Package org.biojava.nbio.structure.ecod

Interface EcodDatabase

All Known Implementing Classes:
EcodInstallation
public interface EcodDatabase
General API for interacting with ECOD.
Author:
Spencer Bliven

  • Method Details

    • getVersion

      String getVersion() throws IOException
      Return the release version.
      Returns:
      version
      Throws:
      IOException

    • getDomainsById

      EcodDomain getDomainsById(String ecodId) throws IOException
      Get a particular ECOD domain by the domain ID (e.g. "e4hhbA1")
      Parameters:
      ecodId -
      Returns:
      Throws:
      IOException

    • getDomainsForPdb

      List<EcodDomain> getDomainsForPdb(String pdbId) throws IOException
      Get a list of all ECOD domains for a particular PDB ID
      Parameters:
      pdbId -
      Returns:
      the list of domains, or null if no matching domains were found
      Throws:
      IOException

    • filterByHierarchy

      List<EcodDomain> filterByHierarchy(String hierarchy) throws IOException
      Get a list of domains within a particular level of the hierarchy
      Parameters:
      hierarchy - A dot-separated list giving the X-group, H-group, and/or T-group (e.g. "1.1" for all members of the RIFT-related H-group)
      Returns:
      Throws:
      IOException

    • getAllDomains

      List<EcodDomain> getAllDomains() throws IOException
      Get all ECOD domains
      Returns:
      Throws:
      IOException