java.lang.Object

org.biojava.nbio.structure.scop.ScopInstallation

All Implemented Interfaces:: LocalScopDatabase, ScopDatabase

Direct Known Subclasses:: BerkeleyScopInstallation

public class ScopInstallation extends Object implements LocalScopDatabase

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

Description

static final String

claFileName

static final String

comFileName

static final String

DEFAULT_VERSION

static final String

desFileName

static final String

FILESPLIT

static final String

hieFileName

static final String

NEWLINE

static final String

SCOP_DOWNLOAD

static final String

SCOP_DOWNLOAD_ALTERNATE

protected String

scopVersion
Constructor Summary

Constructors

Constructor

Description

ScopInstallation()

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

ScopInstallation(String cacheLocation)

Create a new SCOP installation.
Method Summary

Modifier and Type

Method

Description

void

addMirror(String scopDownloadURL)

protected void

downloadClaFile()

protected void

downloadComFile()

protected void

downloadDesFile()

protected void

downloadFileFromRemote(URL remoteURL, File localFile)

protected void

downloadHieFile()

void

ensureClaInstalled()

void

ensureComInstalled()

void

ensureDesInstalled()

void

ensureHieInstalled()

List<ScopDescription>

filterByClassificationId(String query)

Get all scop descriptions that start with a classification ID, e.g.

List<ScopDescription>

filterByDescription(String query)

Get all scop descriptions that start with a certain name.

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()

protected String

getClaFilename()

protected String

getComFilename()

List<String>

getComments(int sunid)

Get comments about a SCOP domain by its sunid

protected String

getDesFilename()

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

protected String

getHieFilename()

List<ScopMirror>

getMirrors()

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

String

getScopDownloadURL()

Deprecated.

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

nullifyComments()

Removes all of the comments (dir.com file) in order to free memory.

void

setCacheLocation(String cacheLocation)

void

setScopDownloadURL(String scopDownloadURL)

Deprecated.
Use addMirror(java.lang.String) instead

void

setScopVersion(String scopVersion)

Sets the scop version used.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- DEFAULT_VERSION
  
  public static final String DEFAULT_VERSION
  See Also:
  
  Constant Field Values
- scopVersion
  
  protected String scopVersion
- 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
- comFileName
  
  public static final String comFileName
  See Also:
  
  Constant Field Values
- SCOP_DOWNLOAD
  
  public static final String SCOP_DOWNLOAD
  See Also:
  
  Constant Field Values
- SCOP_DOWNLOAD_ALTERNATE
  
  public static final String SCOP_DOWNLOAD_ALTERNATE
  See Also:
  
  Constant Field Values
- NEWLINE
  
  public static final String NEWLINE
- FILESPLIT
  
  public static final String FILESPLIT
Constructor Details
- 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 UserConfiguration.PDB_CACHE_DIR, or else will use a temporary directory
Method Details
- nullifyComments
  
  public void nullifyComments()
  
  Removes all of the comments (dir.com file) in order to free memory. The file will need to be reloaded if getComments(int) is called subsequently.
- ensureClaInstalled
  
  public void ensureClaInstalled() throws IOException
  
  Throws:
  
  IOException
- ensureDesInstalled
  
  public void ensureDesInstalled() throws IOException
  
  Throws:
  
  IOException
- ensureComInstalled
  
  public void ensureComInstalled() throws IOException
  
  Throws:
  
  IOException
- ensureHieInstalled
  
  public void ensureHieInstalled() throws IOException
  
  Throws:
  
  IOException
- 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 classification 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) throws ScopIOException
  
  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
  
  Throws:
  
  ScopIOException
- 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
- downloadClaFile
  
  protected void downloadClaFile() throws FileNotFoundException, IOException
  
  Throws:
  
  FileNotFoundException
  
  IOException
- downloadDesFile
  
  protected void downloadDesFile() throws FileNotFoundException, IOException
  
  Throws:
  
  FileNotFoundException
  
  IOException
- downloadHieFile
  
  protected void downloadHieFile() throws IOException
  
  Throws:
  
  IOException
- downloadComFile
  
  protected void downloadComFile() throws FileNotFoundException, IOException
  
  Throws:
  
  FileNotFoundException
  
  IOException
- downloadFileFromRemote
  
  protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException
  
  Throws:
  
  IOException
- getClaFilename
  
  protected String getClaFilename()
- getDesFilename
  
  protected String getDesFilename()
- getHieFilename
  
  protected String getHieFilename()
- getComFilename
  
  protected String getComFilename()
- 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)
  
  Description copied from interface: ScopDatabase
  
  Sets the scop version used.
  
  Specified by:
  
  setScopVersion in interface ScopDatabase
- getScopDownloadURL
  
  @Deprecated public String getScopDownloadURL()
  
  Deprecated.
  
  Get the URL of the first scop mirror being used
  
  Returns:
- setScopDownloadURL
  
  @Deprecated public void setScopDownloadURL(String scopDownloadURL)
  
  Deprecated.
  Use addMirror(java.lang.String) instead
  
  Parameters:
  
  scopDownloadURL - URL to load
- addMirror
  
  public void addMirror(String scopDownloadURL)
- getMirrors
  
  public List<ScopMirror> getMirrors()
- 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
- getComments
  
  public List<String> getComments(int sunid)
  
  Description copied from interface: ScopDatabase
  
  Get comments about a SCOP domain by its sunid
  
  Specified by:
  
  getComments in interface ScopDatabase
  
  Returns:

Class ScopInstallation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

DEFAULT_VERSION

scopVersion

claFileName

desFileName

hieFileName

comFileName

SCOP_DOWNLOAD

SCOP_DOWNLOAD_ALTERNATE

NEWLINE

FILESPLIT

Constructor Details

ScopInstallation

ScopInstallation

Method Details

nullifyComments

ensureClaInstalled

ensureDesInstalled

ensureComInstalled

ensureHieInstalled

getByCategory

filterByClassificationId

getTree

filterByDomainName

filterByDescription

getScopDescriptionBySunid

getDomainsForPDB

getDomainByScopID

getScopNode

downloadClaFile

downloadDesFile

downloadHieFile

downloadComFile

downloadFileFromRemote

getClaFilename

getDesFilename

getHieFilename

getComFilename

getCacheLocation

setCacheLocation

getScopVersion

setScopVersion

getScopDownloadURL

setScopDownloadURL

addMirror

getMirrors

getScopDomainsBySunid

getComments