org.biojava.bio.structure.scop

Class ScopInstallation

java.lang.Object

org.biojava.bio.structure.scop.ScopInstallation

All Implemented Interfaces:

ScopDatabase

public class ScopInstallation
extends Object
implements ScopDatabase

This class provides access to the SCOP protein structure classification. For more information about SCOP see here:

• SCOP: http://scop.mrc-lmb.cam.ac.uk/scop/
• Introduction: http://scop.mrc-lmb.cam.ac.uk/scop/intro.html
• SCOP parsable files: http://scop.mrc-lmb.cam.ac.uk/scop/parse/

This class can automatically download missing files from the SCOP classification.

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static String	claFileName
static String	DEFAULT_VERSION
static String	desFileName
static String	FILESPLIT
static String	hieFileName
static String	NEWLINE
static String	SCOP_DOWNLOAD

Constructor Summary

Constructors

Constructor and Description
ScopInstallation() Create a new SCOP installation, downloading the file to "the right place".
ScopInstallation(String cacheLocation) Create a new SCOP installation.

Method Summary

Methods

Modifier and Type	Method and Description
void	ensureClaInstalled()
void	ensureDesInstalled()
void	ensureHieInstalled()
List<ScopDescription>	filterByClassificationId(String query) Get all scop descriptions that start with a classifcation ID, e.g. b.1.18
List<ScopDescription>	filterByDescription(String query) Get all scop descriptions that start with a certain name. e.g.
List<ScopDomain>	filterByDomainName(String query) search through SCOP and filter based on domain name
List<ScopDescription>	getByCategory(ScopCategory category) Get all records of a particular classification.
String	getCacheLocation()
ScopDomain	getDomainByScopID(String scopId) get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
List<ScopDomain>	getDomainsForPDB(String pdbId) Get a list of ScopDomains that have been assigned to a PDB ID
ScopDescription	getScopDescriptionBySunid(int sunid) Return the SCOP description for a node in the hierarchy by its "sunid" id.
List<ScopDomain>	getScopDomainsBySunid(Integer sunid) Get a SCOP domain by its sunid
ScopNode	getScopNode(int sunid) Access a particular ScopNode.
String	getScopVersion() Returns the SCOP version
List<ScopNode>	getTree(ScopDomain domain) get the SCOP sub-tree for a particular domain.
void	setCacheLocation(String cacheLocation)
void	setScopVersion(String scopVersion)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_VERSION

public static final String DEFAULT_VERSION

See Also:

Constant Field Values

claFileName

public static final String claFileName

See Also:

Constant Field Values

desFileName

public static final String desFileName

See Also:

Constant Field Values

hieFileName

public static final String hieFileName

See Also:

Constant Field Values

SCOP_DOWNLOAD

public static final String SCOP_DOWNLOAD

See Also:

Constant Field Values

NEWLINE

public static final String NEWLINE

FILESPLIT

public static final String FILESPLIT

Constructor Detail

ScopInstallation

public ScopInstallation(String cacheLocation)

Create a new SCOP installation.

Parameters:

cacheLocation - where the SCOP files are stored. If they can't be found at that location they will get automatically downloaded and installed there.

ScopInstallation

public ScopInstallation()

Create a new SCOP installation, downloading the file to "the right place". This will first check for system properties or environmental variables called 'PDB_DIR', or else will use a temporary directory

Method Detail

ensureClaInstalled

public void ensureClaInstalled()

ensureDesInstalled

public void ensureDesInstalled()

ensureHieInstalled

public void ensureHieInstalled()

getByCategory

public List<ScopDescription> getByCategory(ScopCategory category)

Description copied from interface: ScopDatabase

Get all records of a particular classification.

Specified by:

getByCategory in interface ScopDatabase

Parameters:

category - e.g. "superfamily"

Returns:

all records of this type

filterByClassificationId

public List<ScopDescription> filterByClassificationId(String query)

Description copied from interface: ScopDatabase

Get all scop descriptions that start with a classifcation ID, e.g. b.1.18

Specified by:

filterByClassificationId in interface ScopDatabase

Returns:

list of scop descriptions

getTree

public List<ScopNode> getTree(ScopDomain domain)

Description copied from interface: ScopDatabase

get the SCOP sub-tree for a particular domain.

Specified by:

getTree in interface ScopDatabase

Returns:

list of ScopNodes providing the path to this domain

filterByDomainName

public List<ScopDomain> filterByDomainName(String query)

Description copied from interface: ScopDatabase

search through SCOP and filter based on domain name

Specified by:

filterByDomainName in interface ScopDatabase

Parameters:

query - a (part) of a name

Returns:

list of matchin ScopDomains

filterByDescription

public List<ScopDescription> filterByDescription(String query)

Description copied from interface: ScopDatabase

Get all scop descriptions that start with a certain name. e.g. Globin

Specified by:

filterByDescription in interface ScopDatabase

Returns:

list of scop descriptions

getScopDescriptionBySunid

public ScopDescription getScopDescriptionBySunid(int sunid)

Description copied from interface: ScopDatabase

Return the SCOP description for a node in the hierarchy by its "sunid" id.

Specified by:

getScopDescriptionBySunid in interface ScopDatabase

Returns:

a ScopDescription object

getDomainsForPDB

public List<ScopDomain> getDomainsForPDB(String pdbId)

Description copied from interface: ScopDatabase

Get a list of ScopDomains that have been assigned to a PDB ID

Specified by:

getDomainsForPDB in interface ScopDatabase

Parameters:

pdbId - the PDB entry

Returns:

a list of ScopDomains

getDomainByScopID

public ScopDomain getDomainByScopID(String scopId)

Description copied from interface: ScopDatabase

get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)

Specified by:

getDomainByScopID in interface ScopDatabase

Parameters:

scopId - e.g. d2bq6a1

Returns:

a ScopDomain or null if no domain with the particular ID could be found

getScopNode

public ScopNode getScopNode(int sunid)

Description copied from interface: ScopDatabase

Access a particular ScopNode. The scopNode then allows to traverse through the scop hierarchy...

Specified by:

getScopNode in interface ScopDatabase

Parameters:

sunid - the scop unique id

Returns:

a ScopNode that matches this sunid

getCacheLocation

public String getCacheLocation()

setCacheLocation

public void setCacheLocation(String cacheLocation)

getScopVersion

public String getScopVersion()

Description copied from interface: ScopDatabase

Returns the SCOP version

Specified by:

getScopVersion in interface ScopDatabase

Returns:

version of SCOP

setScopVersion

public void setScopVersion(String scopVersion)

getScopDomainsBySunid

public List<ScopDomain> getScopDomainsBySunid(Integer sunid)

Description copied from interface: ScopDatabase

Get a SCOP domain by its sunid

Specified by:

getScopDomainsBySunid in interface ScopDatabase

Parameters:

sunid - the scop unique id

Returns:

a list of scop domains that match this sunid