org.biojava.bio.structure.scop
Class ScopInstallation

java.lang.Object
  org.biojava.bio.structure.scop.ScopInstallation

All Implemented Interfaces:

ScopDatabase

Direct Known Subclasses:

BerkeleyScopInstallation

public class ScopInstallation
extends java.lang.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

static java.lang.String	claFileName
static java.lang.String	DEFAULT_VERSION
static java.lang.String	desFileName
static java.lang.String	FILESPLIT
static java.lang.String	hieFileName
static java.lang.String	NEWLINE
static java.lang.String	SCOP_DOWNLOAD
protected java.lang.String	scopDownloadURL
protected java.lang.String	scopVersion

Constructor Summary

ScopInstallation()
Create a new SCOP installation, downloading the file to "the right place".

ScopInstallation(java.lang.String cacheLocation)
Create a new SCOP installation.

Method Summary

protected void	downloadClaFile()
protected void	downloadDesFile()
protected void	downloadFileFromRemote(java.net.URL remoteURL, java.io.File localFile)
protected void	downloadHieFile()
void	ensureClaInstalled()
void	ensureDesInstalled()
void	ensureHieInstalled()
java.util.List<ScopDescription>	filterByClassificationId(java.lang.String query) Get all scop descriptions that start with a classifcation ID, e.g.
java.util.List<ScopDescription>	filterByDescription(java.lang.String query) Get all scop descriptions that start with a certain name.
java.util.List<ScopDomain>	filterByDomainName(java.lang.String query) search through SCOP and filter based on domain name
java.util.List<ScopDescription>	getByCategory(ScopCategory category) Get all records of a particular classification.
java.lang.String	getCacheLocation()
protected java.lang.String	getClaFilename()
protected java.lang.String	getDesFilename()
ScopDomain	getDomainByScopID(java.lang.String scopId) get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
java.util.List<ScopDomain>	getDomainsForPDB(java.lang.String pdbId) Get a list of ScopDomains that have been assigned to a PDB ID
protected java.lang.String	getHieFilename()
ScopDescription	getScopDescriptionBySunid(int sunid) Return the SCOP description for a node in the hierarchy by its "sunid" id.
java.util.List<ScopDomain>	getScopDomainsBySunid(java.lang.Integer sunid) Get a SCOP domain by its sunid
java.lang.String	getScopDownloadURL()
ScopNode	getScopNode(int sunid) Access a particular ScopNode.
java.lang.String	getScopVersion() Returns the SCOP version
java.util.List<ScopNode>	getTree(ScopDomain domain) get the SCOP sub-tree for a particular domain.
void	setCacheLocation(java.lang.String cacheLocation)
void	setScopDownloadURL(java.lang.String scopDownloadURL)
void	setScopVersion(java.lang.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 java.lang.String DEFAULT_VERSION

See Also:

Constant Field Values

scopVersion

protected java.lang.String scopVersion

claFileName

public static final java.lang.String claFileName

See Also:

Constant Field Values

desFileName

public static final java.lang.String desFileName

See Also:

Constant Field Values

hieFileName

public static final java.lang.String hieFileName

See Also:

Constant Field Values

SCOP_DOWNLOAD

public static final java.lang.String SCOP_DOWNLOAD

See Also:

Constant Field Values

scopDownloadURL

protected java.lang.String scopDownloadURL

NEWLINE

public static final java.lang.String NEWLINE

FILESPLIT

public static final java.lang.String FILESPLIT

Constructor Detail

ScopInstallation

public ScopInstallation(java.lang.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 java.util.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 java.util.List<ScopDescription> filterByClassificationId(java.lang.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 java.util.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 java.util.List<ScopDomain> filterByDomainName(java.lang.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 java.util.List<ScopDescription> filterByDescription(java.lang.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 java.util.List<ScopDomain> getDomainsForPDB(java.lang.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(java.lang.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

downloadClaFile

protected void downloadClaFile()
                        throws java.io.FileNotFoundException,
                               java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

downloadDesFile

protected void downloadDesFile()
                        throws java.io.FileNotFoundException,
                               java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

downloadHieFile

protected void downloadHieFile()
                        throws java.io.FileNotFoundException,
                               java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

downloadFileFromRemote

protected void downloadFileFromRemote(java.net.URL remoteURL,
                                      java.io.File localFile)
                               throws java.io.FileNotFoundException,
                                      java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

getClaFilename

protected java.lang.String getClaFilename()

getDesFilename

protected java.lang.String getDesFilename()

getHieFilename

protected java.lang.String getHieFilename()

getCacheLocation

public java.lang.String getCacheLocation()

setCacheLocation

public void setCacheLocation(java.lang.String cacheLocation)

getScopVersion

public java.lang.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(java.lang.String scopVersion)

getScopDownloadURL

public java.lang.String getScopDownloadURL()

setScopDownloadURL

public void setScopDownloadURL(java.lang.String scopDownloadURL)

getScopDomainsBySunid

public java.util.List<ScopDomain> getScopDomainsBySunid(java.lang.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