VERSION_1_75B

public static final java.lang.String VERSION_1_75B

See Also:

Constant Field Values

VERSION_1_75

public static final java.lang.String VERSION_1_75

See Also:

Constant Field Values

Constructor Detail

ScopFactory

public ScopFactory()

Method Detail

getSCOP

public static ScopDatabase getSCOP()

setScopDatabase

public static void setScopDatabase(java.lang.String s)

Parameters:

s - A version number, such as VERSION_1_75A

setScopDatabase

public static void setScopDatabase(ScopDatabase s)

getSCOP

public static ScopDatabase getSCOP(java.lang.String version,
                   boolean useLocalData)

getSCOP

public static ScopDatabase getSCOP(java.lang.String version)

requests a particular version of SCOP

Parameters:

version -

Returns: