Package org.biojava.nbio.structure.cath

Interface CathDatabase

  • All Known Implementing Classes:
    CathInstallation
    public interface CathDatabase
    General API for interacting with CATH.
    Author:
    Daniel Asarnow

    • Method Detail

      • getCathVersion

        java.lang.String getCathVersion()
        Return the CATH release version.
        Returns:
        CATH version

      • getCathNode

        CathNode getCathNode​(java.lang.String nodeId)
        Return the CathNode for a node ID.
        Parameters:
        nodeId -
        Returns:
        CATH node

      • getByCategory

        java.util.List<CathDomain> getByCategory​(CathCategory category)
        Return list of CATH descriptions for node representatives at a CATH category (e.g. "T").
        Parameters:
        category -
        Returns:
        CATH descriptions

      • filterByCathCode

        java.util.List<CathDomain> filterByCathCode​(java.lang.String query)
        Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query. This is currently redundant with getDescriptionsByNodeId.
        Parameters:
        query -
        Returns:
        CATH descriptions

      • getTree

        java.util.List<CathNode> getTree​(CathDomain domain)
        Return the CATH sub-tree for a particular domain.
        Parameters:
        domain -
        Returns:
        CATH sub-tree

      • filterByNodeName

        java.util.List<CathDomain> filterByNodeName​(java.lang.String query)
        Return list of CATH domains whose node name (e.g. Orthogonal Bundle) starts with the query.
        Parameters:
        query -
        Returns:
        CATH domains

      • filterByDescription

        java.util.List<CathDomain> filterByDescription​(java.lang.String query)
        Return list of CATH descriptions whose descriptions (name field) starts with the query.
        Parameters:
        query -
        Returns:
        CATH descriptions

      • getDescriptionByNodeId

        CathDomain getDescriptionByNodeId​(java.lang.String nodeId)
        Return CATH description for node representative by node ID.
        Parameters:
        nodeId -
        Returns:
        CATH description

      • getDomainsForPdb

        java.util.List<CathDomain> getDomainsForPdb​(java.lang.String pdbId)
        Return all CATH domains for a PDB ID.
        Parameters:
        pdbId -
        Returns:
        CATH domains

      • getDomainByCathId

        CathDomain getDomainByCathId​(java.lang.String cathId)
        Return CATH domain for CATH domain ID.
        Parameters:
        cathId -
        Returns:
        CATH domain

      • getDescriptionByCathId

        CathDomain getDescriptionByCathId​(java.lang.String cathId)
        Return CATH description for CATH domain ID.
        Parameters:
        cathId -
        Returns:

      • getDomainsByNodeId

        java.util.List<CathDomain> getDomainsByNodeId​(java.lang.String nodeId)
        Return all CATH domains for a particular CATH node.
        Parameters:
        nodeId -
        Returns:

      • getFragmentsByPdbId

        java.util.List<CathFragment> getFragmentsByPdbId​(java.lang.String pdbId)