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 Details

    • getCathVersion

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

    • getCathNode

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

    • getByCategory

      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

      List<CathDomain> filterByCathCode(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

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

    • filterByNodeName

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

    • filterByDescription

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

    • getDescriptionByNodeId

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

    • getDomainsForPdb

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

    • getDomainByCathId

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

    • getDescriptionByCathId

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

    • getDomainsByNodeId

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

    • getFragmentsByPdbId

      List<CathFragment> getFragmentsByPdbId(String pdbId)