Package org.biojava.nbio.structure.scop

Interface ScopDatabase

All Known Subinterfaces:
LocalScopDatabase
All Known Implementing Classes:
BerkeleyScopInstallation, ScopInstallation
public interface ScopDatabase
General API how to interact with SCOP
Since:
3.0.2
Author:
Andreas Prlic
See Also:

  • Method Details

    • getByCategory

      List<ScopDescription> getByCategory(ScopCategory category)
      Get all records of a particular classification.
      Parameters:
      category - e.g. "superfamily"
      Returns:
      all records of this type

    • filterByClassificationId

      List<ScopDescription> filterByClassificationId(String query)
      Get all scop descriptions that start with a classification ID, e.g. b.1.18
      Parameters:
      query -
      Returns:
      list of scop descriptions

    • getTree

      List<ScopNode> getTree(ScopDomain domain)
      get the SCOP sub-tree for a particular domain.
      Parameters:
      domain -
      Returns:
      list of ScopNodes providing the path to this domain

    • filterByDomainName

      List<ScopDomain> filterByDomainName(String query)
      search through SCOP and filter based on domain name
      Parameters:
      query - a (part) of a name
      Returns:
      list of matchin ScopDomains

    • filterByDescription

      List<ScopDescription> filterByDescription(String query)
      Get all scop descriptions that start with a certain name. e.g. Globin
      Parameters:
      query -
      Returns:
      list of scop descriptions

    • getScopDescriptionBySunid

      ScopDescription getScopDescriptionBySunid(int sunid)
      Return the SCOP description for a node in the hierarchy by its "sunid" id.
      Parameters:
      sunid -
      Returns:
      a ScopDescription object

    • getDomainsForPDB

      List<ScopDomain> getDomainsForPDB(String pdbId)
      Get a list of ScopDomains that have been assigned to a PDB ID
      Parameters:
      pdbId - the PDB entry
      Returns:
      a list of ScopDomains

    • getDomainByScopID

      ScopDomain getDomainByScopID(String scopId)
      get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
      Parameters:
      scopId - e.g. d2bq6a1
      Returns:
      a ScopDomain or null if no domain with the particular ID could be found

    • getScopNode

      ScopNode getScopNode(int sunid)
      Access a particular ScopNode. The scopNode then allows to traverse through the scop hierarchy...
      Parameters:
      sunid - the scop unique id
      Returns:
      a ScopNode that matches this sunid

    • getScopVersion

      String getScopVersion()
      Returns the SCOP version
      Returns:
      version of SCOP

    • setScopVersion

      void setScopVersion(String version)
      Sets the scop version used.
      Parameters:
      version -
      Throws:
      UnsupportedOperationException - If the version cannot be changed

    • getScopDomainsBySunid

      List<ScopDomain> getScopDomainsBySunid(Integer sunid)
      Get a SCOP domain by its sunid
      Parameters:
      sunid - the scop unique id
      Returns:
      a list of scop domains that match this sunid

    • getComments

      List<String> getComments(int sunid)
      Get comments about a SCOP domain by its sunid
      Parameters:
      sunid -
      Returns: