Interface ScopDatabase

    • Method Detail

      • getTree

        List<ScopNodegetTree​(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<ScopDomainfilterByDomainName​(String query)
        search through SCOP and filter based on domain name
        Parameters:
        query - a (part) of a name
        Returns:
        list of matchin ScopDomains
      • 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<ScopDomaingetDomainsForPDB​(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
      • getComments

        List<StringgetComments​(int sunid)
        Get comments about a SCOP domain by its sunid
        Parameters:
        sunid -
        Returns: